From 8891cc5319fa9bdcfdd8890fbb5a292244c4d959 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Fri, 6 Oct 2023 12:47:32 +0200 Subject: [PATCH 01/95] init draft for Go model --- vermouth/rcsu/contact_map.py | 40 +++++++++++++ vermouth/rcsu/get_go.py | 108 +++++++++++++++++++++++++++++++++++ 2 files changed, 148 insertions(+) create mode 100644 vermouth/rcsu/contact_map.py create mode 100644 vermouth/rcsu/get_go.py diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py new file mode 100644 index 00000000..60fe2415 --- /dev/null +++ b/vermouth/rcsu/contact_map.py @@ -0,0 +1,40 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Read RCSU Go model contact maps. +""" + +def read_contmap(file_path, file_OV, file_rCSU, header_lines=0, cols=[2, 6, 10]): + """ + Read a RCSU contact map. + """ + with open(file_path, "r", encoding='UTF-8') as _file: + lines = _file.readlines() + + contacts = [] + read = False + for line in lines: + tokens = line.strip().splilt() + # we start parsing + # using R1 is super flaky but I don't see a good way to identify + # when the contact map starts ... + if tokens[0] == "R1": + read = True + elif read: + # a contact consits of a resid and the chain ID + contacts.append((int(tokens[1]), tokens[2], int(tokens[4]), tokens[5])) + else: + continue + return contacts diff --git a/vermouth/rcsu/get_go.py b/vermouth/rcsu/get_go.py new file mode 100644 index 00000000..ff0c3a41 --- /dev/null +++ b/vermouth/rcsu/get_go.py @@ -0,0 +1,108 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Process the Go contact pairs. +""" +from vermouth.processors.apply_rubber_bands import self_distance_matrix + +def extract_position_matrix(molecule, selector): + """ + Given a selector extract a distance matrix from + a molecule. + """ + selection = [] + coordinates = [] + missing = [] + node_to_idx = {} + idx_to_node = {} + for node_idx, (node_key, attributes) in enumerate(molecule.nodes.items()): + node_to_idx[node_key] = node_idx + idx_to_node[node_idx] = node_key + if selector(attributes): + selection.append(node_idx) + coordinates.append(attributes.get('position')) + if coordinates[-1] is None: + missing.append(node_key) + node_idx += 1 + + if missing: + raise ValueError('All atoms from the selection must have coordinates. ' + 'The following atoms do not have some: {}.' + .format(' '.join(missing))) + + if not coordinates: + return + + coordinates = np.stack(coordinates) + if np.any(np.isnan(coordinates)): + LOGGER.warning("Found nan coordinates in molecule {}. " + "Will not generate an EN for it. ", + molecule.moltype, + type='unmapped-atom') + return + + distance_matrix = self_distance_matrix(coordinates) + return distance_matrix + +def _get_bb_pos(moleule, nodes): + for node in molecule.nodes: + if molecule.nodes[node]['atomname'] == "BB": + return molecule.nodes[node]['position'] + return None + +class GetGo(): + """ + Generate the Go model interaction parameters. + """ + def __init__(self, + contact_map, + cutoff_short, + cutoff_long, + go_eps, + res_dist, + domain, + selector): + self.contact_map = contact_map + self.cutoff_short = cutoff_short + self.cutoff_long = cutoff_long + self.go_eps = go_eps + self.res_dist = res_dist + self.domain = domain + self.selector = selector + + def run_molecule(molecule): + res_graph = molecule.residue_graph + chain_id_to_resnode = {} + for resnode in res_graph.nodes: + chain = res_graph.nodes[resnode].get('chain', None) + resid = res_graph.nodes[resnode].get('resid') + chain_id_to_resnode[(chain, resid)] = resnode + + # compute the go parameters + for chainA, resA, chainB, resB in self.contact_map: + resA = chain_id_to_resnode[(chainA, resA)] + resB = chain_id_to_resnode[(chainB, resB)] + if graph_distance(resA, resB) > self.res_dist: + posA = _get_bb_pos(molecule, res_graph.nodes[resA]['graph'].nodes) + posB = _get_bb_pos(molecule, res_graph.nodes[resA]['graph'].nodes) + dist = np.linalg.norm(posA, posB) + if dist > self.cutoff_short or dist < self.cutoff_large: + sigma = dist / 1.12246204830 + Vii = 4.0 * pow(sigma, 6) * self.go_eps + Wii = 4.0 * pow(sigma, 12) * self.go_eps + + + + + From ae818e3db7dce6ff6e11bc37017713c0b9d76b38 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Sun, 8 Oct 2023 20:15:14 +0200 Subject: [PATCH 02/95] first implementation Go model --- bin/martinize2 | 63 ++++++++++- vermouth/rcsu/contact_map.py | 8 +- vermouth/rcsu/get_go.py | 196 ++++++++++++++++++++++------------- 3 files changed, 192 insertions(+), 75 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index fb4d620a..e61d89b0 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -49,6 +49,8 @@ from vermouth.map_input import ( generate_all_self_mappings, combine_mappings, ) +from vermouth.rcsu.contact_map import read_go_map +from vermouth.rcsu.get_go import GetGo from vermouth.citation_parser import citation_formatter # TODO Since vermouth's __init__.py does some logging (KDTree), this may or may @@ -618,16 +620,60 @@ def entry(): ) go_group = parser.add_argument_group("Virtual site based GoMartini") go_group.add_argument( - "-govs-includes", + "-go", action="store_true", default=False, - help="Write include statements to use Vitrual Site Go Martini.", + help="Apply the Martini Go model as structural bias.", ) go_group.add_argument( "-govs-moltype", + dest="govs_moltype", default="molecule_0", help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) + go_group.add_argument( + "-govs-includes", + action="store_true", + default=False, + help="Write include statements to use Vitrual Site Go Martini.", + ) + go_group.add_argument( + "-govs-map", + dest="go_map", + required=False, + type=Path, + default=False, + help="Write include statements to use Vitrual Site Go Martini.", + ) + go_group.add_argument( + "-govs-low", + dest="go_low", + type=float, + default=0.3, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-up", + dest="go_up", + type=float, + default=1.1, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-eps", + dest="go_eps", + type=float, + default=0.0, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-res-dist", + dest="go_res_dist", + type=int, + default=3, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + prot_group = parser.add_argument_group("Protein description") prot_group.add_argument( "-scfix", @@ -977,8 +1023,21 @@ def entry(): "The output topology will require files generated by " '"create_goVirt.py".' ) vermouth.MergeAllMolecules().run_system(system) + # not ideal but we need it before making the Go sides + res_graph = vermouth.graph_utils.make_residue_graph(system.molecules[0]) vermouth.SetMoleculeMeta(moltype=args.govs_moltype).run_system(system) vermouth.GoVirtIncludes().run_system(system) + LOGGER.info("Reading Go model contact map.") + go_map = read_go_map(args.go_map) + LOGGER.info("Computing Go interaction table.") + GetGo(contact_map=go_map, + cutoff_short=args.go_low, + cutoff_long=args.go_up, + go_eps=args.go_eps, + res_dist=args.go_res_dist, + prefix=args.govs_moltype, + res_graph=res_graph, + ).run_system(system) defines = ("GO_VIRT",) else: # Merge chains if required. diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index 60fe2415..632d443b 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -16,7 +16,7 @@ Read RCSU Go model contact maps. """ -def read_contmap(file_path, file_OV, file_rCSU, header_lines=0, cols=[2, 6, 10]): +def read_go_map(file_path, header_lines=0, cols=[2, 6, 10]): """ Read a RCSU contact map. """ @@ -26,7 +26,9 @@ def read_contmap(file_path, file_OV, file_rCSU, header_lines=0, cols=[2, 6, 10]) contacts = [] read = False for line in lines: - tokens = line.strip().splilt() + tokens = line.strip().split() + if len(tokens) == 0: + continue # we start parsing # using R1 is super flaky but I don't see a good way to identify # when the contact map starts ... @@ -34,7 +36,7 @@ def read_contmap(file_path, file_OV, file_rCSU, header_lines=0, cols=[2, 6, 10]) read = True elif read: # a contact consits of a resid and the chain ID - contacts.append((int(tokens[1]), tokens[2], int(tokens[4]), tokens[5])) + contacts.append((int(tokens[1]), tokens[2], int(tokens[4]), tokens[5])) else: continue return contacts diff --git a/vermouth/rcsu/get_go.py b/vermouth/rcsu/get_go.py index ff0c3a41..16176e40 100644 --- a/vermouth/rcsu/get_go.py +++ b/vermouth/rcsu/get_go.py @@ -14,95 +14,151 @@ """ Process the Go contact pairs. """ -from vermouth.processors.apply_rubber_bands import self_distance_matrix +import numpy as np +import networkx as nx +from vermouth.molecule import Interaction -def extract_position_matrix(molecule, selector): - """ - Given a selector extract a distance matrix from - a molecule. - """ - selection = [] - coordinates = [] - missing = [] - node_to_idx = {} - idx_to_node = {} - for node_idx, (node_key, attributes) in enumerate(molecule.nodes.items()): - node_to_idx[node_key] = node_idx - idx_to_node[node_idx] = node_key - if selector(attributes): - selection.append(node_idx) - coordinates.append(attributes.get('position')) - if coordinates[-1] is None: - missing.append(node_key) - node_idx += 1 - - if missing: - raise ValueError('All atoms from the selection must have coordinates. ' - 'The following atoms do not have some: {}.' - .format(' '.join(missing))) - - if not coordinates: - return - - coordinates = np.stack(coordinates) - if np.any(np.isnan(coordinates)): - LOGGER.warning("Found nan coordinates in molecule {}. " - "Will not generate an EN for it. ", - molecule.moltype, - type='unmapped-atom') - return - - distance_matrix = self_distance_matrix(coordinates) - return distance_matrix - -def _get_bb_pos(moleule, nodes): - for node in molecule.nodes: +def _get_bb_nodes(molecule, nodes): + for node in nodes: if molecule.nodes[node]['atomname'] == "BB": - return molecule.nodes[node]['position'] + return node return None +def _get_go_type(molecule, resid, chain, prefix): + for node in molecule.nodes: + attrs = molecule.nodes[node] + if attrs['resid'] == resid and attrs['chain'] == chain: + if prefix in attrs['atype']: + return attrs['atype'] + raise IOError(f"Could not find GoVs with resid {resid} in chain {chain}.") + +def _in_region(resid, regions): + """ + Check if resid falls in regions interval. + """ + for low, up in regions: + if low <= resid <= up: + return True + return False + class GetGo(): """ Generate the Go model interaction parameters. """ - def __init__(self, - contact_map, - cutoff_short, - cutoff_long, - go_eps, - res_dist, - domain, - selector): + def __init__(self, + contact_map, + cutoff_short, + cutoff_long, + go_eps, + res_dist, + res_graph, + regions=None, + water_bias=None, + idp_water_bias=None, + prefix="VS"): + self.contact_map = contact_map self.cutoff_short = cutoff_short self.cutoff_long = cutoff_long self.go_eps = go_eps self.res_dist = res_dist - self.domain = domain - self.selector = selector + self.itp_file = open('GoVirtIncludes.itp', "w", encoding='UTF-8') + self.prefix = prefix + self.res_graph = res_graph + self.water_bias = water_bias + self.idp_water_bias = idp_water_bias + self.regions = regions - def run_molecule(molecule): - res_graph = molecule.residue_graph + def write_go_structural_bias(self, molecule): chain_id_to_resnode = {} - for resnode in res_graph.nodes: - chain = res_graph.nodes[resnode].get('chain', None) - resid = res_graph.nodes[resnode].get('resid') + # find all pairs of residues that are within bonded distance of + # self.res_dist + connected_pairs = dict(nx.all_pairs_shortest_path_length(self.res_graph, + cutoff=self.res_dist)) + + # for each residue collect the chain and residue in a dict + # we use this later for identifying the residues from the + # contact map + for resnode in self.res_graph.nodes: + chain = self.res_graph.nodes[resnode].get('chain', None) + # in vermouth within a molecule all resid are unique + # when merging multiple chains we store the old resid + # the go model always references the input resid i.e. + # the _old_resid + resid = self.res_graph.nodes[resnode].get('_old_resid') chain_id_to_resnode[(chain, resid)] = resnode - - # compute the go parameters - for chainA, resA, chainB, resB in self.contact_map: - resA = chain_id_to_resnode[(chainA, resA)] - resB = chain_id_to_resnode[(chainB, resB)] - if graph_distance(resA, resB) > self.res_dist: - posA = _get_bb_pos(molecule, res_graph.nodes[resA]['graph'].nodes) - posB = _get_bb_pos(molecule, res_graph.nodes[resA]['graph'].nodes) - dist = np.linalg.norm(posA, posB) - if dist > self.cutoff_short or dist < self.cutoff_large: + + for contact in self.contact_map: + resIDA, chainA, resIDB, chainB = contact + # identify the contact in the residue graph based on + # chain ID and resid + resA = chain_id_to_resnode[(chainA, resIDA)] + resB = chain_id_to_resnode[(chainB, resIDB)] + # make sure that both residues are not connected + # note: contacts should be symmteric so we should be + # able to get rid of the second if clause + if resB not in connected_pairs[resA] and resA not in connected_pairs[resB]: + # now we lookup the backbone nodes within the residue contact + bb_node_A = _get_bb_nodes(molecule, self.res_graph.nodes[resA]['graph'].nodes) + bb_node_B = _get_bb_nodes(molecule, self.res_graph.nodes[resB]['graph'].nodes) + # compute the distance between bb-beads + dist = np.linalg.norm(molecule.nodes[bb_node_A]['position'] - + molecule.nodes[bb_node_B]['position']) + # verify that the distance between BB-beads satisfies the + # cut-off criteria + if dist > self.cutoff_short or dist < self.cutoff_long: + # compute the LJ sigma paramter for this contact sigma = dist / 1.12246204830 - Vii = 4.0 * pow(sigma, 6) * self.go_eps - Wii = 4.0 * pow(sigma, 12) * self.go_eps + # find the go virtual-sites for this residue + # probably can be done smarter but mehhhh + nodeA = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) + nodeB = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) + # write itp file with go interaction parameters + self.itp_file.write(f"{nodeA} {nodeB} 1 {sigma:3.8F} {self.go_eps:3.8F} ; structural Go bias\n") + # generate the exclusions between pairs of bb beads + excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) + molecule.interactions['exclusions'].append(excl) + + def write_water_bias_auto(self, molecule): + """ + Automatically calculate the water bias depending on the secondary structure. + """ + self.itp_file.write('; additional Lennard-Jones interaction between virtual BB bead and W\n') + for res_node in self.res_graph.nodes: + resid = self.res_graph.nodes[res_node]['resid'] + chain = self.res_graph.nodes[res_node]['chain'] + vs_go_node = _get_go_type(molecule, resid=resid, chain=chain, prefix=self.prefix) + sec_struc = self.res_graph.nodes[res_node]['sec_struc'] + eps = self.water_bias.get(sec_struc, 0.0) + if self.res_graph.nodes[res_node]['resname'] in ['GLY', 'ALA', 'VAL', 'PRO']: + sigma = 0.430 + else: + sigma = 0.470 + self.itp_file.write(f"W {vs_go_node} 1 {sigma:3.8F} {eps:3.8F} ; secondary structure water bias\n") + def write_water_bias_idr(self, molecule): + """ + Write bias for intrinsically disordered domains from manual selection. + """ + self.itp_file.write('; additional Lennard-Jones interaction between virtual BB bead and W\n') + for res_node in self.res_graph.nodes: + if _in_region(self.res_graph.nodes[res_node], self.regions): + resid = self.res_graph.nodes[res_node]['resid'] + chain = self.res_graph.nodes[res_node]['chain'] + vs_go_node = _get_go_type(molecule, resid=resid, chain=chain, prefix=self.prefix) + eps = self.idp_water_bias + if self.res_graph.nodes[res_node]['resname'] in ['GLY', 'ALA', 'VAL', 'PRO']: + sigma = 0.430 + else: + sigma = 0.470 + self.itp_file.write(f"W {vs_go_node} 1 {sigma:3.8F} {eps:3.8F} ; idp water bias\n") + def run_system(self, system): + for molecule in system.molecules: + self.write_go_structural_bias(molecule) + if self.water_bias: + self.write_water_bias_auto(self, molecule) + self.itp_file.close() From d2ed0f65cbe180c9df904bb5d4a7091f1e66068f Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:22:56 +0200 Subject: [PATCH 03/95] implement structural bias processor --- bin/martinize2 | 30 ++++ vermouth/rcsu/go_structure_bias.py | 219 +++++++++++++++++++++++++++++ 2 files changed, 249 insertions(+) create mode 100644 vermouth/rcsu/go_structure_bias.py diff --git a/bin/martinize2 b/bin/martinize2 index e61d89b0..11d31ef6 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -673,6 +673,36 @@ def entry(): default=3, help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) + go_group.add_argument( + "-govs-bias-auto", + dest="go_water", + type=float, + default=0.0, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-auto-bias", + dest="go_water", + type=float, + default=0.0, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-idrs", + dest="go_idrs", + type=float, + default=0.0, + help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + ) + go_group.add_argument( + "-govs-bias-auto", + dest="water-bias", + action="append", + type=lambda s: s.split(":"), + default=[], + help=("Define the water bias for the Go model by secondary structure type. " + "For example, use H:3.6, C:2.1 to bias helixes and coils."), + ) prot_group = parser.add_argument_group("Protein description") prot_group.add_argument( diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py new file mode 100644 index 00000000..666a94c9 --- /dev/null +++ b/vermouth/rcsu/go_structure_bias.py @@ -0,0 +1,219 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Obtain the structural bias for the Go model. +""" +import numpy as np +import networkx as nx +from vermouth.molecule import Interaction, attributes_match +from vermouth.processors import Procssor + +class ComputeStructuralGoBias(Processor): + """ + Generate the Go model structural bias for a system + of molecules. This processor class has two main + functions: .contact_selector and .compute_bias. + The .run_molecule function simply loops over all + molecules in the system and calls the other two + functions. The computed structural bias parameters + are stored in `system.gmx_topology_params` and can + be written out using the `vermouth.gmx.write_topology` + function. + + ** Subclassing ** + In order to customize the Go-model structural bias + it is recommended to subclass this function and + overwrite the .contact_selector method and/or + the .compute_bias method. This subclassed Processor + then has to be added to the into the /bin/martinize2 + pipline in place of the StructuralBiasWriter or as + replacement in the GoPipeline. + """ + def __init__(self, + contact_map, + cutoff_short, + cutoff_long, + go_eps, + res_dist, + res_graph=None, + prefix="VS"): + """ + Initialize the Processor with arguments required + to setup the Go model structural bias. + + Parameters + ---------- + contact_map: list[(str, int, str, int)] + list of contacts defined as by the chain + identifier and residue index + cutoff_short: float + distances smaller than this are ignored + cutoff_long: float + distances larger than this are ignored + go_eps: float + epsilon value of the structural bias in + kJ/mol + res_dist: int + if nodes are closer than res_dist along + the residue graph they are ignored; this + is similar to sequence distance but takes + into account disulfide bridges for example + res_graph: :class:vermouth.Molecule + residue graph of the molecule; if None it + get's generated automatically + prefix: str + prefix for all virtual-site atomtypes + """ + self.contact_map = contact_map + self.cutoff_short = cutoff_short + self.cutoff_long = cutoff_long + self.go_eps = go_eps + self.res_dist = res_dist + self.prefix = prefix + self.res_graph = res_graph + # don't modify + self.__chain_id_to_resnode = {} + + # do not overwrite when subclassing + def _chain_id_to_resnode(self, chain, resid): + """ + Return the node corresponding to the chain and + resid. First time the function is run the dict + is being created. + + Parameters + ---------- + chain: str + chain identifier + resid: int + residue index + + Returns + ------- + dict + a dict matching the chain,resid to the self.res_graph node + """ + if self.__chain_id_to_resnode: + return self.__chain_id_to_resnode + + # for each residue collect the chain and residue in a dict + # we use this later for identifying the residues from the + # contact map + for resnode in self.res_graph.nodes: + chain = self.res_graph.nodes[resnode].get('chain', None) + # in vermouth within a molecule all resid are unique + # when merging multiple chains we store the old resid + # the go model always references the input resid i.e. + # the _old_resid + resid = self.res_graph.nodes[resnode].get('_old_resid') + self.__chain_id_to_resnode[(chain, resid)] = resnode + return self.__chain_id_to_resnode + + def contact_selector(self, molecule): + """ + Select all contacts from the contact map + that according to their distance and graph + connectivity are elegible to form a Go + bond and create exclusions between the + backbone beads of those contacts. + + Parameters + ---------- + molecule: :class:vermouth.Molecule + + Returns + ------- + list[(abc.hashable, abc.hashable, float)] + list of node keys and distance + """ + # distance_matrix of elegible pairs as tuple(node, node, dist) + contact_matrix = [] + # find all pairs of residues that are within bonded distance of + # self.res_dist + connected_pairs = dict(nx.all_pairs_shortest_path_length(self.res_graph, + cutoff=self.res_dist)) + for contact in self.contact_map: + resIDA, chainA, resIDB, chainB = contact + # identify the contact in the residue graph based on + # chain ID and resid + resA = self.chain_id_to_resnode[(chainA, resIDA)] + resB = self.chain_id_to_resnode[(chainB, resIDB)] + # make sure that both residues are not connected + # note: contacts should be symmteric so we only + # check against one + if resB not in connected_pairs[resA]: + # now we lookup the backbone nodes within the residue contact + bb_node_A = next(filter_minimal(self.res_graph.nodes[resB], select_backbone)) + bb_node_B = next(filter_minimal(self.res_graph.nodes[resB], select_backbone)) + # compute the distance between bb-beads + dist = np.linalg.norm(molecule.nodes[bb_node_A]['position'] - + molecule.nodes[bb_node_B]['position']) + # verify that the distance between BB-beads satisfies the + # cut-off criteria + if self.cut_off_large > dist > self.cutoff_short: + # find the go virtual-sites for this residue + # probably can be done smarter but mehhhh + nodeA = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) + nodeB = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) + # generate backbone backbone exclusions + # perhaps one day can be it's own function + excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) + molecule.interactions['exclusions'].append(excl) + + contact_matrix.append((nodeA, nodeB, dist)) + return contact_matrix + + def compute_go_interaction(self, contacts): + """ + Compute the epsilon value given a distance between + two nodes, figure out the atomtype name and store + it in the systems attribute gmx_topology_params. + + Parameters + ---------- + contacts: list[(str, str, float)] + list of node-keys and their distance + + Returns + ---------- + dict[frozenset(str, str): float] + dict of interaction parameters indexed by atomtype + """ + go_inters = {} + for node_a, node_b, dist in contacts: + # compute the LJ sigma paramter for this contact + # 1.12246204830 is a magic number by Sebastian + sigma = dist / 1.12246204830 + # find the go virtual-sites for this residue + # probably can be done smarter but mehhhh + go_inters[frozenset(atype_a, atype_b)] = (sigma, self.go_eps) + return go_inters + + def run_system(self, system): + """ + Process `system`. + + Parameters + ---------- + system: vermouth.system.System + The system to process. Is modified in-place. + """ + for molecule in system.molecules: + # compute the contacts; this also creates + # the exclusions + contacts = self.contact_selector(molecule) + # compute the interaction parameters + inters = self.compute_go_interaction(contacts) + # update the contacts for the system + self.system.gmx_topology_params.upadte(inters) From ab9303bc0632682ed6f1d84d53ba83c2511c203d Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:23:14 +0200 Subject: [PATCH 04/95] have some handy utilites for the Go pipeline --- vermouth/rcsu/go_utils.py | 70 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 vermouth/rcsu/go_utils.py diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py new file mode 100644 index 00000000..d50b49f3 --- /dev/null +++ b/vermouth/rcsu/go_utils.py @@ -0,0 +1,70 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Utilities for Go model processors. +""" +from vermouth.molecule import attributes_match + +def get_go_type_from_attributes(molecule, prefix, kwargs): + """ + Find all nodes that satisfy a number of attributes specified + as kwargs and have a specific atomtype prefix. + + Parameters + ---------- + molecule: :class:vermouth.Molecule + prefix: str + the atom-type prefix of the Go virtual side + kwargs: + any number of attributes + + Yields + ------ + str + the atom-type + + Raises + ------ + IOError + If no node can be found that matches attributes + and prefix an IOError is raised. + """ + for node in molecule.nodes: + if attributes_match(molecule.nodes[node], kwargs) and\ + attrs['atype'].startswith(prefix): + yield attrs['atype'] + + resid = kwargs['resid'] + chain = kwargs['chain'] + raise IOError(f"Could not find GoVs with resid {resid} in chain {chain}.") + +def _in_resid_region(resid, regions): + """ + Check if resid falls in regions interval. + + Parameters + ---------- + resid: int + the resid of a molecule + regions: list[tuple(int)] + a list of the intervals + + Returns + ------- + bool + """ + for low, up in regions: + if low <= resid <= up: + return True + return False From b3156038f742d48e18f7b472dbec73b9ce7ee0e5 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:57:37 +0200 Subject: [PATCH 05/95] add water bias functionality --- vermouth/rcsu/go_water_bias.py | 113 +++++++++++++++++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 vermouth/rcsu/go_water_bias.py diff --git a/vermouth/rcsu/go_water_bias.py b/vermouth/rcsu/go_water_bias.py new file mode 100644 index 00000000..3d98c0bc --- /dev/null +++ b/vermouth/rcsu/go_water_bias.py @@ -0,0 +1,113 @@ +from vermouth.processor import Processor + +class ComputeWaterGoBias(Processor): + """ + Processor which computes the water bias for + the Martini Go and Martini IDP model. + + The water bias streght is defined per secondary + structure element in `water_bias` and assinged if + `auto_bias` is set to True. Using the `selector` + argument the water_bias can be changed for + intrinsically disordered regions (IDRs). The IDR + bias superseeds the auto bias. + + This Processor updates the system.gmx_topology_params + attribute. + + ** Subclassing ** + If the procedure by which to assign the water bias is + to be changed this processor is best subclassed and the + assign_residue_water_bias method overwritten. + """ + + def __init__(self, + water_bias, + auto_bias + selector, + prefix=""): + """ + + + Parameters + ---------- + water_bias: dict[str, float] + a dict of secondary structure codes and + epsilon value for the water bias in kJ/mol + auto_bias: bool + selector: + selector for IDRs + prefix: str + prefix of the Go virtual-site atomtypes + """ + self.water_bias = water_bias + self.auto_bias = auto_bias + self.selector = selecor + self.prefix = prefix + + def assign_residue_water_bias(self, molecule, res_graph): + """ + Assign the residue water bias for all residues + with a secondary structure element or that are + defined by the region selector. Region selectors + superceed the auto assignement. + + Parameters + ---------- + molecule: :class:vermouth.Molecule + the molecule + res_graph: :class:vermouth.Molecule + the residue graph of the molecule + """ + bias_params = {} + for res_node in self.res_graph.nodes: + resid = self.res_graph.nodes[res_node]['resid'] + chain = self.res_graph.nodes[res_node]['chain'] + resname = self.res_gaph.nodes[res_node]['resname'] + + if self.selector(res_graph, res_node): + eps = self.water_bias.get('idr', 0.0) + elif: + sec_struc = self.res_graph.nodes[res_node]['sec_struc'] + eps = self.water_bias.get(sec_struc, 0.0) + else: + continue + + vs_go_node = _get_go_type(res_graph.nodes[res_node], + resid=resid, + chain=chain, + prefix=self.prefix) + + # what is the blocks bb-type + bb_type = molecule.forcefield.blocks[resname]['BB']['atype'] + if bb_type.startswith('S'): + size = _get_bead_size(bb_type) + sigma = molecule.forcefield.variables['bead_sizes'][size] + elif bb_type.startswith('T'): + sigma = 0.41 + else: + sigma = 0.47 + + bias_params[frozenset([forcefield.water_name, vs_go_node])] = (sigma, eps) + return bias_params + + def run_system(self, system): + """ + Assign the water bias of the Go model to file. Biasing + is always molecule specific i.e. no two different + vermouth molecules can have the same bias. + + Parameters + ---------- + molecule: :class:`vermouth.Molecule` + """ + if self.selector or self.auto: + for molecule in system.molecules: + if hasattr(molecule.res_graph): + res_graph = molecule.res_graph + else: + make_residue_graph(molecule) + + bias_params = self.determine_residue_water_bias(self, res_graph) + system.gmx_topology_params["nonbond_params"].update(bias_params) + return system From 77d7c70a25d8bddb4b4bf791497486c1cdeb5d59 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:57:56 +0200 Subject: [PATCH 06/95] use new contact map format --- vermouth/rcsu/contact_map.py | 30 +++++++++++++++++++----------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index 632d443b..a232d661 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -16,9 +16,21 @@ Read RCSU Go model contact maps. """ -def read_go_map(file_path, header_lines=0, cols=[2, 6, 10]): +def read_go_map(file_path): """ - Read a RCSU contact map. + Read a RCSU contact map from the c code as published in + doi:zzzz. The format requires all contacts to have 18 + columns and the first column to be a capital R. + + Paraemters + --------- + file_path: :cls:pathlib.Path + path to the contact map file + + Returns + ------- + list(tuple(4)) + contact as chain id, res id, chain id, res id """ with open(file_path, "r", encoding='UTF-8') as _file: lines = _file.readlines() @@ -29,14 +41,10 @@ def read_go_map(file_path, header_lines=0, cols=[2, 6, 10]): tokens = line.strip().split() if len(tokens) == 0: continue - # we start parsing - # using R1 is super flaky but I don't see a good way to identify - # when the contact map starts ... - if tokens[0] == "R1": - read = True - elif read: - # a contact consits of a resid and the chain ID + + if tokens[0] == "R" and len(tokens) == 18: contacts.append((int(tokens[1]), tokens[2], int(tokens[4]), tokens[5])) - else: - continue + + if len(contacts) == 0: + raise IOError("You contact map is empty. Are you sure it has the right formatting?") return contacts From 96be469f01c5e1aff19644b2ced3a116b9fabbd0 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:58:24 +0200 Subject: [PATCH 07/95] rename get go --- vermouth/rcsu/get_go.py | 164 ---------------------------------------- 1 file changed, 164 deletions(-) delete mode 100644 vermouth/rcsu/get_go.py diff --git a/vermouth/rcsu/get_go.py b/vermouth/rcsu/get_go.py deleted file mode 100644 index 16176e40..00000000 --- a/vermouth/rcsu/get_go.py +++ /dev/null @@ -1,164 +0,0 @@ -# Copyright 2023 University of Groningen -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -""" -Process the Go contact pairs. -""" -import numpy as np -import networkx as nx -from vermouth.molecule import Interaction - -def _get_bb_nodes(molecule, nodes): - for node in nodes: - if molecule.nodes[node]['atomname'] == "BB": - return node - return None - -def _get_go_type(molecule, resid, chain, prefix): - for node in molecule.nodes: - attrs = molecule.nodes[node] - if attrs['resid'] == resid and attrs['chain'] == chain: - if prefix in attrs['atype']: - return attrs['atype'] - raise IOError(f"Could not find GoVs with resid {resid} in chain {chain}.") - -def _in_region(resid, regions): - """ - Check if resid falls in regions interval. - """ - for low, up in regions: - if low <= resid <= up: - return True - return False - -class GetGo(): - """ - Generate the Go model interaction parameters. - """ - def __init__(self, - contact_map, - cutoff_short, - cutoff_long, - go_eps, - res_dist, - res_graph, - regions=None, - water_bias=None, - idp_water_bias=None, - prefix="VS"): - - self.contact_map = contact_map - self.cutoff_short = cutoff_short - self.cutoff_long = cutoff_long - self.go_eps = go_eps - self.res_dist = res_dist - self.itp_file = open('GoVirtIncludes.itp', "w", encoding='UTF-8') - self.prefix = prefix - self.res_graph = res_graph - self.water_bias = water_bias - self.idp_water_bias = idp_water_bias - self.regions = regions - - def write_go_structural_bias(self, molecule): - chain_id_to_resnode = {} - # find all pairs of residues that are within bonded distance of - # self.res_dist - connected_pairs = dict(nx.all_pairs_shortest_path_length(self.res_graph, - cutoff=self.res_dist)) - - # for each residue collect the chain and residue in a dict - # we use this later for identifying the residues from the - # contact map - for resnode in self.res_graph.nodes: - chain = self.res_graph.nodes[resnode].get('chain', None) - # in vermouth within a molecule all resid are unique - # when merging multiple chains we store the old resid - # the go model always references the input resid i.e. - # the _old_resid - resid = self.res_graph.nodes[resnode].get('_old_resid') - chain_id_to_resnode[(chain, resid)] = resnode - - for contact in self.contact_map: - resIDA, chainA, resIDB, chainB = contact - # identify the contact in the residue graph based on - # chain ID and resid - resA = chain_id_to_resnode[(chainA, resIDA)] - resB = chain_id_to_resnode[(chainB, resIDB)] - # make sure that both residues are not connected - # note: contacts should be symmteric so we should be - # able to get rid of the second if clause - if resB not in connected_pairs[resA] and resA not in connected_pairs[resB]: - # now we lookup the backbone nodes within the residue contact - bb_node_A = _get_bb_nodes(molecule, self.res_graph.nodes[resA]['graph'].nodes) - bb_node_B = _get_bb_nodes(molecule, self.res_graph.nodes[resB]['graph'].nodes) - # compute the distance between bb-beads - dist = np.linalg.norm(molecule.nodes[bb_node_A]['position'] - - molecule.nodes[bb_node_B]['position']) - # verify that the distance between BB-beads satisfies the - # cut-off criteria - if dist > self.cutoff_short or dist < self.cutoff_long: - # compute the LJ sigma paramter for this contact - sigma = dist / 1.12246204830 - # find the go virtual-sites for this residue - # probably can be done smarter but mehhhh - nodeA = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) - nodeB = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) - # write itp file with go interaction parameters - self.itp_file.write(f"{nodeA} {nodeB} 1 {sigma:3.8F} {self.go_eps:3.8F} ; structural Go bias\n") - # generate the exclusions between pairs of bb beads - excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) - molecule.interactions['exclusions'].append(excl) - - def write_water_bias_auto(self, molecule): - """ - Automatically calculate the water bias depending on the secondary structure. - """ - self.itp_file.write('; additional Lennard-Jones interaction between virtual BB bead and W\n') - for res_node in self.res_graph.nodes: - resid = self.res_graph.nodes[res_node]['resid'] - chain = self.res_graph.nodes[res_node]['chain'] - vs_go_node = _get_go_type(molecule, resid=resid, chain=chain, prefix=self.prefix) - sec_struc = self.res_graph.nodes[res_node]['sec_struc'] - eps = self.water_bias.get(sec_struc, 0.0) - if self.res_graph.nodes[res_node]['resname'] in ['GLY', 'ALA', 'VAL', 'PRO']: - sigma = 0.430 - else: - sigma = 0.470 - - self.itp_file.write(f"W {vs_go_node} 1 {sigma:3.8F} {eps:3.8F} ; secondary structure water bias\n") - - def write_water_bias_idr(self, molecule): - """ - Write bias for intrinsically disordered domains from manual selection. - """ - self.itp_file.write('; additional Lennard-Jones interaction between virtual BB bead and W\n') - for res_node in self.res_graph.nodes: - if _in_region(self.res_graph.nodes[res_node], self.regions): - resid = self.res_graph.nodes[res_node]['resid'] - chain = self.res_graph.nodes[res_node]['chain'] - vs_go_node = _get_go_type(molecule, resid=resid, chain=chain, prefix=self.prefix) - eps = self.idp_water_bias - if self.res_graph.nodes[res_node]['resname'] in ['GLY', 'ALA', 'VAL', 'PRO']: - sigma = 0.430 - else: - sigma = 0.470 - - self.itp_file.write(f"W {vs_go_node} 1 {sigma:3.8F} {eps:3.8F} ; idp water bias\n") - - def run_system(self, system): - for molecule in system.molecules: - self.write_go_structural_bias(molecule) - if self.water_bias: - self.write_water_bias_auto(self, molecule) - - self.itp_file.close() From 6e05c098f9acec60bbad218512820b1d3a1cbee1 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 15:59:13 +0200 Subject: [PATCH 08/95] add licensce header --- vermouth/rcsu/go_water_bias.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/vermouth/rcsu/go_water_bias.py b/vermouth/rcsu/go_water_bias.py index 3d98c0bc..ead3aa99 100644 --- a/vermouth/rcsu/go_water_bias.py +++ b/vermouth/rcsu/go_water_bias.py @@ -1,3 +1,17 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from vermouth.processor import Processor class ComputeWaterGoBias(Processor): From 92fb9b90045ae0308ab6f3b240e4be223f008d79 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 16:21:00 +0200 Subject: [PATCH 09/95] move the go_vs_includes --- vermouth/{processors => rcsu}/go_vs_includes.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename vermouth/{processors => rcsu}/go_vs_includes.py (99%) diff --git a/vermouth/processors/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py similarity index 99% rename from vermouth/processors/go_vs_includes.py rename to vermouth/rcsu/go_vs_includes.py index 60548b70..704a5f3a 100644 --- a/vermouth/processors/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -41,8 +41,7 @@ import networkx as nx from ..molecule import Interaction -from .processor import Processor - +from ..processors.processor import Processor class GoVirtIncludes(Processor): """ From 462d033f395641db93c4451ba433a6678c49bcbe Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 16:21:15 +0200 Subject: [PATCH 10/95] add go_pipeline --- vermouth/rcsu/go_pipeline.py | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 vermouth/rcsu/go_pipeline.py diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py new file mode 100644 index 00000000..9698c6b2 --- /dev/null +++ b/vermouth/rcsu/go_pipeline.py @@ -0,0 +1,36 @@ +# Copyright 2023 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Wrapper of Processors defining the GoPipline. +""" +from vermouth.processors import Processor +from .go_vs_includes import GoVirtIncludes +from .go_structure_bias import ComputeStructuralGoBias +from .go_water_bias import ComputeWaterGoBias + +class ProcessorPipline(Processor): + """ + Wrapping all processors for the go model. + """ + def __init__(self, processor_list, **kwargs): + self.processor_list = processor_list + + def run_system(self, system): + for processor in processor_list: + process_args = inspect.getfullargspec(processor).args + process_args_values = {self.kwargs[arg] for arg in process_args} + processor(**process_args_values).run_system(system) + return system + +GoPipeline = ProcessorPipline([GoVirtIncludes, ComputeStructuralGoBias, ComputeWaterGoBias]) From 01b617b0a307acd3e36d37dc788c46b211e00f48 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 16:36:05 +0200 Subject: [PATCH 11/95] implement go_pipeline --- bin/martinize2 | 39 +++++++++++------------------------- vermouth/rcsu/go_pipeline.py | 24 ++++++++++++++++++++-- 2 files changed, 34 insertions(+), 29 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 11d31ef6..b8379994 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -1040,34 +1040,19 @@ def entry(): vermouth.ApplyPosres(node_selector, args.posres_fc).run_system(system) if args.govs_includes: - # The way Virtual Site GoMartini works has to be in sync with - # Sebastian's create_goVirt.py script, until the method is fully - # implemented in vermouth. One call of martinize2 must create a single - # molecule, regardless of the number of fragments in the input. - # The molecule type name is provided as an input with the -govs-moltype - # flag to be consistent with the name provided to Sebastian's script. - # The name cannot be guessed because a system may need to be composed - # from multiple calls to martinize2 and create_goVirt.py. - LOGGER.info("Adding includes for Virtual Site Go Martini.", type="step") - LOGGER.info( - "The output topology will require files generated by " '"create_goVirt.py".' - ) - vermouth.MergeAllMolecules().run_system(system) - # not ideal but we need it before making the Go sides - res_graph = vermouth.graph_utils.make_residue_graph(system.molecules[0]) - vermouth.SetMoleculeMeta(moltype=args.govs_moltype).run_system(system) - vermouth.GoVirtIncludes().run_system(system) - LOGGER.info("Reading Go model contact map.") + LOGGER.info("Reading Go model contact map.", type="step") go_map = read_go_map(args.go_map) - LOGGER.info("Computing Go interaction table.") - GetGo(contact_map=go_map, - cutoff_short=args.go_low, - cutoff_long=args.go_up, - go_eps=args.go_eps, - res_dist=args.go_res_dist, - prefix=args.govs_moltype, - res_graph=res_graph, - ).run_system(system) + LOGGER.info("Generating the Go model.", type="step") + GoPipeline(moltype=args.govs_moltype, + contact_map=go_map, + cutoff_short=args.go_low, + cutoff_long=args.go_up, + go_eps=args.go_eps, + res_dist=args.go_res_dist, + prefix=args.govs_moltype, + res_graph=res_graph, + ).run_system(system) + defines = ("GO_VIRT",) else: # Merge chains if required. diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 9698c6b2..9f0e9c60 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -18,19 +18,39 @@ from .go_vs_includes import GoVirtIncludes from .go_structure_bias import ComputeStructuralGoBias from .go_water_bias import ComputeWaterGoBias +from ..processors import SetMoleculeMeta -class ProcessorPipline(Processor): +class GoProcessorPipline(Processor): """ Wrapping all processors for the go model. """ def __init__(self, processor_list, **kwargs): self.processor_list = processor_list + def prepare_run(self, system): + """ + Things to do before running the pipeline. + """ + # merge all molecules in the system + # this will eventually become deprecated + # with the proper Go-model for multimers + vermouth.MergeAllMolecules().run_system(system) + for molecule in system.molecules: + res_graph = vermouth.graph_utils.make_residue_graph(system.molecules[0]) + molecule.residue_graph = res_graph + + def postprocess_run(self, system): + """ + Do required post-processing. + """ + pass + def run_system(self, system): + self.prepare_run(self, system) for processor in processor_list: process_args = inspect.getfullargspec(processor).args process_args_values = {self.kwargs[arg] for arg in process_args} processor(**process_args_values).run_system(system) return system -GoPipeline = ProcessorPipline([GoVirtIncludes, ComputeStructuralGoBias, ComputeWaterGoBias]) +GoPipeline = ProcessorPipline([SetMoleculeMeta, GoVirtIncludes, ComputeStructuralGoBias, ComputeWaterGoBias]) From f0bc07fea7d95d3b756c85c32f04142348aeb3aa Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 16:36:26 +0200 Subject: [PATCH 12/95] move logging to processor --- vermouth/rcsu/go_vs_includes.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 704a5f3a..92726a53 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -82,6 +82,10 @@ def run_molecule(self, molecule): molecule.meta['post_section_lines'] = includes return molecule + def run_system(self, system): + LOGGER.info("Adding includes for Virtual Site Go Martini.", type="step") + for molecule in system.molecules: + self.run_molecule(system) def add_virtual_sites(molecule, prefix, backbone='BB', atomname='CA', charge=0): """ From 1fd451a0cab1028018d673f6636def713a0a16c9 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 12 Oct 2023 17:06:45 +0200 Subject: [PATCH 13/95] lining --- vermouth/rcsu/contact_map.py | 1 - vermouth/rcsu/go_pipeline.py | 12 ++++++-- vermouth/rcsu/go_structure_bias.py | 14 ++++++---- vermouth/rcsu/go_utils.py | 9 ++++++ vermouth/rcsu/go_water_bias.py | 45 ++++++++++++++---------------- 5 files changed, 47 insertions(+), 34 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index a232d661..b22305fc 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -36,7 +36,6 @@ def read_go_map(file_path): lines = _file.readlines() contacts = [] - read = False for line in lines: tokens = line.strip().split() if len(tokens) == 0: diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 9f0e9c60..93b39e7c 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -14,6 +14,8 @@ """ Wrapper of Processors defining the GoPipline. """ +import inspect +import vermouth from vermouth.processors import Processor from .go_vs_includes import GoVirtIncludes from .go_structure_bias import ComputeStructuralGoBias @@ -26,6 +28,7 @@ class GoProcessorPipline(Processor): """ def __init__(self, processor_list, **kwargs): self.processor_list = processor_list + self.kwargs = kwargs def prepare_run(self, system): """ @@ -47,10 +50,13 @@ def postprocess_run(self, system): def run_system(self, system): self.prepare_run(self, system) - for processor in processor_list: + for processor in self.processor_list: process_args = inspect.getfullargspec(processor).args process_args_values = {self.kwargs[arg] for arg in process_args} processor(**process_args_values).run_system(system) - return system + return system -GoPipeline = ProcessorPipline([SetMoleculeMeta, GoVirtIncludes, ComputeStructuralGoBias, ComputeWaterGoBias]) +GoPipeline = GoProcessorPipline([SetMoleculeMeta, + GoVirtIncludes, + ComputeStructuralGoBias, + ComputeWaterGoBias]) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 666a94c9..ed448950 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -16,8 +16,10 @@ """ import numpy as np import networkx as nx -from vermouth.molecule import Interaction, attributes_match -from vermouth.processors import Procssor +from ..molecule import Interaction +from .. import Processor +from ..selectors import filter_minimal, select_backbone +from .go_utils import _get_go_type class ComputeStructuralGoBias(Processor): """ @@ -164,14 +166,14 @@ def contact_selector(self, molecule): if self.cut_off_large > dist > self.cutoff_short: # find the go virtual-sites for this residue # probably can be done smarter but mehhhh - nodeA = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) - nodeB = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) + atype_a = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) + atype_b = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) # generate backbone backbone exclusions # perhaps one day can be it's own function excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) molecule.interactions['exclusions'].append(excl) - contact_matrix.append((nodeA, nodeB, dist)) + contact_matrix.append((atype_a, atype_b, dist)) return contact_matrix def compute_go_interaction(self, contacts): @@ -191,7 +193,7 @@ def compute_go_interaction(self, contacts): dict of interaction parameters indexed by atomtype """ go_inters = {} - for node_a, node_b, dist in contacts: + for atype_a, atype_b, dist in contacts: # compute the LJ sigma paramter for this contact # 1.12246204830 is a magic number by Sebastian sigma = dist / 1.12246204830 diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index d50b49f3..2d231191 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -68,3 +68,12 @@ def _in_resid_region(resid, regions): if low <= resid <= up: return True return False + +def _get_bead_size(atype): + if atype.startswith("S"): + bead_size = "small" + elif atype.startswith("T"): + bead_size = "tiny" + else: + bead_size = "regular" + return bead_size diff --git a/vermouth/rcsu/go_water_bias.py b/vermouth/rcsu/go_water_bias.py index ead3aa99..d1ff386c 100644 --- a/vermouth/rcsu/go_water_bias.py +++ b/vermouth/rcsu/go_water_bias.py @@ -12,7 +12,9 @@ # See the License for the specific language governing permissions and # limitations under the License. -from vermouth.processor import Processor +from ..processors.processor import Processor +from ..graph_utils import make_residue_graph +from .go_utils import get_go_type_from_attributes, _get_bead_size class ComputeWaterGoBias(Processor): """ @@ -21,7 +23,7 @@ class ComputeWaterGoBias(Processor): The water bias streght is defined per secondary structure element in `water_bias` and assinged if - `auto_bias` is set to True. Using the `selector` + `auto_bias` is set to True. Using the `idr_regions` argument the water_bias can be changed for intrinsically disordered regions (IDRs). The IDR bias superseeds the auto bias. @@ -37,8 +39,8 @@ class ComputeWaterGoBias(Processor): def __init__(self, water_bias, - auto_bias - selector, + auto_bias, + idr_regions, prefix=""): """ @@ -49,14 +51,14 @@ def __init__(self, a dict of secondary structure codes and epsilon value for the water bias in kJ/mol auto_bias: bool - selector: - selector for IDRs + idr_regions: + regions defining the IDRs prefix: str prefix of the Go virtual-site atomtypes """ self.water_bias = water_bias self.auto_bias = auto_bias - self.selector = selecor + self.idr_regions = idr_regions self.prefix = prefix def assign_residue_water_bias(self, molecule, res_graph): @@ -81,28 +83,23 @@ def assign_residue_water_bias(self, molecule, res_graph): if self.selector(res_graph, res_node): eps = self.water_bias.get('idr', 0.0) - elif: + elif self.auto_bias: sec_struc = self.res_graph.nodes[res_node]['sec_struc'] eps = self.water_bias.get(sec_struc, 0.0) else: continue - vs_go_node = _get_go_type(res_graph.nodes[res_node], - resid=resid, - chain=chain, - prefix=self.prefix) - - # what is the blocks bb-type - bb_type = molecule.forcefield.blocks[resname]['BB']['atype'] - if bb_type.startswith('S'): - size = _get_bead_size(bb_type) - sigma = molecule.forcefield.variables['bead_sizes'][size] - elif bb_type.startswith('T'): - sigma = 0.41 - else: - sigma = 0.47 + vs_go_node = get_go_type_from_attributes(res_graph.nodes[res_node], + resid=resid, + chain=chain, + prefix=self.prefix) + + # what is the blocks bb-type + bb_type = molecule.force_field.blocks[resname]['BB']['atype'] + size = _get_bead_size(bb_type) + sigma = molecule.force_field.variables['bead_sizes'][size] + bias_params[frozenset([molecule.force_field.water_name, vs_go_node])] = (sigma, eps) - bias_params[frozenset([forcefield.water_name, vs_go_node])] = (sigma, eps) return bias_params def run_system(self, system): @@ -115,7 +112,7 @@ def run_system(self, system): ---------- molecule: :class:`vermouth.Molecule` """ - if self.selector or self.auto: + if self.idr_regions or self.auto: for molecule in system.molecules: if hasattr(molecule.res_graph): res_graph = molecule.res_graph From e60e120bdcd44860241c580ff95efc9b3a41b616 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 13 Oct 2023 13:42:48 +0200 Subject: [PATCH 14/95] refactor topology writing --- vermouth/gmx/topology.py | 210 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 210 insertions(+) create mode 100644 vermouth/gmx/topology.py diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py new file mode 100644 index 00000000..7d358345 --- /dev/null +++ b/vermouth/gmx/topology.py @@ -0,0 +1,210 @@ +""" +I/O of topology parameters that are not molecules. +""" +import itertools +from collections import namedtuple +import textwrap +import vermouth +from vermouth.file_writer import deferred_open +from vermouth.citation_parser import citation_formatter +from ..log_helpers import StyleAdapter, get_logger +from .itp import _interaction_sorting_key + +LOGGER = StyleAdapter(get_logger(__name__)) + +Atomtype = namedtuple('Atomtype', 'molecule node sigma epsilon meta') +NonbondParam = namedtuple('NonbondParam', 'sigma epsilon meta') + +def _group_by_conditionals(interactions): + interactions_group_sorted = sorted(interactions, + key=_interaction_sorting_key + ) + interaction_grouped = itertools.groupby( + interactions_group_sorted, + key=_interaction_sorting_key + ) + return interaction_grouped + +def convert_sigma_epsilon(sigma, epsilon): + """ + Convert the LJ potential from sigma epsilon + form to C6 C12 form. + """ + C6 = 4*sigma*epsilon**6 + C12 = 4*sigma*epsilon**12 + return C6, C12 + +def write_atomtypes(system, itp_path, C6C12=False): + """ + Writes the [atomtypes] directive to file. + All atomtypes are defined in system.gmx_topology_params. + Masses and further information are taken from the molecule + directly. + """ + conditional_keys = {True: '#ifdef', False: '#ifndef'} + with deferred_open(itp_path, "w") as itp_file: + grouped_types = _group_by_conditionals(system.gmx_topology_params['atomtypes']) + for (conditional, group), interactions_in_group in grouped_types: + if conditional: + conditional_key = conditional_keys[conditional[1]] + itp_file.write('{} {}\n'.format(conditional_key, conditional[0])) + if group: + itp_file.write('; {}\n'.format(group)) + + for atomtype in interactions_in_group: + atype = atomtype.molecule.nodes[atomtype.node]['atype'] + charge = atomtype.molecule.nodes[atomtype.node]['charge'] + mass = atomtype.molecule.nodes[atomtype.node]['mass'] + + if C6C12: + nb1, nb2 = convert_sigma_epsilon(atomtype.sigma, atomtype.epsilon) + else: + nb1, nb2 = atomtype.sigma, atomtype.epsilon + + comments = ";" + " ".join(atomtype.meta['comment']) + itp_file.write(f"{atype} {mass} {charge} A {nb1:3.8F} {nb2:3.8F} {comments}\n") + +def write_nonbond_params(system, itp_path, C6C12=False): + """ + Writes the [nonbond_params] directive to file. + All atomtypes are defined in system.gmx_topology_params. + Masses and further information are taken from the molecule + directly. + """ + conditional_keys = {True: '#ifdef', False: '#ifndef'} + with deferred_open(itp_path, "w") as itp_file: + grouped_types = _group_by_conditionals(system.gmx_topology_params['nonbond_params']) + for (conditional, group), interactions_in_group in grouped_types: + if conditional: + conditional_key = conditional_keys[conditional[1]] + itp_file.write('{} {}\n'.format(conditional_key, conditional[0])) + if group: + itp_file.write('; {}\n'.format(group)) + + + for atoms, nb_params in interactions_in_group: + if len(atoms) == 2: + a1, a2 = atoms + # self interaction + else: + a1 = atoms[0] + a2 = atoms[0] + + if C6C12: + nb1, nb2 = convert_sigma_epsilon(nb_params.sigma, nb_params.epsilon) + else: + nb1, nb2 = nb_params.sigma, nb_params.epsilon + + comments = ";" + " ".join(nb_params.meta['comment']) + itp_path.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n") + +def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), header=()): + """ + Writes a Gromacs .top file for the specified system. Gromacs topology + files are defined by directives for example `[ atomtypes ]`. However, + Gromacs supports writing parts of the topology to so called .itp + files which can be inculded into a toplevel topology file with the + extension .top using #include statements. The topology writer will + generate such a toplevel topology file where the different directives + are written to seperate .itp files and included into the toplevel + file. + + Parameters + ---------- + system: :class:vermouth.System + top_path: pathlib.Path + path for topology file + defines: tuple(str) + define statments to include in the topology + header: tuple(str) + any comment lines to include at the beginning + """ + if not system.molecules: + raise ValueError("No molecule in the system. Nothing to write.") + + # First we write the atomtypes and nonbondparams directive + if itp_paths: + write_nonbond_params(system, C6C12, itp_paths[0]) + write_atomtypes(system, C6C12, itp_paths[1]) + include_string = "\n".join('#include "{}.itp"'.format(path) for path in itp_paths[:2]) + + # Write the ITP files for the molecule types, and prepare writing the + # [ molecules ] section of the top file. + # * We write one ITP file for each different moltype in the system, the + # moltype being defined by the name provided under the "moltype" meta of + # the molecules. If more than one molecule share the same moltype, we use + # the first one to write the ITP file. + moltype_written = set() + # * We keep track of the length of the longer moltype name, to align the + # [ molecules ] section. + max_name_length = 0 + # * We keep track of groups of successive molecules with the same moltypes. + moltype_count = [] # items will be [moltype, number of molecules] + + # Iterate over groups of successive molecules with the same moltypes. We + # shall *NOT* sort the molecules before hand, as groups of successive + # molecules with the same moltype can be interupted by other moltypes, and + # we want to reflect these interuptions in the [ molecules ] section of the + # top file. + molecule_groups = itertools.groupby( + system.molecules, key=lambda x: x.meta["moltype"] + ) + for moltype, molecules in molecule_groups: + molecule = next(molecules) + if moltype not in moltype_written: + # A given moltype can appear more than once in the sequence of + # molecules, without being uninterupted by other moltypes. Even in + # that case, we want to write the ITP only once. + with deferred_open("{}.itp".format(moltype), "w") as outfile: + # here we format and merge all citations + header[-1] = header[-1] + "\n" + header.append("Pleas cite the following papers:") + for citation in molecule.citations: + cite_string = citation_formatter( + molecule.force_field.citations[citation] + ) + LOGGER.info("Please cite: " + cite_string) + header.append(cite_string) + vermouth.gmx.itp.write_molecule_itp(molecule, outfile, header=header) + this_moltype_len = len(molecule.meta["moltype"]) + if this_moltype_len > max_name_length: + max_name_length = this_moltype_len + moltype_written.add(moltype) + # We already removed one element from the "molecules" generator, do not + # forget to count it in the number of molecules in that group. + moltype_count.append([moltype, 1 + len(list(molecules))]) + + # Write the top file + template = textwrap.dedent( + """\ + {defines} + #include "martini.itp" + {includes} + + [ system ] + Title of the system + + [ molecules ] + {molecules} + """ + ) + include_string = include_string + "\n".join( + '#include "{}.itp"'.format(molecule_type) for molecule_type, _ in moltype_count + ) + molecule_string = "\n".join( + "{mtype:<{length}} {num}".format( + mtype=mtype, num=num, length=max_name_length + ) + for mtype, num in moltype_count + ) + define_string = "\n".join("#define {}".format(define) for define in defines) + with deferred_open(str(top_path), "w") as outfile: + outfile.write( + textwrap.dedent( + template.format( + includes=include_string, + molecules=molecule_string, + defines=define_string, + ) + ) + ) From e01dc30c48118d27c58b8383e81494f383978b54 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 13 Oct 2023 15:49:03 +0200 Subject: [PATCH 15/95] some clean up --- bin/martinize2 | 194 ++++++++--------------------- vermouth/processors/__init__.py | 1 - vermouth/rcsu/go_pipeline.py | 6 +- vermouth/rcsu/go_structure_bias.py | 14 ++- vermouth/rcsu/go_vs_includes.py | 36 ++---- 5 files changed, 77 insertions(+), 174 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index b8379994..20ca00f6 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -50,8 +50,9 @@ from vermouth.map_input import ( combine_mappings, ) from vermouth.rcsu.contact_map import read_go_map -from vermouth.rcsu.get_go import GetGo +from vermouth.rcsu.go_pipeline import GoPipeline from vermouth.citation_parser import citation_formatter +from vermouth.gmx.topology import write_gmx_topology # TODO Since vermouth's __init__.py does some logging (KDTree), this may or may # not work as intended. Investigation required. @@ -190,96 +191,6 @@ def martinize(system, mappings, to_ff, delete_unknown=False): vermouth.LocateChargeDummies().run_system(system) return system - -def write_gmx_topology(system, top_path, defines=(), header=()): - """ - Writes a Gromacs .top file for the specified system. - """ - if not system.molecules: - raise ValueError("No molecule in the system. Nothing to write.") - - # Write the ITP files for the molecule types, and prepare writing the - # [ molecules ] section of the top file. - # * We write one ITP file for each different moltype in the system, the - # moltype being defined by the name provided under the "moltype" meta of - # the molecules. If more than one molecule share the same moltype, we use - # the first one to write the ITP file. - moltype_written = set() - # * We keep track of the length of the longer moltype name, to align the - # [ molecules ] section. - max_name_length = 0 - # * We keep track of groups of successive molecules with the same moltypes. - moltype_count = [] # items will be [moltype, number of molecules] - - # Iterate over groups of successive molecules with the same moltypes. We - # shall *NOT* sort the molecules before hand, as groups of successive - # molecules with the same moltype can be interupted by other moltypes, and - # we want to reflect these interuptions in the [ molecules ] section of the - # top file. - molecule_groups = itertools.groupby( - system.molecules, key=lambda x: x.meta["moltype"] - ) - for moltype, molecules in molecule_groups: - molecule = next(molecules) - if moltype not in moltype_written: - # A given moltype can appear more than once in the sequence of - # molecules, without being uninterupted by other moltypes. Even in - # that case, we want to write the ITP only once. - with deferred_open("{}.itp".format(moltype), "w") as outfile: - # here we format and merge all citations - header[-1] = header[-1] + "\n" - header.append("Pleas cite the following papers:") - for citation in molecule.citations: - cite_string = citation_formatter( - molecule.force_field.citations[citation] - ) - LOGGER.info("Please cite: " + cite_string) - header.append(cite_string) - vermouth.gmx.itp.write_molecule_itp(molecule, outfile, header=header) - this_moltype_len = len(molecule.meta["moltype"]) - if this_moltype_len > max_name_length: - max_name_length = this_moltype_len - moltype_written.add(moltype) - # We already removed one element from the "molecules" generator, do not - # forget to count it in the number of molecules in that group. - moltype_count.append([moltype, 1 + len(list(molecules))]) - - # Write the top file - template = textwrap.dedent( - """\ - {defines} - #include "martini.itp" - {includes} - - [ system ] - Title of the system - - [ molecules ] - {molecules} - """ - ) - include_string = "\n".join( - '#include "{}.itp"'.format(molecule_type) for molecule_type, _ in moltype_count - ) - molecule_string = "\n".join( - "{mtype:<{length}} {num}".format( - mtype=mtype, num=num, length=max_name_length - ) - for mtype, num in moltype_count - ) - define_string = "\n".join("#define {}".format(define) for define in defines) - with deferred_open(str(top_path), "w") as outfile: - outfile.write( - textwrap.dedent( - template.format( - includes=include_string, - molecules=molecule_string, - defines=define_string, - ) - ) - ) - - def _cys_argument(value): """ Convert and validate the value of the cys option for argparse. @@ -623,22 +534,10 @@ def entry(): "-go", action="store_true", default=False, - help="Apply the Martini Go model as structural bias.", - ) - go_group.add_argument( - "-govs-moltype", - dest="govs_moltype", - default="molecule_0", - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), - ) - go_group.add_argument( - "-govs-includes", - action="store_true", - default=False, - help="Write include statements to use Vitrual Site Go Martini.", + help="Apply the Martini Go model as structural bias and/or water bias.", ) go_group.add_argument( - "-govs-map", + "-go-map", dest="go_map", required=False, type=Path, @@ -646,64 +545,71 @@ def entry(): help="Write include statements to use Vitrual Site Go Martini.", ) go_group.add_argument( - "-govs-low", - dest="go_low", - type=float, - default=0.3, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), - ) - go_group.add_argument( - "-govs-up", - dest="go_up", - type=float, - default=1.1, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), - ) - go_group.add_argument( - "-govs-eps", + "-go-eps", dest="go_eps", type=float, default=0.0, help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) go_group.add_argument( - "-govs-res-dist", - dest="go_res_dist", - type=int, - default=3, + "-go-moltype", + dest="govs_moltype", + default="molecule_0", help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) go_group.add_argument( - "-govs-bias-auto", - dest="go_water", + "-go-low", + dest="go_low", type=float, - default=0.0, + default=0.3, help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) go_group.add_argument( - "-govs-auto-bias", - dest="go_water", + "-go-up", + dest="go_up", type=float, - default=0.0, + default=1.1, help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) go_group.add_argument( - "-govs-idrs", - dest="go_idrs", - type=float, - default=0.0, + "-go-res-dist", + dest="go_res_dist", + type=int, + default=3, help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), ) - go_group.add_argument( - "-govs-bias-auto", - dest="water-bias", + + water_group = parser.add_argument_group("Apply water bias.") + water_group.add_argument( + "-water-bias-auto", + dest="water_bias_auto", + action="store_true", + default=False, + help=("Automatically apply water bias to different secondary structure elements."), + ) + water_group.add_argument( + "-water-bias-eps", + dest="water_bias_eps", action="append", type=lambda s: s.split(":"), default=[], - help=("Define the water bias for the Go model by secondary structure type. " - "For example, use H:3.6, C:2.1 to bias helixes and coils."), + help=("Define the strength of the water bias by secondary structure type. " + "For example, use H:3.6, C:2.1 to bias helixes and coils. " + "Using the idr option (e.g. idr:2.1) intrinsically disordered regions " + "are biased seperately."), + ) + water_group.add_argument( + "-id-regions", + dest="water_idrs", + type=lambda s: s.split(":"), + default=[], + help=("Regions of resid defining the intrinsically disordered parts of the protein." + "These parts are biased differently when applying a water bias." + "format: :, :..." + ), ) + prot_group = parser.add_argument_group("Protein description") prot_group.add_argument( "-scfix", @@ -1054,7 +960,10 @@ def entry(): ).run_system(system) defines = ("GO_VIRT",) + itp_paths = ["go_atomtypes.itp", "go_nbparams.itp"] else: + # don't write non-bonded interactions + itp_paths = [] # Merge chains if required. if args.merge_chains: for chain_set in args.merge_chains: @@ -1157,7 +1066,12 @@ def entry(): ] if args.top_path is not None: - write_gmx_topology(system, args.top_path, defines=defines, header=header) + write_gmx_topology(system, + args.top_path, + itp_paths=itp_paths, + C6C12=False, + defines=defines, + header=header) # Write a PDB file. vermouth.pdb.write_pdb(system, str(args.outpath), omit_charges=True) diff --git a/vermouth/processors/__init__.py b/vermouth/processors/__init__.py index 9445c62f..c4f63335 100644 --- a/vermouth/processors/__init__.py +++ b/vermouth/processors/__init__.py @@ -40,7 +40,6 @@ from .add_molecule_edges import AddMoleculeEdgesAtDistance, MergeNucleicStrands from .name_moltype import NameMolType from .quote import Quoter -from .go_vs_includes import GoVirtIncludes from .sort_molecule_atoms import SortMoleculeAtoms from .merge_all_molecules import MergeAllMolecules from .annotate_mut_mod import AnnotateMutMod diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 93b39e7c..0618657e 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -16,8 +16,8 @@ """ import inspect import vermouth -from vermouth.processors import Processor -from .go_vs_includes import GoVirtIncludes +from ..processors.processor import Processor +from .go_vs_includes import VirtualSideCreator from .go_structure_bias import ComputeStructuralGoBias from .go_water_bias import ComputeWaterGoBias from ..processors import SetMoleculeMeta @@ -57,6 +57,6 @@ def run_system(self, system): return system GoPipeline = GoProcessorPipline([SetMoleculeMeta, - GoVirtIncludes, + VirtualSideCreator, ComputeStructuralGoBias, ComputeWaterGoBias]) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index ed448950..bdd3907d 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -17,9 +17,9 @@ import numpy as np import networkx as nx from ..molecule import Interaction -from .. import Processor +from ..processors.processor import Processor from ..selectors import filter_minimal, select_backbone -from .go_utils import _get_go_type +from .go_utils import get_go_type_from_attributes class ComputeStructuralGoBias(Processor): """ @@ -166,8 +166,14 @@ def contact_selector(self, molecule): if self.cut_off_large > dist > self.cutoff_short: # find the go virtual-sites for this residue # probably can be done smarter but mehhhh - atype_a = _get_go_type(molecule, resid=resIDA, chain=chainA, prefix=self.prefix) - atype_b = _get_go_type(molecule, resid=resIDB, chain=chainB, prefix=self.prefix) + atype_a = get_go_type_from_attributes(molecule, + resid=resIDA, + chain=chainA, + prefix=self.prefix) + atype_b = get_go_type_from_attributes(molecule, + resid=resIDB, + chain=chainB, + prefix=self.prefix) # generate backbone backbone exclusions # perhaps one day can be it's own function excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 92726a53..fd64947b 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -13,39 +13,17 @@ # limitations under the License. """ -Add the include statements and the virtual sites for Virtual Site Go model. - -The VirtualGoSite model allows to stabilize the ternary structure of Martini -proteins by applying Go potentials maintaining the contacts within the -backbone. The Go potentials are not applied on the backbone beads directly, -instead, they are applied on virtual sites overlapping with the backbone. - -The processor defined in this module does not generate the Go potentials. -Instead, they the potential is generated by a third party program. The third -party program generate the interaction matrix for the Go potentials, and the -exclusions as ITP files to be included in the right place in the protein ITP -file. The processor adds an include statement at the end of the `[ exclusions -]` section. Would the third party program need the addition of other include -statements, they can be added by adjusting the `sections` argument of the -processor. To incorporate the include statements, the processor adds the -required lines in the "post_section_lines" meta attribute of the molecules. -This meta attribute is read by :func:`vermouth.gmx.itp.write_molecule_itp`. The -include files are called "_
_VirtGoSite.itp". - -In addition of writing the include statements, the processor adds virtual sites -on top of the backbone beads. The virtual sites are added at the end of the -molecule, they share the residue name, residue id, chain, and position of the -underlying backbone bead. They are also added in the `[ virtual_sitesn ]` -section. """ import networkx as nx from ..molecule import Interaction from ..processors.processor import Processor +from ..gmx.topology import Atomtype -class GoVirtIncludes(Processor): +class VirtualSideCreator(Processor): """ - Add the include statements and the virtual sites for Virtual Site Go model. + Create virtual-sites for the Martini Go model implementation. + This processor also updates the gmx See :mod:`vermouth.processors.go_vs_includes` for more details. @@ -139,13 +117,19 @@ def add_virtual_sites(molecule, prefix, backbone='BB', atomname='CA', charge=0): 'position': atom['position'], 'atomname': atomname, 'charge': charge, + 'mass': 0.0, })) virtual_sites.append(Interaction( atoms=[new_node_id, node_id], parameters=['1'], meta={'go_vs': True, 'group': 'Virtual go site'}, )) + vs_params = Atomtype(node=new_node_id, molecule=molecule, sigma=0.0, epsilon=0.0) + system.gmx_topology_params['atomtypes'].update(vs_params) + molecule.add_nodes_from(virtual_site_nodes) + if 'virtual_sitesn' not in molecule.interactions: molecule.interactions['virtual_sitesn'] = [] + molecule.interactions['virtual_sitesn'] += virtual_sites From b0b4b6c292a2091e619b9c94518b8ccbbf14e549 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Mon, 16 Oct 2023 08:45:33 +0200 Subject: [PATCH 16/95] refactor water bias --- bin/martinize2 | 13 ++++++++++--- .../go_water_bias.py => processors/water_bias.py} | 6 +++--- vermouth/rcsu/go_pipeline.py | 3 +-- vermouth/rcsu/go_vs_includes.py | 2 +- 4 files changed, 15 insertions(+), 9 deletions(-) rename vermouth/{rcsu/go_water_bias.py => processors/water_bias.py} (96%) diff --git a/bin/martinize2 b/bin/martinize2 index 20ca00f6..f8a5128b 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -581,8 +581,8 @@ def entry(): water_group = parser.add_argument_group("Apply water bias.") water_group.add_argument( - "-water-bias-auto", - dest="water_bias_auto", + "-water-bias", + dest="water_bias", action="store_true", default=False, help=("Automatically apply water bias to different secondary structure elements."), @@ -945,7 +945,8 @@ def entry(): node_selector = node_selectors[args.posres] vermouth.ApplyPosres(node_selector, args.posres_fc).run_system(system) - if args.govs_includes: + # Generate the Go model if required + if args.go: LOGGER.info("Reading Go model contact map.", type="step") go_map = read_go_map(args.go_map) LOGGER.info("Generating the Go model.", type="step") @@ -1022,6 +1023,12 @@ def entry(): ) rubber_band_processor.run_system(system) + # If required add some water bias + if args.water_bias: + if not args.go: + Create + ComputeWaterBias().run_system(system) + # Here we need to add the resids from the PDB back if that is needed if args.resid_handling == "input": for molecule in system.molecules: diff --git a/vermouth/rcsu/go_water_bias.py b/vermouth/processors/water_bias.py similarity index 96% rename from vermouth/rcsu/go_water_bias.py rename to vermouth/processors/water_bias.py index d1ff386c..18bca749 100644 --- a/vermouth/rcsu/go_water_bias.py +++ b/vermouth/processors/water_bias.py @@ -12,11 +12,11 @@ # See the License for the specific language governing permissions and # limitations under the License. -from ..processors.processor import Processor +from .processors.processor import Processor from ..graph_utils import make_residue_graph -from .go_utils import get_go_type_from_attributes, _get_bead_size +from ..rcsu.go_utils import get_go_type_from_attributes, _get_bead_size -class ComputeWaterGoBias(Processor): +class ComputeWaterBias(Processor): """ Processor which computes the water bias for the Martini Go and Martini IDP model. diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 0618657e..194ee00d 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -58,5 +58,4 @@ def run_system(self, system): GoPipeline = GoProcessorPipline([SetMoleculeMeta, VirtualSideCreator, - ComputeStructuralGoBias, - ComputeWaterGoBias]) + ComputeStructuralGoBias]) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index fd64947b..787d066c 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -61,7 +61,7 @@ def run_molecule(self, molecule): return molecule def run_system(self, system): - LOGGER.info("Adding includes for Virtual Site Go Martini.", type="step") + LOGGER.info("Adding Virtual Sites to backbone beads.", type="step") for molecule in system.molecules: self.run_molecule(system) From 5cd2c82925fe6a94604c21ad5ea6f7a5eb062c49 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Mon, 16 Oct 2023 11:48:38 +0200 Subject: [PATCH 17/95] make water bias workflow worl --- bin/martinize2 | 30 ++-- .../data/force_fields/martini3001/general.ff | 4 + vermouth/gmx/topology.py | 30 ++-- vermouth/processors/__init__.py | 1 + vermouth/processors/water_bias.py | 93 +++++++---- vermouth/rcsu/go_pipeline.py | 1 - vermouth/rcsu/go_utils.py | 6 +- vermouth/rcsu/go_vs_includes.py | 154 ++++++++++-------- vermouth/system.py | 3 +- 9 files changed, 194 insertions(+), 128 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index f8a5128b..668e1734 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -542,14 +542,15 @@ def entry(): required=False, type=Path, default=False, - help="Write include statements to use Vitrual Site Go Martini.", + help="Contact map to be used for the Martini Go model." + "Currently, only one format is supported. See docs.", ) go_group.add_argument( "-go-eps", dest="go_eps", type=float, default=0.0, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + help=("The strength of the Go model structural bias in kJ/mol."), ) go_group.add_argument( "-go-moltype", @@ -562,21 +563,22 @@ def entry(): dest="go_low", type=float, default=0.3, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + help=("Minimum distance (nm) below which contacts are removed."), ) go_group.add_argument( "-go-up", dest="go_up", type=float, default=1.1, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + help=("Maximum distance (nm) above which contacts are removed."), ) go_group.add_argument( "-go-res-dist", dest="go_res_dist", type=int, default=3, - help=("Set the name of the molecule when using " "Virtual Sites GoMartini."), + help=("Minimum graph distance (similar seqeuence distance) below which" + "contacts are removed. "), ) water_group = parser.add_argument_group("Apply water bias.") @@ -590,7 +592,7 @@ def entry(): water_group.add_argument( "-water-bias-eps", dest="water_bias_eps", - action="append", + nargs='+', type=lambda s: s.split(":"), default=[], help=("Define the strength of the water bias by secondary structure type. " @@ -603,7 +605,8 @@ def entry(): dest="water_idrs", type=lambda s: s.split(":"), default=[], - help=("Regions of resid defining the intrinsically disordered parts of the protein." + nargs='+', + help=("Intrinsically disordered regions specified by resid." "These parts are biased differently when applying a water bias." "format: :, :..." ), @@ -1025,9 +1028,16 @@ def entry(): # If required add some water bias if args.water_bias: + # if the go model hasn't been used we need to create virtual + # sites for the biasing if not args.go: - Create - ComputeWaterBias().run_system(system) + vermouth.rcsu.go_vs_includes.VirtualSideCreator().run_system(system) + itp_paths = ["virtual_sites_atomtypes.itp", "virtual_sites_nonbond_params.itp"] + # now we add a bias by defining specific virtual-site water interactions + vermouth.processors.ComputeWaterBias(args.water_bias, + { s:float(eps) for s, eps in args.water_bias_eps}, + [(int(start), int(stop)) for start, stop in args.water_idrs], + ).run_system(system) # Here we need to add the resids from the PDB back if that is needed if args.resid_handling == "input": @@ -1038,7 +1048,7 @@ def entry(): # The Martini Go model assumes that we do not mess with the order of # particles in any way especially the virtual sites needed for the Go # model, thus we skip the sorting here altogether. - if not args.govs_includes: + if not args.go: LOGGER.info("Sorting atomids", type="step") vermouth.SortMoleculeAtoms().run_system(system) diff --git a/vermouth/data/force_fields/martini3001/general.ff b/vermouth/data/force_fields/martini3001/general.ff index ac40de4c..8ed42b37 100644 --- a/vermouth/data/force_fields/martini3001/general.ff +++ b/vermouth/data/force_fields/martini3001/general.ff @@ -14,3 +14,7 @@ [ variables ] center_weight "mass" +regular "0.47" +small "0.41" +tiny "0.34" +water_type "W" diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 7d358345..41812ff1 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -13,7 +13,7 @@ LOGGER = StyleAdapter(get_logger(__name__)) Atomtype = namedtuple('Atomtype', 'molecule node sigma epsilon meta') -NonbondParam = namedtuple('NonbondParam', 'sigma epsilon meta') +NonbondParam = namedtuple('NonbondParam', 'atoms sigma epsilon meta') def _group_by_conditionals(interactions): interactions_group_sorted = sorted(interactions, @@ -43,6 +43,7 @@ def write_atomtypes(system, itp_path, C6C12=False): """ conditional_keys = {True: '#ifdef', False: '#ifndef'} with deferred_open(itp_path, "w") as itp_file: + itp_file.write("[ atomtypes ]\n") grouped_types = _group_by_conditionals(system.gmx_topology_params['atomtypes']) for (conditional, group), interactions_in_group in grouped_types: if conditional: @@ -61,7 +62,10 @@ def write_atomtypes(system, itp_path, C6C12=False): else: nb1, nb2 = atomtype.sigma, atomtype.epsilon - comments = ";" + " ".join(atomtype.meta['comment']) + if 'comment' in atomtype.meta: + comments = ";" + " ".join(atomtype.meta['comment']) + else: + comments = "" itp_file.write(f"{atype} {mass} {charge} A {nb1:3.8F} {nb2:3.8F} {comments}\n") def write_nonbond_params(system, itp_path, C6C12=False): @@ -73,6 +77,7 @@ def write_nonbond_params(system, itp_path, C6C12=False): """ conditional_keys = {True: '#ifdef', False: '#ifndef'} with deferred_open(itp_path, "w") as itp_file: + itp_file.write("[ nonbond_params ]\n") grouped_types = _group_by_conditionals(system.gmx_topology_params['nonbond_params']) for (conditional, group), interactions_in_group in grouped_types: if conditional: @@ -82,13 +87,13 @@ def write_nonbond_params(system, itp_path, C6C12=False): itp_file.write('; {}\n'.format(group)) - for atoms, nb_params in interactions_in_group: - if len(atoms) == 2: - a1, a2 = atoms + for nb_params in interactions_in_group: + if len(nb_params.atoms) == 2: + a1, a2 = nb_params.atoms # self interaction else: - a1 = atoms[0] - a2 = atoms[0] + a1 = nb_params.atoms[0] + a2 = nb_params.atoms[0] if C6C12: nb1, nb2 = convert_sigma_epsilon(nb_params.sigma, nb_params.epsilon) @@ -96,7 +101,7 @@ def write_nonbond_params(system, itp_path, C6C12=False): nb1, nb2 = nb_params.sigma, nb_params.epsilon comments = ";" + " ".join(nb_params.meta['comment']) - itp_path.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n") + itp_file.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n") def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), header=()): """ @@ -122,12 +127,13 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), if not system.molecules: raise ValueError("No molecule in the system. Nothing to write.") + include_string = "" # First we write the atomtypes and nonbondparams directive if itp_paths: - write_nonbond_params(system, C6C12, itp_paths[0]) - write_atomtypes(system, C6C12, itp_paths[1]) - include_string = "\n".join('#include "{}.itp"'.format(path) for path in itp_paths[:2]) - + write_atomtypes(system, itp_paths[0], C6C12) + write_nonbond_params(system, itp_paths[1], C6C12) + include_string = "\n".join('#include "{}"'.format(path) for path in itp_paths[:2]) + include_string += "\n" # Write the ITP files for the molecule types, and prepare writing the # [ molecules ] section of the top file. # * We write one ITP file for each different moltype in the system, the diff --git a/vermouth/processors/__init__.py b/vermouth/processors/__init__.py index c4f63335..4cdcc58e 100644 --- a/vermouth/processors/__init__.py +++ b/vermouth/processors/__init__.py @@ -43,3 +43,4 @@ from .sort_molecule_atoms import SortMoleculeAtoms from .merge_all_molecules import MergeAllMolecules from .annotate_mut_mod import AnnotateMutMod +from .water_bias import ComputeWaterBias diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 18bca749..c272497c 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -12,9 +12,16 @@ # See the License for the specific language governing permissions and # limitations under the License. -from .processors.processor import Processor +from .processor import Processor from ..graph_utils import make_residue_graph from ..rcsu.go_utils import get_go_type_from_attributes, _get_bead_size +from ..gmx.topology import NonbondParam + +def _in_region(resid, regions): + for start, stop in regions: + if start <= resid <= stop: + return True + return False class ComputeWaterBias(Processor): """ @@ -38,28 +45,32 @@ class ComputeWaterBias(Processor): """ def __init__(self, - water_bias, auto_bias, - idr_regions, - prefix=""): + water_bias, + idr_regions): """ Parameters ---------- + auto_bias: bool + apply the automatic secondary structure + dependent water biasing water_bias: dict[str, float] a dict of secondary structure codes and epsilon value for the water bias in kJ/mol - auto_bias: bool idr_regions: regions defining the IDRs prefix: str prefix of the Go virtual-site atomtypes + system: :class:vermouth.System + the system of the molecules is used for + storing the nonbonded parameters """ self.water_bias = water_bias self.auto_bias = auto_bias self.idr_regions = idr_regions - self.prefix = prefix + self.system = None def assign_residue_water_bias(self, molecule, res_graph): """ @@ -75,32 +86,59 @@ def assign_residue_water_bias(self, molecule, res_graph): res_graph: :class:vermouth.Molecule the residue graph of the molecule """ - bias_params = {} - for res_node in self.res_graph.nodes: - resid = self.res_graph.nodes[res_node]['resid'] - chain = self.res_graph.nodes[res_node]['chain'] - resname = self.res_gaph.nodes[res_node]['resname'] + for res_node in res_graph.nodes: + resid = res_graph.nodes[res_node]['resid'] + chain = res_graph.nodes[res_node]['chain'] + resname = res_graph.nodes[res_node]['resname'] - if self.selector(res_graph, res_node): + if _in_region(resid, self.idr_regions): eps = self.water_bias.get('idr', 0.0) elif self.auto_bias: - sec_struc = self.res_graph.nodes[res_node]['sec_struc'] + sec_struc = res_graph.nodes[res_node]['cgsecstruct'] eps = self.water_bias.get(sec_struc, 0.0) else: continue - vs_go_node = get_go_type_from_attributes(res_graph.nodes[res_node], - resid=resid, - chain=chain, - prefix=self.prefix) + if eps == 0.0: + continue + + vs_go_node = next(get_go_type_from_attributes(res_graph.nodes[res_node]['graph'], + resid=resid, + chain=chain, + prefix=molecule.meta.get('moltype'))) # what is the blocks bb-type - bb_type = molecule.force_field.blocks[resname]['BB']['atype'] + bb_type = molecule.force_field.blocks[resname].nodes['BB']['atype'] size = _get_bead_size(bb_type) - sigma = molecule.force_field.variables['bead_sizes'][size] - bias_params[frozenset([molecule.force_field.water_name, vs_go_node])] = (sigma, eps) + # bead sizes are defined in the force-field file as + # regular, small and tiny + sigma = float(molecule.force_field.variables[size]) + # update interaction parameters + atoms = (molecule.force_field.variables['water_type'], vs_go_node) + water_bias = NonbondParam(atoms=atoms, + sigma=sigma, + epsilon=eps, + meta={"comment": ["water bias", sec_struc]}) + self.system.gmx_topology_params["nonbond_params"].append(water_bias) + + def run_molecule(self, molecule): + """ + Assign water bias for a single molecule + """ + if not self.system: + raise IOError('This processor requires a system.') + + if not molecule.meta.get('moltype'): + raise ValueError('The molecule does not have a moltype name.') - return bias_params + if hasattr(molecule, 'res_graph'): + res_graph = molecule.res_graph + else: + res_graph = make_residue_graph(molecule) + + self.assign_residue_water_bias(molecule, res_graph) + + return molecule def run_system(self, system): """ @@ -110,15 +148,10 @@ def run_system(self, system): Parameters ---------- - molecule: :class:`vermouth.Molecule` + system: :class:`vermouth.System` """ - if self.idr_regions or self.auto: + if self.idr_regions or self.auto_bias: + self.system = system for molecule in system.molecules: - if hasattr(molecule.res_graph): - res_graph = molecule.res_graph - else: - make_residue_graph(molecule) - - bias_params = self.determine_residue_water_bias(self, res_graph) - system.gmx_topology_params["nonbond_params"].update(bias_params) + self.run_molecule(molecule) return system diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 194ee00d..72385f50 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -19,7 +19,6 @@ from ..processors.processor import Processor from .go_vs_includes import VirtualSideCreator from .go_structure_bias import ComputeStructuralGoBias -from .go_water_bias import ComputeWaterGoBias from ..processors import SetMoleculeMeta class GoProcessorPipline(Processor): diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index 2d231191..c160ce45 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -16,7 +16,7 @@ """ from vermouth.molecule import attributes_match -def get_go_type_from_attributes(molecule, prefix, kwargs): +def get_go_type_from_attributes(molecule, prefix, **kwargs): """ Find all nodes that satisfy a number of attributes specified as kwargs and have a specific atomtype prefix. @@ -41,8 +41,8 @@ def get_go_type_from_attributes(molecule, prefix, kwargs): and prefix an IOError is raised. """ for node in molecule.nodes: - if attributes_match(molecule.nodes[node], kwargs) and\ - attrs['atype'].startswith(prefix): + attrs = molecule.nodes[node] + if attributes_match(attrs, kwargs) and attrs['atype'].startswith(prefix): yield attrs['atype'] resid = kwargs['resid'] diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 787d066c..db9c44b0 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -19,6 +19,10 @@ from ..molecule import Interaction from ..processors.processor import Processor from ..gmx.topology import Atomtype +from ..log_helpers import StyleAdapter, get_logger + +LOGGER = StyleAdapter(get_logger(__name__)) + class VirtualSideCreator(Processor): """ @@ -43,13 +47,17 @@ class VirtualSideCreator(Processor): """ def __init__(self, sections=('exclusions', )): self.sections = sections + self.system = None def run_molecule(self, molecule): moltype = molecule.meta.get('moltype') if not moltype: raise ValueError('The molecule does not have a moltype name.') - add_virtual_sites(molecule, prefix=moltype) + if not self.system: + raise IOError('This processor requires a system.') + + self.add_virtual_sites(molecule, prefix=moltype) includes = molecule.meta.get('post_section_lines', {}) for section in self.sections: @@ -61,75 +69,79 @@ def run_molecule(self, molecule): return molecule def run_system(self, system): + self.system = system LOGGER.info("Adding Virtual Sites to backbone beads.", type="step") for molecule in system.molecules: - self.run_molecule(system) - -def add_virtual_sites(molecule, prefix, backbone='BB', atomname='CA', charge=0): - """ - Add the virtual sites for GoMartini in the molecule. - - One virtual site is added per backbone bead of the the Martini protein. - Each virtual site copies the resid, resname, and chain of the backbone - bead. It also copies the *reference* to the position array, so the virtual - site position follows if the backbone bead is translated. The virtual sites - are added *after* all the other atoms of the molecule, each in its own - charge group, with "CA" as atomname, and a charge of 0. The atomname and - charge can be set with the `atomname` and `charge` argument, respectively. - - The bead type of the virtual sites is names "_". Where - `prefix` is provided as an argument of the function, and is expected to be - the molecule type name. - - Parameters - ---------- - molecule: vermouth.molecule.Molecule - The molecule to augment with virtual sites. - prefix: str - The prefix to use for bead type names. Usually the molecule type name. - backbone: str - The atomname of the backbone beads. - atomname: str - The atomname of the virtual sites. - charge: float or int - The charge of the virtual sites. - """ - # If there are no atoms, then there is nothing to do. We can exit early, - # avoiding to deal with empty iterators. - if not molecule.nodes: - return - virtual_site_nodes = [] - virtual_sites = [] - new_node_id = max(molecule.nodes) - charge_groups = nx.get_node_attributes(molecule, 'charge_group').values() - new_charge_group = max(charge_groups) if charge_groups else 0 - for node_id, atom in molecule.nodes(data=True): - if atom.get('atomname') == backbone: - new_node_id += 1 - new_charge_group += 1 - virtual_site_nodes.append((new_node_id, { - 'resid': atom['resid'], - '_old_resid': atom['_old_resid'], - 'resname': atom['resname'], - 'atype': '{}_{}'.format(prefix, atom['resid']), - 'charge_group': new_charge_group, - 'chain': atom['chain'], - 'position': atom['position'], - 'atomname': atomname, - 'charge': charge, - 'mass': 0.0, - })) - virtual_sites.append(Interaction( - atoms=[new_node_id, node_id], - parameters=['1'], - meta={'go_vs': True, 'group': 'Virtual go site'}, - )) - vs_params = Atomtype(node=new_node_id, molecule=molecule, sigma=0.0, epsilon=0.0) - system.gmx_topology_params['atomtypes'].update(vs_params) - - molecule.add_nodes_from(virtual_site_nodes) - - if 'virtual_sitesn' not in molecule.interactions: - molecule.interactions['virtual_sitesn'] = [] - - molecule.interactions['virtual_sitesn'] += virtual_sites + self.run_molecule(molecule) + + def add_virtual_sites(self, molecule, prefix, backbone='BB', atomname='CA', charge=0): + """ + Add the virtual sites for GoMartini in the molecule. + + One virtual site is added per backbone bead of the the Martini protein. + Each virtual site copies the resid, resname, and chain of the backbone + bead. It also copies the *reference* to the position array, so the virtual + site position follows if the backbone bead is translated. The virtual sites + are added *after* all the other atoms of the molecule, each in its own + charge group, with "CA" as atomname, and a charge of 0. The atomname and + charge can be set with the `atomname` and `charge` argument, respectively. + + The bead type of the virtual sites is names "_". Where + `prefix` is provided as an argument of the function, and is expected to be + the molecule type name. + + Parameters + ---------- + molecule: vermouth.molecule.Molecule + The molecule to augment with virtual sites. + prefix: str + The prefix to use for bead type names. Usually the molecule type name. + backbone: str + The atomname of the backbone beads. + atomname: str + The atomname of the virtual sites. + charge: float or int + The charge of the virtual sites. + """ + # If there are no atoms, then there is nothing to do. We can exit early, + # avoiding to deal with empty iterators. + if not molecule.nodes: + return + virtual_site_nodes = [] + virtual_sites = [] + atomtypes = {} + new_node_id = max(molecule.nodes) + charge_groups = nx.get_node_attributes(molecule, 'charge_group').values() + new_charge_group = max(charge_groups) if charge_groups else 0 + for node_id, atom in molecule.nodes(data=True): + if atom.get('atomname') == backbone: + new_node_id += 1 + new_charge_group += 1 + + virtual_site_nodes.append((new_node_id, { + 'resid': atom['resid'], + '_old_resid': atom['_old_resid'], + 'resname': atom['resname'], + 'atype': '{}_{}'.format(prefix, atom['resid']), + 'charge_group': new_charge_group, + 'chain': atom['chain'], + 'position': atom['position'], + 'atomname': atomname, + 'charge': charge, + 'mass': 0.0, + 'cgsecstruct': atom.get('cgsecstruct', None), + })) + virtual_sites.append(Interaction( + atoms=[new_node_id, node_id], + parameters=['1'], + meta={'go_vs': True, 'group': 'Virtual go site'}, + )) + vs_params = Atomtype(node=new_node_id, molecule=molecule, sigma=0.0, epsilon=0.0, meta={}) + self.system.gmx_topology_params['atomtypes'].append(vs_params) + + molecule.add_nodes_from(virtual_site_nodes) + + if 'virtual_sitesn' not in molecule.interactions: + molecule.interactions['virtual_sitesn'] = [] + + molecule.interactions['virtual_sitesn'] += virtual_sites diff --git a/vermouth/system.py b/vermouth/system.py index f6d8be10..b1e7d9fa 100644 --- a/vermouth/system.py +++ b/vermouth/system.py @@ -16,7 +16,7 @@ """ Provides a class to describe a system. """ - +from collections import defaultdict class System: """ @@ -31,6 +31,7 @@ def __init__(self, force_field=None): self.molecules = [] self._force_field = None self.force_field = force_field + self.gmx_topology_params = defaultdict(list) @property def force_field(self): From c7eb8c9cc6d06e657217f58050f340577126972b Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 14:59:49 +0200 Subject: [PATCH 18/95] baseline for including tests --- bin/martinize2 | 2 +- vermouth/tests/test_go_vs_includes.py | 88 --------------------------- 2 files changed, 1 insertion(+), 89 deletions(-) delete mode 100644 vermouth/tests/test_go_vs_includes.py diff --git a/bin/martinize2 b/bin/martinize2 index 668e1734..8ee52868 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -800,7 +800,7 @@ def entry(): print(", ".join(known_force_fields[args.to_ff].modifications)) parser.exit() - if args.elastic and args.govs_includes: + if args.elastic and args.go: parser.error( "A rubber band elastic network and GoMartini are not " "compatible. The -elastic and -govs-include flags cannot " diff --git a/vermouth/tests/test_go_vs_includes.py b/vermouth/tests/test_go_vs_includes.py deleted file mode 100644 index 9108338d..00000000 --- a/vermouth/tests/test_go_vs_includes.py +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 2018 University of Groningen -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -""" -Test the :class:`vermouth.processors.go_vs_includes.GoVirtIncludes` processor. -""" - -# Pylint issues false warnings because of pytest's fixtures. -# pylint: disable=redefined-outer-name - -import pytest -from vermouth import Molecule -from vermouth.processors import GoVirtIncludes - -@pytest.fixture(params=(0, 4)) -def molecule_for_go(request): - """ - Molecule to test virtual site-based GoMartini. - - The molecule has a variable number of residue set in the fixture parameter. - Each residue has a backbone and a side chain beads. It also has some post - sections lines that should not disapear when running the processor, and a - moltype name as this is required. - """ - n_residues = request.param - molecule = Molecule() - for residue_idx in range(n_residues): - base_atom_idx = residue_idx * 2 - for relative_atom_idx, atomname in enumerate(('BB', 'SC1')): - molecule.add_node( - base_atom_idx + relative_atom_idx, - resid=residue_idx, - _old_resid=residue_idx, - resname='XX', - atomname=atomname, - charge_group=base_atom_idx, - chain='A', - # Should be an array, but it is not relevant for the test - position=[0, 0, 0], - ) - molecule.meta['post_section_lines'] = { - 'exclusions': ['I exist'], - 'other': ['Hello'], - } - molecule.meta['moltype'] = 'TEST' - return molecule - - -def test_go_virt_includes(molecule_for_go): - """ - Test the processor in normal conditions. - """ - molecule = molecule_for_go - initial_n_backbone = len(molecule.nodes) // 2 # Each residues has 2 atoms - processor = GoVirtIncludes() - processor.run_molecule(molecule) - - expected_post = { - 'exclusions': ['I exist', '#include "TEST_exclusions_VirtGoSites.itp"'], - 'other': ['Hello'], - } - - assert molecule.meta['post_section_lines'] == expected_post - # Each residue in the initial molecule has a backbone and a side chain - # beads. We create one virtual site per backbone beads, so we expect to - # have a side chain and a virtual site for each backbone bead. - assert len(molecule.nodes) == initial_n_backbone * 3 - - -def test_go_virt_includes_no_moltype(): - """ - Test the processor raises an exception if the moltype is not defined. - """ - molecule = Molecule() - processor = GoVirtIncludes() - with pytest.raises(ValueError): - processor.run_molecule(molecule) From f7e43387e4551199ac0e9c663b3ca12a3592ec2a Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Mon, 16 Oct 2023 13:57:04 +0200 Subject: [PATCH 19/95] working Go flow --- bin/martinize2 | 16 +++--- vermouth/rcsu/contact_map.py | 3 +- vermouth/rcsu/go_pipeline.py | 26 +++++----- vermouth/rcsu/go_structure_bias.py | 78 ++++++++++++++++++------------ vermouth/rcsu/go_utils.py | 1 - vermouth/rcsu/go_vs_includes.py | 2 +- 6 files changed, 68 insertions(+), 58 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 8ee52868..49eecd88 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -953,15 +953,13 @@ def entry(): LOGGER.info("Reading Go model contact map.", type="step") go_map = read_go_map(args.go_map) LOGGER.info("Generating the Go model.", type="step") - GoPipeline(moltype=args.govs_moltype, - contact_map=go_map, - cutoff_short=args.go_low, - cutoff_long=args.go_up, - go_eps=args.go_eps, - res_dist=args.go_res_dist, - prefix=args.govs_moltype, - res_graph=res_graph, - ).run_system(system) + GoPipeline.run_system(system, + moltype=args.govs_moltype, + contact_map=go_map, + cutoff_short=args.go_low, + cutoff_long=args.go_up, + go_eps=args.go_eps, + res_dist=args.go_res_dist,) defines = ("GO_VIRT",) itp_paths = ["go_atomtypes.itp", "go_nbparams.itp"] diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index b22305fc..b8ee5936 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -42,8 +42,9 @@ def read_go_map(file_path): continue if tokens[0] == "R" and len(tokens) == 18: - contacts.append((int(tokens[1]), tokens[2], int(tokens[4]), tokens[5])) + contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) if len(contacts) == 0: raise IOError("You contact map is empty. Are you sure it has the right formatting?") + return contacts diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 72385f50..f30bba10 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -25,11 +25,11 @@ class GoProcessorPipline(Processor): """ Wrapping all processors for the go model. """ - def __init__(self, processor_list, **kwargs): + def __init__(self, processor_list): self.processor_list = processor_list - self.kwargs = kwargs + self.kwargs = {} - def prepare_run(self, system): + def prepare_run(self, system, moltype): """ Things to do before running the pipeline. """ @@ -37,21 +37,17 @@ def prepare_run(self, system): # this will eventually become deprecated # with the proper Go-model for multimers vermouth.MergeAllMolecules().run_system(system) - for molecule in system.molecules: - res_graph = vermouth.graph_utils.make_residue_graph(system.molecules[0]) - molecule.residue_graph = res_graph + molecule = system.molecules[0] +# res_graph = vermouth.graph_utils.make_residue_graph(molecule) +# molecule.res_graph = res_graph + molecule.meta['moltype'] = moltype - def postprocess_run(self, system): - """ - Do required post-processing. - """ - pass - - def run_system(self, system): - self.prepare_run(self, system) + def run_system(self, system, **kwargs): + self.kwargs = kwargs + self.prepare_run(system, moltype=kwargs['moltype']) for processor in self.processor_list: process_args = inspect.getfullargspec(processor).args - process_args_values = {self.kwargs[arg] for arg in process_args} + process_args_values = {arg:self.kwargs[arg] for arg in kwargs.keys() if arg in process_args} processor(**process_args_values).run_system(system) return system diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index bdd3907d..0569b7b9 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -16,9 +16,11 @@ """ import numpy as np import networkx as nx +from ..graph_utils import make_residue_graph from ..molecule import Interaction from ..processors.processor import Processor from ..selectors import filter_minimal, select_backbone +from ..gmx.topology import NonbondParam from .go_utils import get_go_type_from_attributes class ComputeStructuralGoBias(Processor): @@ -48,8 +50,8 @@ def __init__(self, cutoff_long, go_eps, res_dist, - res_graph=None, - prefix="VS"): + moltype, + res_graph=None): """ Initialize the Processor with arguments required to setup the Go model structural bias. @@ -71,21 +73,28 @@ def __init__(self, the residue graph they are ignored; this is similar to sequence distance but takes into account disulfide bridges for example + moltype: str + name of the molecule to treat res_graph: :class:vermouth.Molecule residue graph of the molecule; if None it get's generated automatically - prefix: str - prefix for all virtual-site atomtypes + system: :class:vermouth.System + the system + magic_number: float + magic number for Go contacts from the old + GoVirt script. """ self.contact_map = contact_map self.cutoff_short = cutoff_short self.cutoff_long = cutoff_long self.go_eps = go_eps self.res_dist = res_dist - self.prefix = prefix - self.res_graph = res_graph + self.moltype = moltype # don't modify + self.res_graph = None + self.system = None self.__chain_id_to_resnode = {} + self.magic_number = 1.12246204830 # do not overwrite when subclassing def _chain_id_to_resnode(self, chain, resid): @@ -107,7 +116,7 @@ def _chain_id_to_resnode(self, chain, resid): a dict matching the chain,resid to the self.res_graph node """ if self.__chain_id_to_resnode: - return self.__chain_id_to_resnode + return self.__chain_id_to_resnode[(chain, resid)] # for each residue collect the chain and residue in a dict # we use this later for identifying the residues from the @@ -120,7 +129,7 @@ def _chain_id_to_resnode(self, chain, resid): # the _old_resid resid = self.res_graph.nodes[resnode].get('_old_resid') self.__chain_id_to_resnode[(chain, resid)] = resnode - return self.__chain_id_to_resnode + return self.__chain_id_to_resnode[(chain, resid)] def contact_selector(self, molecule): """ @@ -149,31 +158,31 @@ def contact_selector(self, molecule): resIDA, chainA, resIDB, chainB = contact # identify the contact in the residue graph based on # chain ID and resid - resA = self.chain_id_to_resnode[(chainA, resIDA)] - resB = self.chain_id_to_resnode[(chainB, resIDB)] + resA = self._chain_id_to_resnode(chainA, resIDA) + resB = self._chain_id_to_resnode(chainB, resIDB) # make sure that both residues are not connected # note: contacts should be symmteric so we only # check against one if resB not in connected_pairs[resA]: # now we lookup the backbone nodes within the residue contact - bb_node_A = next(filter_minimal(self.res_graph.nodes[resB], select_backbone)) - bb_node_B = next(filter_minimal(self.res_graph.nodes[resB], select_backbone)) + bb_node_A = next(filter_minimal(self.res_graph.nodes[resA]['graph'], select_backbone)) + bb_node_B = next(filter_minimal(self.res_graph.nodes[resB]['graph'], select_backbone)) # compute the distance between bb-beads dist = np.linalg.norm(molecule.nodes[bb_node_A]['position'] - molecule.nodes[bb_node_B]['position']) # verify that the distance between BB-beads satisfies the # cut-off criteria - if self.cut_off_large > dist > self.cutoff_short: + if self.cutoff_long > dist > self.cutoff_short: # find the go virtual-sites for this residue # probably can be done smarter but mehhhh - atype_a = get_go_type_from_attributes(molecule, - resid=resIDA, - chain=chainA, - prefix=self.prefix) - atype_b = get_go_type_from_attributes(molecule, - resid=resIDB, - chain=chainB, - prefix=self.prefix) + atype_a = next(get_go_type_from_attributes(self.res_graph.nodes[resA]['graph'], + resid=resIDA, + chain=chainA, + prefix=self.moltype)) + atype_b = next(get_go_type_from_attributes(self.res_graph.nodes[resB]['graph'], + resid=resIDB, + chain=chainB, + prefix=self.moltype)) # generate backbone backbone exclusions # perhaps one day can be it's own function excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) @@ -202,11 +211,23 @@ def compute_go_interaction(self, contacts): for atype_a, atype_b, dist in contacts: # compute the LJ sigma paramter for this contact # 1.12246204830 is a magic number by Sebastian - sigma = dist / 1.12246204830 + sigma = dist / self.magic_number # find the go virtual-sites for this residue # probably can be done smarter but mehhhh - go_inters[frozenset(atype_a, atype_b)] = (sigma, self.go_eps) - return go_inters + contact_bias = NonbondParam(atoms=(atype_a, atype_b), + sigma=sigma, + epsilon=self.go_eps, + meta={"comment": ["go bond {resid_a} {resid_b}"]}) + self.system.gmx_topology_params["nonbond_params"].append(contact_bias) + + def run_molecule(self, molecule): + self.res_graph = make_residue_graph(molecule) + # compute the contacts; this also creates + # the exclusions + contacts = self.contact_selector(molecule) + # compute the interaction parameters + self.compute_go_interaction(contacts) + return molecule def run_system(self, system): """ @@ -217,11 +238,6 @@ def run_system(self, system): system: vermouth.system.System The system to process. Is modified in-place. """ + self.system = system for molecule in system.molecules: - # compute the contacts; this also creates - # the exclusions - contacts = self.contact_selector(molecule) - # compute the interaction parameters - inters = self.compute_go_interaction(contacts) - # update the contacts for the system - self.system.gmx_topology_params.upadte(inters) + self.run_molecule(molecule) diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index c160ce45..fe44ad44 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -44,7 +44,6 @@ def get_go_type_from_attributes(molecule, prefix, **kwargs): attrs = molecule.nodes[node] if attributes_match(attrs, kwargs) and attrs['atype'].startswith(prefix): yield attrs['atype'] - resid = kwargs['resid'] chain = kwargs['chain'] raise IOError(f"Could not find GoVs with resid {resid} in chain {chain}.") diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index db9c44b0..3c79e0ac 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -45,7 +45,7 @@ class VirtualSideCreator(Processor): Assign molecule type names to the molecules in a system. :func:`add_virtual_sites` """ - def __init__(self, sections=('exclusions', )): + def __init__(self, sections=()): self.sections = sections self.system = None From f06b2908ddeea54d339eb1352ec90ed70783d072 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 15:17:49 +0200 Subject: [PATCH 20/95] contact map tes --- vermouth/tests/rcsu/test_read_go_map.py | 53 +++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 vermouth/tests/rcsu/test_read_go_map.py diff --git a/vermouth/tests/rcsu/test_read_go_map.py b/vermouth/tests/rcsu/test_read_go_map.py new file mode 100644 index 00000000..5899e9d2 --- /dev/null +++ b/vermouth/tests/rcsu/test_read_go_map.py @@ -0,0 +1,53 @@ +# -*- coding: utf-8 -*- +# Copyright 2022 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Unit tests for the Go contact map reader. +""" +import pytest +from vermouth.rcsu.contact_map import read_go_map + +@pytest.mark.parametrize('lines, contacts', + # two sets of contacts same chain + ((""" + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model + ============================================================================================ + R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 + R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 + R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 + R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 + """, + [(1, "A", 2, "A"), (1, "A", 40, "A"), (2, "A", 37, "A"), (2, "A", 39, "A")] + ), + # two sets of contacts different chains + ((""" + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model + ============================================================================================ + R 1 1 LYS A 1 2 VAL B 2 3.8094 1 1 1 1 11 369 0 + R 6 1 LYS A 1 40 THR B 40 5.4657 1 1 1 1 222 238 0 + R 13 2 VAL C 2 37 ASN D 37 7.9443 0 1 0 0 -75 75 0 + R 15 2 VAL C 2 39 ASN D 39 4.2809 1 1 1 0 -13 121 0 + """), + [(1, "A", 2, "B"), (1, "A", 40, "B"), (2, "C", 37, "D"), (2, "C", 39, "D")] + ))) +def test_go_map(tmp_path, lines, contacts): + + # write the go contact map file + with open(tmp_path / "go_file.txt", "w") as in_file: + in_file.write(lines) + + # read go map + contact_map = read_go_map(tmp_path / "go_file.txt") + assert contact_map == contacts From 257600a932326b9404ee05e33b4dae59fd196a12 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 15:22:20 +0200 Subject: [PATCH 21/95] test for reading and error in go map --- vermouth/tests/rcsu/test_read_go_map.py | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/vermouth/tests/rcsu/test_read_go_map.py b/vermouth/tests/rcsu/test_read_go_map.py index 5899e9d2..54049f59 100644 --- a/vermouth/tests/rcsu/test_read_go_map.py +++ b/vermouth/tests/rcsu/test_read_go_map.py @@ -25,6 +25,7 @@ ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model ============================================================================================ R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 + R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 @@ -43,11 +44,23 @@ [(1, "A", 2, "B"), (1, "A", 40, "B"), (2, "C", 37, "D"), (2, "C", 39, "D")] ))) def test_go_map(tmp_path, lines, contacts): + # write the go contact map file + with open(tmp_path / "go_file.txt", "w") as in_file: + in_file.write(lines) + + # read go map + contact_map = read_go_map(tmp_path / "go_file.txt") + assert contact_map == contacts - # write the go contact map file - with open(tmp_path / "go_file.txt", "w") as in_file: - in_file.write(lines) +def test_go_error(tmp_path): + lines=""" + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model + ============================================================================================ + No valid contacts in this file. + """ + # write the go contact map file + with open(tmp_path / "go_file.txt", "w") as in_file: + in_file.write(lines) - # read go map - contact_map = read_go_map(tmp_path / "go_file.txt") - assert contact_map == contacts + with pytest.raises(IOError): + read_go_map(tmp_path / "go_file.txt") From 4f45d810880f91443be78390913731091c8e9b93 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 15:49:37 +0200 Subject: [PATCH 22/95] test for go utils --- vermouth/tests/rcsu/test_go_utils.py | 56 ++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 vermouth/tests/rcsu/test_go_utils.py diff --git a/vermouth/tests/rcsu/test_go_utils.py b/vermouth/tests/rcsu/test_go_utils.py new file mode 100644 index 00000000..00eb887e --- /dev/null +++ b/vermouth/tests/rcsu/test_go_utils.py @@ -0,0 +1,56 @@ +# -*- coding: utf-8 -*- +# Copyright 2022 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Unit tests for the Go contact map reader. +""" +import pytest +import hypothesis +import hypothesis.strategies as st +from vermouth.rcsu.go_utils import _get_bead_size, _in_resid_region, get_go_type_from_attributes +from vermouth.tests.molecule_strategies import random_molecule + +@pytest.mark.parametrize('atype, size', ( + ("SN4a", "small"), + ("P3", "regular"), + ("Tq4d", "tiny") + )) +def test_get_bead_size(atype, size): + assert size == _get_bead_size(atype) + + +@pytest.mark.parametrize('regions, resid, result', ( + # single region true + ([(101, 120)], 115, True), + # two regions true + ([(101, 120), (180, 210)], 115, True), + # two regions true; but inaccurate sorting + ([(120, 101), (180, 210)], 115, True), + # single region false + ([(101, 120)], 15, False), + # two regions false + ([(101, 120), (180, 210)], 15, False), + )) +def test_get_bead_size(regions, resid, result): + assert result == _in_resid_region(resid, regions) + + +@hypothesis.settings(suppress_health_check=[hypothesis.HealthCheck.too_slow]) +@hypothesis.given(random_molecule()) +def test_get_go_type_from_attributes(mol): + vs_node = len(mol.nodes) + mol.add_node(vs_node, atype="prefix_0", chain="A", resid=5) + found_atype = next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) + assert found_atype == "prefix_0" From 0d7cc942649cad43921aa9875a781f7d1263a42d Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 16:55:58 +0200 Subject: [PATCH 23/95] add test for atomtypes --- vermouth/tests/gmx/test_topology.py | 85 +++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 vermouth/tests/gmx/test_topology.py diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py new file mode 100644 index 00000000..54657904 --- /dev/null +++ b/vermouth/tests/gmx/test_topology.py @@ -0,0 +1,85 @@ +# Copyright 2018 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Test the writing of TOP file. +""" +import pytest +import vermouth +from vermouth.file_writer import DeferredFileWriter +from vermouth.gmx.topology import (convert_sigma_epsilon, + write_atomtypes, + write_nonbond_params, + write_gmx_topology, + Atomtype, + NonbondParam) +from vermouth.tests.gmx.test_itp import dummy_molecule + +@pytest.mark.parametrize('atomtypes, expected', + # simple atomtype + #'Atomtype', 'molecule node sigma epsilon meta + (( + [{"node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {}}], + ["[ atomtypes ]\n", + "A 72 0 A 0.43000000 2.30000000 \n"]), + ( + [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {}}, + {"node":1, "sigma": 0.47, "epsilon": 2.5, "meta": {}}], + ["[ atomtypes ]\n", + "A 72 0 A 0.43000000 2.30000000 \n", + "B 72 0 A 0.47000000 2.50000000 \n"]), + ( + [{"node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {"comment": ["comment"]}}], + ["[ atomtypes ]\n", + "A 72 0 A 0.43000000 2.30000000 ;comment\n"]), + ( + [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {"group": "g1"}}, + {"node":1, "sigma": 0.44, "epsilon": 3.3, "meta": {}}, + {"node":2, "sigma": 0.47, "epsilon": 2.5, "meta": {"group": "g1"}}], + ['[ atomtypes ]\n', + 'B 72 0 A 0.44000000 3.30000000 \n', + '; g1\n', + 'A 72 0 A 0.43000000 2.30000000 \n', + 'C 72 0 A 0.47000000 2.50000000 \n'] + ), + ( + [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {"ifdef": "g1"}}, + {"node":1, "sigma": 0.44, "epsilon": 3.3, "meta": {}}, + {"node":2, "sigma": 0.47, "epsilon": 2.5, "meta": {"ifdef": "g1"}}], + ['[ atomtypes ]\n', + 'B 72 0 A 0.44000000 3.30000000 \n', + '#ifdef g1\n', + 'A 72 0 A 0.43000000 2.30000000 \n', + 'C 72 0 A 0.47000000 2.50000000 \n', + '#endif'] + ), + )) +def test_no_header(tmp_path, dummy_molecule, atomtypes, expected): + """ + Test that the atomtypes directive is properly written. + """ + dummy_sys = vermouth.system.System("") + for atype in atomtypes: + # somewhat hacky workaround because pytest doesn't + # allow the use of fixtures in parametrize + atype['molecule'] = dummy_molecule + dummy_sys.gmx_topology_params['atomtypes'].append(Atomtype(**atype)) + + outpath = tmp_path / 'out.itp' + write_atomtypes(dummy_sys, outpath) + DeferredFileWriter().write() + + with open(str(outpath)) as infile: + for line, ref_line in zip(infile.readlines(), expected): + assert line == ref_line From 90fca98d479dc26efd75d661b684df0cea3a224b Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 16:59:30 +0200 Subject: [PATCH 24/95] add test for atomtypes --- vermouth/tests/gmx/test_topology.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index 54657904..ac5f1754 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -26,23 +26,27 @@ NonbondParam) from vermouth.tests.gmx.test_itp import dummy_molecule -@pytest.mark.parametrize('atomtypes, expected', +@pytest.mark.parametrize('atomtypes, expected, C6C12', # simple atomtype #'Atomtype', 'molecule node sigma epsilon meta (( [{"node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {}}], ["[ atomtypes ]\n", - "A 72 0 A 0.43000000 2.30000000 \n"]), + "A 72 0 A 0.43000000 2.30000000 \n"], False), + ( + [{"node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {}}], + ["[ atomtypes ]\n", + "A 72 0 A 254.62172908 37693.15402307 \n"], True), ( [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {}}, {"node":1, "sigma": 0.47, "epsilon": 2.5, "meta": {}}], ["[ atomtypes ]\n", "A 72 0 A 0.43000000 2.30000000 \n", - "B 72 0 A 0.47000000 2.50000000 \n"]), + "B 72 0 A 0.47000000 2.50000000 \n"], False), ( [{"node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {"comment": ["comment"]}}], ["[ atomtypes ]\n", - "A 72 0 A 0.43000000 2.30000000 ;comment\n"]), + "A 72 0 A 0.43000000 2.30000000 ;comment\n"], False), ( [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {"group": "g1"}}, {"node":1, "sigma": 0.44, "epsilon": 3.3, "meta": {}}, @@ -51,7 +55,7 @@ 'B 72 0 A 0.44000000 3.30000000 \n', '; g1\n', 'A 72 0 A 0.43000000 2.30000000 \n', - 'C 72 0 A 0.47000000 2.50000000 \n'] + 'C 72 0 A 0.47000000 2.50000000 \n'], False ), ( [{"node":0, "sigma": 0.43, "epsilon": 2.3, "meta": {"ifdef": "g1"}}, @@ -62,10 +66,10 @@ '#ifdef g1\n', 'A 72 0 A 0.43000000 2.30000000 \n', 'C 72 0 A 0.47000000 2.50000000 \n', - '#endif'] + '#endif'], False ), )) -def test_no_header(tmp_path, dummy_molecule, atomtypes, expected): +def test_no_header(tmp_path, dummy_molecule, atomtypes, expected, C6C12): """ Test that the atomtypes directive is properly written. """ @@ -77,7 +81,7 @@ def test_no_header(tmp_path, dummy_molecule, atomtypes, expected): dummy_sys.gmx_topology_params['atomtypes'].append(Atomtype(**atype)) outpath = tmp_path / 'out.itp' - write_atomtypes(dummy_sys, outpath) + write_atomtypes(dummy_sys, outpath, C6C12=C6C12) DeferredFileWriter().write() with open(str(outpath)) as infile: From 31fa775aab56c4bfecd900ff0a00c27bcf3d7d3f Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:00:16 +0200 Subject: [PATCH 25/95] change name test atomtypes --- vermouth/tests/gmx/test_topology.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index ac5f1754..d12cdfc2 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -69,7 +69,7 @@ '#endif'], False ), )) -def test_no_header(tmp_path, dummy_molecule, atomtypes, expected, C6C12): +def test_atomtypes(tmp_path, dummy_molecule, atomtypes, expected, C6C12): """ Test that the atomtypes directive is properly written. """ From b96113ed20bc24aca0069655f663e77dc7fab504 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:13:29 +0200 Subject: [PATCH 26/95] add tests nonbond_params --- vermouth/tests/gmx/test_topology.py | 60 +++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index d12cdfc2..1ad93b5f 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -87,3 +87,63 @@ def test_atomtypes(tmp_path, dummy_molecule, atomtypes, expected, C6C12): with open(str(outpath)) as infile: for line, ref_line in zip(infile.readlines(), expected): assert line == ref_line + + +@pytest.mark.parametrize('nbparams, expected, C6C12', + # simple atomtype + #'Atomtype', 'molecule node sigma epsilon meta + (( + [{"atoms": ("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {}}], + ["[ nonbond_params ]\n", + "A B 1 0.43000000 2.30000000 \n"], False), + ( + [{"atoms": ("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {}}], + ["[ nonbond_params ]\n", + "A B 1 254.62172908 37693.15402307 \n"], True), + ( + [{"atoms": ("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {}}, + {"atoms": ("A", "C"), "sigma": 0.47, "epsilon": 2.5, "meta": {}}], + ["[ nonbond_params ]\n", + "A B 1 0.43000000 2.30000000 \n", + "A C 1 0.47000000 2.50000000 \n"], False), + ( + [{"atoms": ("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {"comment": ["comment"]}}], + ["[ nonbond_params ]\n", + "A B 1 0.43000000 2.30000000 ;comment\n"], False), + ( + [{"atoms":("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {"group": "g1"}}, + {"atoms":("B", "C"), "sigma": 0.44, "epsilon": 3.3, "meta": {}}, + {"atoms":("A", "C"), "sigma": 0.47, "epsilon": 2.5, "meta": {"group": "g1"}}], + ['[ nonbond_params ]\n', + 'B C 1 0.44000000 3.30000000 \n', + '; g1\n', + 'A B 1 0.43000000 2.30000000 \n', + 'A C 1 0.47000000 2.50000000 \n'], False + ), + ( + [{"atoms":("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {"ifdef": "g1"}}, + {"atoms":("B", "C"), "sigma": 0.44, "epsilon": 3.3, "meta": {}}, + {"atoms":("A", "C"), "sigma": 0.47, "epsilon": 2.5, "meta": {"ifdef": "g1"}}], + ['[ nonbond_params ]\n', + 'B C 1 0.44000000 3.30000000 \n', + '#ifdef g1\n', + 'A B 1 0.43000000 2.30000000 \n', + 'A C 1 0.47000000 2.50000000 \n', + '#endif'], False + ), + )) +def test_nonbond_params(tmp_path, nbparams, expected, C6C12): + """ + Test that the atomtypes directive is properly written. + """ + dummy_sys = vermouth.system.System("") + for nbparam in nbparams: + dummy_sys.gmx_topology_params['nonbond_params'].append(NonbondParam(**nbparam)) + + outpath = tmp_path / 'out.itp' + write_nonbond_params(dummy_sys, outpath, C6C12=C6C12) + DeferredFileWriter().write() + + with open(str(outpath)) as infile: + for line, ref_line in zip(infile.readlines(), expected): + assert line == ref_line From 6f59271c09b999493c3455af338c707636c9316e Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:31:22 +0200 Subject: [PATCH 27/95] fix comment handling --- vermouth/gmx/topology.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 41812ff1..89fe40e6 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -100,7 +100,10 @@ def write_nonbond_params(system, itp_path, C6C12=False): else: nb1, nb2 = nb_params.sigma, nb_params.epsilon - comments = ";" + " ".join(nb_params.meta['comment']) + if nb_params.meta.get('comment'): + comments = ";" + " ".join(nb_params.meta['comment']) + else: + comments = "" itp_file.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n") def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), header=()): From 7e11ddcb8dd61118bb62c89245ab82a3fc75117c Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:31:43 +0200 Subject: [PATCH 28/95] use resid function from go_utils --- vermouth/processors/water_bias.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index c272497c..ff8e68d8 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -14,15 +14,9 @@ from .processor import Processor from ..graph_utils import make_residue_graph -from ..rcsu.go_utils import get_go_type_from_attributes, _get_bead_size +from ..rcsu.go_utils import get_go_type_from_attributes, _get_bead_size, _in_resid_region from ..gmx.topology import NonbondParam -def _in_region(resid, regions): - for start, stop in regions: - if start <= resid <= stop: - return True - return False - class ComputeWaterBias(Processor): """ Processor which computes the water bias for @@ -91,7 +85,7 @@ def assign_residue_water_bias(self, molecule, res_graph): chain = res_graph.nodes[res_node]['chain'] resname = res_graph.nodes[res_node]['resname'] - if _in_region(resid, self.idr_regions): + if _in_resid_region(resid, self.idr_regions): eps = self.water_bias.get('idr', 0.0) elif self.auto_bias: sec_struc = res_graph.nodes[res_node]['cgsecstruct'] From c072b925cfeb83f0f8d68d285a653a460ddbe0cb Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:32:13 +0200 Subject: [PATCH 29/95] idot safe in resid handling --- vermouth/rcsu/go_utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index fe44ad44..83335169 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -63,7 +63,9 @@ def _in_resid_region(resid, regions): ------- bool """ - for low, up in regions: + for limits in regions: + # perhaps someone gives them as reversed + low, up = sorted(limits) if low <= resid <= up: return True return False From cba5f78bb7f4b7ab58e3483d154638e2c7cdd138 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 16 Oct 2023 17:32:31 +0200 Subject: [PATCH 30/95] update dummy molecule --- vermouth/tests/gmx/test_itp.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/vermouth/tests/gmx/test_itp.py b/vermouth/tests/gmx/test_itp.py index 6125c2d5..720c30f8 100644 --- a/vermouth/tests/gmx/test_itp.py +++ b/vermouth/tests/gmx/test_itp.py @@ -41,7 +41,11 @@ def dummy_molecule(): 'charge_group': 1, 'charge': 0, 'mass': 72 }), (1, { - 'atype': 'A', 'resid': 1, 'resname': 'X', 'atomname': 'A', + 'atype': 'B', 'resid': 1, 'resname': 'X', 'atomname': 'B', + 'charge_group': 1, 'charge': 0, 'mass': 72 + }), + (2, { + 'atype': 'C', 'resid': 1, 'resname': 'X', 'atomname': 'C', 'charge_group': 1, 'charge': 0, 'mass': 72 }), )) From 7fc412d5588e40d5daf19bf1115338cab3585de0 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Tue, 17 Oct 2023 08:57:18 +0200 Subject: [PATCH 31/95] topology writing test --- vermouth/tests/gmx/test_topology.py | 54 +++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index 1ad93b5f..c7c69239 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -15,6 +15,7 @@ """ Test the writing of TOP file. """ +import textwrap import pytest import vermouth from vermouth.file_writer import DeferredFileWriter @@ -147,3 +148,56 @@ def test_nonbond_params(tmp_path, nbparams, expected, C6C12): with open(str(outpath)) as infile: for line, ref_line in zip(infile.readlines(), expected): assert line == ref_line + +def test_toplevel_topology(tmp_path, dummy_molecule): + """ + Make sure the toplevel topology file + is correctly written. Note that the individual + molecule itp files are seperately checked in + gmx itp module or in the previous tests. + """ + system = vermouth.System() + system.molecules.append(dummy_molecule) + dummy_molecule.meta['moltype'] = "molecule_0" + # "node": 0, "sigma": 0.43, "epsilon": 2.3, "meta": {}} + system.gmx_topology_params['atomtypes'].append(Atomtype(node=0, + molecule=dummy_molecule, + sigma=0.43, + meta={}, + epsilon=2.3)) + system.gmx_topology_params['nonbond_params'].append(NonbondParam(atoms=("A", "B"), + sigma=0.43, + epsilon=2.3, + meta={})) + outpath = tmp_path / 'out.itp' + atompath = tmp_path / 'atomtypes.itp' + nbpath = tmp_path / 'nonbond_params.itp' + write_gmx_topology(system, + outpath, + header=['first header comment', 'second header comment'], + defines=('random', ), + itp_paths=[atompath, nbpath], + # at this level C6C12 doesn't matter; it gets + # checked in previous texts + C6C12=False) + DeferredFileWriter().write() + + reference =f"""#define random +#include "martini.itp" + +#include "{tmp_path}/atomtypes.itp" +#include "{tmp_path}/nonbond_params.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 +""" + ref_lines = textwrap.dedent(reference).splitlines() + with open(str(outpath)) as infile: + for line, ref_line in zip(infile.readlines(), ref_lines): + print('l', line.strip()) + print('lr', ref_line.strip()) + assert line.strip() == ref_line From f368a38bc216e942977461af6e95460d16fd36fe Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Tue, 17 Oct 2023 08:59:22 +0200 Subject: [PATCH 32/95] do writing test in tmp dir --- vermouth/tests/gmx/test_topology.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index c7c69239..f15c8575 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -15,6 +15,7 @@ """ Test the writing of TOP file. """ +import os import textwrap import pytest import vermouth @@ -156,6 +157,7 @@ def test_toplevel_topology(tmp_path, dummy_molecule): molecule itp files are seperately checked in gmx itp module or in the previous tests. """ + os.chdir(tmp_path) system = vermouth.System() system.molecules.append(dummy_molecule) dummy_molecule.meta['moltype'] = "molecule_0" From 82ca6af6a2800c25019caf0641e687b43d43352c Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Tue, 17 Oct 2023 09:36:09 +0200 Subject: [PATCH 33/95] address comment in topology file writing --- vermouth/gmx/topology.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 89fe40e6..170a77fe 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -130,13 +130,18 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), if not system.molecules: raise ValueError("No molecule in the system. Nothing to write.") + itp_paths = itp_paths[::-1] include_string = "" - # First we write the atomtypes and nonbondparams directive - if itp_paths: - write_atomtypes(system, itp_paths[0], C6C12) - write_nonbond_params(system, itp_paths[1], C6C12) - include_string = "\n".join('#include "{}"'.format(path) for path in itp_paths[:2]) - include_string += "\n" + # First we write the atomtypes directive + if "atomtypes" in system.gmx_topology_params: + _path = itp_paths.pop() + write_atomtypes(system, _path, C6C12) + include_string += f'\n #include "{_path}"' + # Next we write the nonbond_params directive + if "nonbond_params" in system.gmx_topology_params: + _path = itp_paths.pop() + write_nonbond_params(system, _path, C6C12) + include_string += f'\n #include "{_path}"\n' # Write the ITP files for the molecule types, and prepare writing the # [ molecules ] section of the top file. # * We write one ITP file for each different moltype in the system, the From af6de4981ca9484f16e878f60199fe38539ad0f9 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 09:45:31 +0200 Subject: [PATCH 34/95] update doc-string --- vermouth/gmx/topology.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 170a77fe..e4d98750 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -122,6 +122,12 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), system: :class:vermouth.System top_path: pathlib.Path path for topology file + itp_paths: list[pathlib.Path] + list of paths for writing the topology parameters + like atomtypes. + C6C12: bool + write non-bonded interaction parameters using LJ + C6C12 form defines: tuple(str) define statments to include in the topology header: tuple(str) From 403ec92ba01ffd866de96c50c67a9185971eeb82 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 10:56:08 +0200 Subject: [PATCH 35/95] test-water bias --- vermouth/tests/test_water_bias.py | 125 ++++++++++++++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 vermouth/tests/test_water_bias.py diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py new file mode 100644 index 00000000..67daed9e --- /dev/null +++ b/vermouth/tests/test_water_bias.py @@ -0,0 +1,125 @@ +# Copyright 2022 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Test for the water bias processor. +""" +import pytest +import networkx as nx +import vermouth +from vermouth.rcsu.go_vs_includes import VirtualSideCreator +from vermouth.system import System +from vermouth.forcefield import ForceField +from vermouth.processors.water_bias import ComputeWaterBias +from vermouth.tests.test_apply_rubber_band import test_molecule + +@pytest.mark.parametrize('secstruc, water_bias, idr_regions, expected', + (( + # only auto-bias single sec struct + {1: "H", 2: "H", 3: "H", 4: "H"}, + {"H": 2.1}, + [], + {0: "H", 3: "H", 5: "H", 6: "H"} + ), + # only auto-bias two sec struct + ({1: "H", 2: "H", 3: "C", 4: "C"}, + {"H": 2.1, "C": 3.1}, + [], + {0: "H", 3: "H", 5: "C", 6: "C"} + ), + # only idp bias + ({1: "H", 2: "H", 3: "C", 4: "C"}, + {"idr": 2.1}, + [(2, 3)], + {2: "idr", 3: "idr"} + ), + # idp and sec struc bias + ({1: "H", 2: "H", 3: "C", 4: "C"}, + {"idr": 1.1, "C": 3.1, "H": 2.1}, + [(2, 3)], + {0: "H", 2: "idr", 3: "idr", 4: "C"} + ) + )) +def test_assign_residue_water_bias(test_molecule, + secstruc, + water_bias, + idr_regions, + expected): + + # set mol meta + test_molecule.meta['moltype'] = "molecule_0" + # assign some atomtypes; as the molecule is rather + # complex we don't need to redo it every time + atypes = {0: "P1", 1: "SN4a", 2: "SN4a", + 3: "SP1", 4: "C1", + 5: "TP1", + 6: "P1", 7: "SN3a", 8: "SP4"} + nx.set_node_attributes(test_molecule, atypes, "atype") + sizes = {0: 0.47, 3: 0.41, 5: 0.38, 6: 0.47} + # assign residue names + resnames = {0: "A", 1: "A", 2: "A", + 3: "B", 4: "B", + 5: "C", + 6: "D", 7: "D", 8: "D"} + nx.set_node_attributes(test_molecule, resnames, "resname") + # assign resids + resids = nx.get_node_attributes(test_molecule, "resid") + nx.set_node_attributes(test_molecule, resids, "_old_resid") + # assign chain ids + nx.set_node_attributes(test_molecule, "A", "chain") + + # make the proper force-field + ff = ForceField("test") + ff.variables['water_type'] = "W" + ff.variables['regular'] = 0.47 + ff.variables['small'] = 0.41 + ff.variables['tiny'] = 0.38 + + res_graph = vermouth.graph_utils.make_residue_graph(test_molecule) + for node in res_graph.nodes: + mol_nodes = res_graph.nodes[node]['graph'].nodes + block = vermouth.molecule.Block() + resname = res_graph.nodes[node]['resname'] + resid = res_graph.nodes[node]['resid'] + # assign secondary structure + for mol_node in mol_nodes: + test_molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid] + block.add_node(test_molecule.nodes[mol_node]['atomname'], + atype=test_molecule.nodes[mol_node]['atype']) + + ff.blocks[resname] = block + + + # create the system + test_molecule._force_field = ff + system = System() + system.molecules.append(test_molecule) + + # generate the virtual sites + VirtualSideCreator().run_system(system) + + processor = ComputeWaterBias(water_bias=water_bias, + auto_bias=True, + idr_regions=idr_regions) + processor.run_system(system) + for nb_params in system.gmx_topology_params['nonbond_params']: + assert nb_params.atoms[0] == "W" + vs_node = nb_params.atoms[1] + for vs in system.molecules[0].interactions['virtual_sitesn']: + if vs.atoms[0] == vs_node: + bb_node = vs.atoms[1] + water_eps = water_bias[expected[bb_node]] + water_sig = sizes[bb_node] + assert water_eps == nb_params.epsilon + assert water_sig == nb_params.sigma From 8ed3e8484675f90d3617d4b79ac6eb8e3e7523f4 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 11:18:15 +0200 Subject: [PATCH 36/95] refactor water bias test --- vermouth/tests/test_water_bias.py | 116 +++++++++++++++++++----------- 1 file changed, 76 insertions(+), 40 deletions(-) diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index 67daed9e..1d6a7428 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -24,6 +24,72 @@ from vermouth.processors.water_bias import ComputeWaterBias from vermouth.tests.test_apply_rubber_band import test_molecule +def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): + """ + Generate a test system from a molecule + with all attributes set and blocks in + force-field. + + Parameters + ---------- + molecule: :class:vermouth.Molecule + moltype: str + sets meta['moltype'] + secstruc: dict[int, str] + secondary structure attributes + as resid str pairs + defauts: dict + dict of attribute default value + attrs: dict + dict of attribute name and dict + of node value pairs + + Returns + ------- + :class:vermouth.System + """ + # set mol meta + molecule.meta['moltype'] = moltype + # assign default node attributes + for attr, value in defaults.items(): + nx.set_node_attributes(molecule, value, attr) + + # assign node attributes + for attr, values in attrs.items(): + nx.set_node_attributes(molecule, values, attr) + + # assign resids + resids = nx.get_node_attributes(molecule, "resid") + nx.set_node_attributes(molecule, resids, "_old_resid") + + # make the proper force-field + ff = ForceField("test") + ff.variables['water_type'] = "W" + ff.variables['regular'] = 0.47 + ff.variables['small'] = 0.41 + ff.variables['tiny'] = 0.38 + + res_graph = vermouth.graph_utils.make_residue_graph(molecule) + for node in res_graph.nodes: + mol_nodes = res_graph.nodes[node]['graph'].nodes + block = vermouth.molecule.Block() + resname = res_graph.nodes[node]['resname'] + resid = res_graph.nodes[node]['resid'] + # assign secondary structure + for mol_node in mol_nodes: + molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid] + block.add_node(molecule.nodes[mol_node]['atomname'], + atype=molecule.nodes[mol_node]['atype']) + + ff.blocks[resname] = block + + + # create the system + molecule._force_field = ff + system = System() + system.molecules.append(molecule) + return system + @pytest.mark.parametrize('secstruc, water_bias, idr_regions, expected', (( # only auto-bias single sec struct @@ -56,55 +122,25 @@ def test_assign_residue_water_bias(test_molecule, water_bias, idr_regions, expected): - - # set mol meta - test_molecule.meta['moltype'] = "molecule_0" - # assign some atomtypes; as the molecule is rather - # complex we don't need to redo it every time + # bead sizes + sizes = {0: 0.47, 3: 0.41, 5: 0.38, 6: 0.47} + # the molecule atomtypes atypes = {0: "P1", 1: "SN4a", 2: "SN4a", 3: "SP1", 4: "C1", 5: "TP1", 6: "P1", 7: "SN3a", 8: "SP4"} - nx.set_node_attributes(test_molecule, atypes, "atype") - sizes = {0: 0.47, 3: 0.41, 5: 0.38, 6: 0.47} - # assign residue names + # the molecule resnames resnames = {0: "A", 1: "A", 2: "A", 3: "B", 4: "B", 5: "C", 6: "D", 7: "D", 8: "D"} - nx.set_node_attributes(test_molecule, resnames, "resname") - # assign resids - resids = nx.get_node_attributes(test_molecule, "resid") - nx.set_node_attributes(test_molecule, resids, "_old_resid") - # assign chain ids - nx.set_node_attributes(test_molecule, "A", "chain") - - # make the proper force-field - ff = ForceField("test") - ff.variables['water_type'] = "W" - ff.variables['regular'] = 0.47 - ff.variables['small'] = 0.41 - ff.variables['tiny'] = 0.38 - res_graph = vermouth.graph_utils.make_residue_graph(test_molecule) - for node in res_graph.nodes: - mol_nodes = res_graph.nodes[node]['graph'].nodes - block = vermouth.molecule.Block() - resname = res_graph.nodes[node]['resname'] - resid = res_graph.nodes[node]['resid'] - # assign secondary structure - for mol_node in mol_nodes: - test_molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid] - block.add_node(test_molecule.nodes[mol_node]['atomname'], - atype=test_molecule.nodes[mol_node]['atype']) - - ff.blocks[resname] = block - - - # create the system - test_molecule._force_field = ff - system = System() - system.molecules.append(test_molecule) + system = create_sys_all_attrs(test_molecule, + moltype="molecule_0", + secstruc=secstruc, + defaults={"chain": "A"}, + attrs={"resname": resnames, + "atype": atypes}) # generate the virtual sites VirtualSideCreator().run_system(system) From f4f97a9e954cf57310fbcaafca3dbecaf1807568 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 14:42:50 +0200 Subject: [PATCH 37/95] fix go processor chain accounting --- vermouth/rcsu/go_structure_bias.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 0569b7b9..d9b837f1 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -122,13 +122,14 @@ def _chain_id_to_resnode(self, chain, resid): # we use this later for identifying the residues from the # contact map for resnode in self.res_graph.nodes: - chain = self.res_graph.nodes[resnode].get('chain', None) + chain_key = self.res_graph.nodes[resnode].get('chain', None) # in vermouth within a molecule all resid are unique # when merging multiple chains we store the old resid # the go model always references the input resid i.e. # the _old_resid - resid = self.res_graph.nodes[resnode].get('_old_resid') - self.__chain_id_to_resnode[(chain, resid)] = resnode + resid_key = self.res_graph.nodes[resnode].get('_old_resid') + self.__chain_id_to_resnode[(chain_key, resid_key)] = resnode + return self.__chain_id_to_resnode[(chain, resid)] def contact_selector(self, molecule): @@ -217,7 +218,7 @@ def compute_go_interaction(self, contacts): contact_bias = NonbondParam(atoms=(atype_a, atype_b), sigma=sigma, epsilon=self.go_eps, - meta={"comment": ["go bond {resid_a} {resid_b}"]}) + meta={"comment": ["go bond"]}) self.system.gmx_topology_params["nonbond_params"].append(contact_bias) def run_molecule(self, molecule): From 65106b054b49186f79b1524e2b0a17a2ee5d75f8 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 14:43:03 +0200 Subject: [PATCH 38/95] test for go processor structure bias --- vermouth/tests/rcsu/test_go_structure_bias.py | 132 ++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 vermouth/tests/rcsu/test_go_structure_bias.py diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py new file mode 100644 index 00000000..4529231a --- /dev/null +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -0,0 +1,132 @@ +""" +Test for the water bias processor. +""" +import pytest +import numpy as np +import networkx as nx +import vermouth +from vermouth.rcsu.go_vs_includes import VirtualSideCreator +from vermouth.tests.test_water_bias import create_sys_all_attrs +from vermouth.tests.test_apply_rubber_band import test_molecule +from vermouth.rcsu.go_structure_bias import ComputeStructuralGoBias + +def test_compute_go_interaction(test_molecule): + contacts = [("atom_a", "atom_b", 2.3), + ("atom_a", "atom_c", 4.1), + ("atom_q", "atom_p", 0.0)] + denom = 2**(1/6.) + expected = {("atom_a", "atom_b"): 2.3/denom, + ("atom_a", "atom_c"): 4.1/denom, + ("atom_q", "atom_p"): 0/denom} + + + system = vermouth.System() + system.molecules.append(test_molecule) + go_processor = ComputeStructuralGoBias(contact_map=None, + cutoff_short=None, + cutoff_long=None, + go_eps=2.1, + res_dist=None, + moltype="molecule_0") + go_processor.system = system + + go_processor.compute_go_interaction(contacts) + for nb_params in system.gmx_topology_params['nonbond_params']: + assert nb_params.atoms in expected + assert np.isclose(nb_params.sigma, expected[nb_params.atoms]) + assert nb_params.epsilon == 2.1 + +@pytest.mark.parametrize('cmap, cshort, clong, rdist, expected',( + # single contact good + ([(1, 'A', 4, 'A')], + 0.3, + 2.0, + 0, + [("mol_0_1", "mol_0_4", 1.5)]), + # single contact bad -> cshort + ([(1, 'A', 3, 'A')], + 1.5, + 2.0, + 0, + []), + # single contact bad -> clong + ([(1, 'A', 4, 'A')], + 0.5, + 0.8, + 0, + []), + # single contact bad -> rdist + ([(1, 'A', 4, 'A')], + 0.3, + 2.0, + 5, + []), + # two contacts good + ([(1, 'A', 3, 'A'), (1, 'A', 4, 'A')], + 0.3, + 2.0, + 1, + [("mol_0_1", "mol_0_3", 1.0), + ("mol_0_1", "mol_0_4", 1.5), + ]), + # one good one bad rdist + ([(1, 'A', 4, 'A'), (1, 'A', 2, 'A')], + 0.3, + 2.0, + 2, + [("mol_0_1", "mol_0_4", 1.5)]), + )) +def test_contact_selector(test_molecule, + cmap, + cshort, + clong, + rdist, + expected): + + # define some possible positions + pos = np.array([[0.0, 0.0, 0.0], + [0.0, 0.4, 0.0], + [0.0, 0.8, 0.0], + [0.5, 0.0, 0.0], + [0.5, 0.4, 0.0], + [1.0, 0.0, 0.0], + [1.5, 0.0, 0.0], + [1.5, 0.4, 0.0], + [1.5, 0.8, 0.0]]) + for node in test_molecule.nodes: + test_molecule.nodes[node]['position'] = pos[node] + + # bead sizes + sizes = {0: 0.47, 3: 0.41, 5: 0.38, 6: 0.47} + # the molecule atomtypes + atypes = {0: "P1", 1: "SN4a", 2: "SN4a", + 3: "SP1", 4: "C1", + 5: "TP1", + 6: "P1", 7: "SN3a", 8: "SP4"} + # the molecule resnames + resnames = {0: "A", 1: "A", 2: "A", + 3: "B", 4: "B", + 5: "C", + 6: "D", 7: "D", 8: "D"} + + secstruc = {1: "H", 2: "H", 3: "H", 4: "H"} + system = create_sys_all_attrs(test_molecule, + moltype="mol_0", + secstruc=secstruc, + defaults={"chain": "A"}, + attrs={"resname": resnames, + "atype": atypes}) + + # generate the virtual sites + VirtualSideCreator().run_system(system) + # initialize the Go processor + go_processor = ComputeStructuralGoBias(contact_map=cmap, + cutoff_short=cshort, + cutoff_long=clong, + go_eps=2.1, + res_dist=rdist, + moltype="mol_0") + go_processor.res_graph = vermouth.graph_utils.make_residue_graph(test_molecule) + # run the contact map selector + contact_matrix = go_processor.contact_selector(test_molecule) + assert contact_matrix == expected From fbbf8f5f12a29f15f98a64c5cc14162246f9352c Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 14:51:31 +0200 Subject: [PATCH 39/95] fix indent in vs creator --- vermouth/rcsu/go_vs_includes.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 3c79e0ac..4a3400cb 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -136,8 +136,8 @@ def add_virtual_sites(self, molecule, prefix, backbone='BB', atomname='CA', char parameters=['1'], meta={'go_vs': True, 'group': 'Virtual go site'}, )) - vs_params = Atomtype(node=new_node_id, molecule=molecule, sigma=0.0, epsilon=0.0, meta={}) - self.system.gmx_topology_params['atomtypes'].append(vs_params) + vs_params = Atomtype(node=new_node_id, molecule=molecule, sigma=0.0, epsilon=0.0, meta={}) + self.system.gmx_topology_params['atomtypes'].append(vs_params) molecule.add_nodes_from(virtual_site_nodes) From 71a8d2e60bd31c436a1626046eb38f6dbf2f0f94 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 16:01:35 +0200 Subject: [PATCH 40/95] fix some more issues --- bin/martinize2 | 2 +- vermouth/rcsu/contact_map.py | 14 +++++++++++++- vermouth/rcsu/go_structure_bias.py | 4 +++- 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 49eecd88..b7979fa2 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -549,7 +549,7 @@ def entry(): "-go-eps", dest="go_eps", type=float, - default=0.0, + default=9.414, help=("The strength of the Go model structural bias in kJ/mol."), ) go_group.add_argument( diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index b8ee5936..f4a9fb36 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -36,15 +36,27 @@ def read_go_map(file_path): lines = _file.readlines() contacts = [] + OV=0 + rCSU=0 for line in lines: tokens = line.strip().split() if len(tokens) == 0: continue if tokens[0] == "R" and len(tokens) == 18: - contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) + # this is a bad place to filter but follows + # the old script + if tokens[11] == "1": + # this is a OV contact we take it + contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) + OV+=1 + if tokens[11] == "0" and tokens[14] == "1": + # this is a rCSU contact we take it + contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) + rCSU+=1 if len(contacts) == 0: raise IOError("You contact map is empty. Are you sure it has the right formatting?") + print(len(contacts), OV, rCSU) return contacts diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index d9b837f1..de95eeb4 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -184,6 +184,8 @@ def contact_selector(self, molecule): resid=resIDB, chain=chainB, prefix=self.moltype)) + if (atype_b, atype_a, dist) in contact_matrix: + continue # generate backbone backbone exclusions # perhaps one day can be it's own function excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) @@ -218,7 +220,7 @@ def compute_go_interaction(self, contacts): contact_bias = NonbondParam(atoms=(atype_a, atype_b), sigma=sigma, epsilon=self.go_eps, - meta={"comment": ["go bond"]}) + meta={"comment": [f"go bond {dist}"]}) self.system.gmx_topology_params["nonbond_params"].append(contact_bias) def run_molecule(self, molecule): From cae03e9e40f0fb040e639746eb8aaf2ab6617684 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 16:09:01 +0200 Subject: [PATCH 41/95] adjust test to skip no OV/rCSU contacts --- vermouth/tests/rcsu/test_read_go_map.py | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/vermouth/tests/rcsu/test_read_go_map.py b/vermouth/tests/rcsu/test_read_go_map.py index 54049f59..942c8eed 100644 --- a/vermouth/tests/rcsu/test_read_go_map.py +++ b/vermouth/tests/rcsu/test_read_go_map.py @@ -27,20 +27,32 @@ R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 - R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 - R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 + R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 1 -75 75 0 + R 15 2 VAL A 2 39 ASN A 39 4.2809 0 1 1 1 -13 121 0 """, [(1, "A", 2, "A"), (1, "A", 40, "A"), (2, "A", 37, "A"), (2, "A", 39, "A")] ), + # two sets of contacts same chain but skip two non-OV/rCSU + (""" + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model + ============================================================================================ + R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 + + R 6 1 LYS A 1 40 THR A 40 5.4657 0 1 1 0 222 238 0 + R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 + R 15 2 VAL A 2 39 ASN A 39 4.2809 0 1 1 1 -13 121 0 + """, + [(1, "A", 2, "A"), (2, "A", 39, "A")] + ), # two sets of contacts different chains - ((""" + (""" ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model ============================================================================================ R 1 1 LYS A 1 2 VAL B 2 3.8094 1 1 1 1 11 369 0 R 6 1 LYS A 1 40 THR B 40 5.4657 1 1 1 1 222 238 0 - R 13 2 VAL C 2 37 ASN D 37 7.9443 0 1 0 0 -75 75 0 - R 15 2 VAL C 2 39 ASN D 39 4.2809 1 1 1 0 -13 121 0 - """), + R 13 2 VAL C 2 37 ASN D 37 7.9443 0 1 0 1 -75 75 0 + R 15 2 VAL C 2 39 ASN D 39 4.2809 0 1 1 1 -13 121 0 + """, [(1, "A", 2, "B"), (1, "A", 40, "B"), (2, "C", 37, "D"), (2, "C", 39, "D")] ))) def test_go_map(tmp_path, lines, contacts): From f01261b65031e0e1e4c4144436dc71a27ee19997 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 16:29:27 +0200 Subject: [PATCH 42/95] remove debug --- vermouth/rcsu/contact_map.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index f4a9fb36..f0e303f5 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -36,8 +36,6 @@ def read_go_map(file_path): lines = _file.readlines() contacts = [] - OV=0 - rCSU=0 for line in lines: tokens = line.strip().split() if len(tokens) == 0: @@ -49,14 +47,11 @@ def read_go_map(file_path): if tokens[11] == "1": # this is a OV contact we take it contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) - OV+=1 if tokens[11] == "0" and tokens[14] == "1": # this is a rCSU contact we take it contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) - rCSU+=1 if len(contacts) == 0: raise IOError("You contact map is empty. Are you sure it has the right formatting?") - print(len(contacts), OV, rCSU) return contacts From 293b73e1c30700baee9aa43ddd730f692a1a43e9 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Tue, 17 Oct 2023 16:34:39 +0200 Subject: [PATCH 43/95] add test for symmetric contact --- vermouth/tests/rcsu/test_go_structure_bias.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 4529231a..3cfefb60 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -43,6 +43,12 @@ def test_compute_go_interaction(test_molecule): 2.0, 0, [("mol_0_1", "mol_0_4", 1.5)]), + # add symmetric contact good + ([(1, 'A', 4, 'A'), (4, 'A', 1, 'A')], + 0.3, + 2.0, + 0, + [("mol_0_1", "mol_0_4", 1.5)]), # single contact bad -> cshort ([(1, 'A', 3, 'A')], 1.5, From c87d24505f4a8559f7db5b19c409544dece1219f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Thu, 19 Oct 2023 13:01:35 +0200 Subject: [PATCH 44/95] VirtualSideCreator to VirtualSiteCreator --- bin/martinize2 | 2 +- vermouth/rcsu/go_pipeline.py | 4 ++-- vermouth/rcsu/go_vs_includes.py | 2 +- vermouth/tests/rcsu/test_go_structure_bias.py | 4 ++-- vermouth/tests/test_water_bias.py | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index b7979fa2..d6e521b3 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -1029,7 +1029,7 @@ def entry(): # if the go model hasn't been used we need to create virtual # sites for the biasing if not args.go: - vermouth.rcsu.go_vs_includes.VirtualSideCreator().run_system(system) + vermouth.rcsu.go_vs_includes.VirtualSiteCreator().run_system(system) itp_paths = ["virtual_sites_atomtypes.itp", "virtual_sites_nonbond_params.itp"] # now we add a bias by defining specific virtual-site water interactions vermouth.processors.ComputeWaterBias(args.water_bias, diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index f30bba10..557e542c 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -17,7 +17,7 @@ import inspect import vermouth from ..processors.processor import Processor -from .go_vs_includes import VirtualSideCreator +from .go_vs_includes import VirtualSiteCreator from .go_structure_bias import ComputeStructuralGoBias from ..processors import SetMoleculeMeta @@ -52,5 +52,5 @@ def run_system(self, system, **kwargs): return system GoPipeline = GoProcessorPipline([SetMoleculeMeta, - VirtualSideCreator, + VirtualSiteCreator, ComputeStructuralGoBias]) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 4a3400cb..92bb6528 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -24,7 +24,7 @@ LOGGER = StyleAdapter(get_logger(__name__)) -class VirtualSideCreator(Processor): +class VirtualSiteCreator(Processor): """ Create virtual-sites for the Martini Go model implementation. This processor also updates the gmx diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 3cfefb60..260779ec 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -5,7 +5,7 @@ import numpy as np import networkx as nx import vermouth -from vermouth.rcsu.go_vs_includes import VirtualSideCreator +from vermouth.rcsu.go_vs_includes import VirtualSiteCreator from vermouth.tests.test_water_bias import create_sys_all_attrs from vermouth.tests.test_apply_rubber_band import test_molecule from vermouth.rcsu.go_structure_bias import ComputeStructuralGoBias @@ -124,7 +124,7 @@ def test_contact_selector(test_molecule, "atype": atypes}) # generate the virtual sites - VirtualSideCreator().run_system(system) + VirtualSiteCreator().run_system(system) # initialize the Go processor go_processor = ComputeStructuralGoBias(contact_map=cmap, cutoff_short=cshort, diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index 1d6a7428..8ca6c227 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -18,7 +18,7 @@ import pytest import networkx as nx import vermouth -from vermouth.rcsu.go_vs_includes import VirtualSideCreator +from vermouth.rcsu.go_vs_includes import VirtualSiteCreator from vermouth.system import System from vermouth.forcefield import ForceField from vermouth.processors.water_bias import ComputeWaterBias @@ -143,7 +143,7 @@ def test_assign_residue_water_bias(test_molecule, "atype": atypes}) # generate the virtual sites - VirtualSideCreator().run_system(system) + VirtualSiteCreator().run_system(system) processor = ComputeWaterBias(water_bias=water_bias, auto_bias=True, From 662ecfa638426fee85aaaf6b224eeebb8bfb638c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Thu, 19 Oct 2023 13:20:14 +0200 Subject: [PATCH 45/95] Moved create_sys_all_attrs to helperfunctions --- vermouth/tests/helper_functions.py | 73 ++++++++++++++++++++++++- vermouth/tests/test_water_bias.py | 85 +++--------------------------- 2 files changed, 79 insertions(+), 79 deletions(-) diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index d199bc3c..9af47620 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -17,8 +17,11 @@ """ import operator import os +import networkx as nx import networkx.algorithms.isomorphism as iso - +import vermouth +from vermouth.system import System +from vermouth.forcefield import ForceField def make_into_set(iter_of_dict): """ @@ -78,4 +81,70 @@ def find_in_path(names=('martinize2', 'martinize2.py')): for name in names: fullpath = os.path.join(folder, name) if os.path.isfile(fullpath): - return fullpath \ No newline at end of file + return fullpath + +def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): + """ + Generate a test system from a molecule + with all attributes set and blocks in + force-field. + + Parameters + ---------- + molecule: :class:vermouth.Molecule + moltype: str + sets meta['moltype'] + secstruc: dict[int, str] + secondary structure attributes + as resid str pairs + defaults: dict + dict of attribute default value + attrs: dict + dict of attribute name and dict + of node value pairs + + Returns + ------- + :class:vermouth.System + """ + # set mol meta + molecule.meta['moltype'] = moltype + # assign default node attributes + for attr, value in defaults.items(): + nx.set_node_attributes(molecule, value, attr) + + # assign node attributes + for attr, values in attrs.items(): + nx.set_node_attributes(molecule, values, attr) + + # assign resids + resids = nx.get_node_attributes(molecule, "resid") + nx.set_node_attributes(molecule, resids, "_old_resid") + + # make the proper force-field + ff = ForceField("test") + ff.variables['water_type'] = "W" + ff.variables['regular'] = 0.47 + ff.variables['small'] = 0.41 + ff.variables['tiny'] = 0.38 + + res_graph = vermouth.graph_utils.make_residue_graph(molecule) + for node in res_graph.nodes: + mol_nodes = res_graph.nodes[node]['graph'].nodes + block = vermouth.molecule.Block() + resname = res_graph.nodes[node]['resname'] + resid = res_graph.nodes[node]['resid'] + # assign secondary structure + for mol_node in mol_nodes: + molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid] + block.add_node(molecule.nodes[mol_node]['atomname'], + atype=molecule.nodes[mol_node]['atype']) + + ff.blocks[resname] = block + + + # create the system + molecule._force_field = ff + system = System() + system.molecules.append(molecule) + return system diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index 8ca6c227..1810457f 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -16,79 +16,10 @@ Test for the water bias processor. """ import pytest -import networkx as nx -import vermouth from vermouth.rcsu.go_vs_includes import VirtualSiteCreator -from vermouth.system import System -from vermouth.forcefield import ForceField from vermouth.processors.water_bias import ComputeWaterBias from vermouth.tests.test_apply_rubber_band import test_molecule - -def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): - """ - Generate a test system from a molecule - with all attributes set and blocks in - force-field. - - Parameters - ---------- - molecule: :class:vermouth.Molecule - moltype: str - sets meta['moltype'] - secstruc: dict[int, str] - secondary structure attributes - as resid str pairs - defauts: dict - dict of attribute default value - attrs: dict - dict of attribute name and dict - of node value pairs - - Returns - ------- - :class:vermouth.System - """ - # set mol meta - molecule.meta['moltype'] = moltype - # assign default node attributes - for attr, value in defaults.items(): - nx.set_node_attributes(molecule, value, attr) - - # assign node attributes - for attr, values in attrs.items(): - nx.set_node_attributes(molecule, values, attr) - - # assign resids - resids = nx.get_node_attributes(molecule, "resid") - nx.set_node_attributes(molecule, resids, "_old_resid") - - # make the proper force-field - ff = ForceField("test") - ff.variables['water_type'] = "W" - ff.variables['regular'] = 0.47 - ff.variables['small'] = 0.41 - ff.variables['tiny'] = 0.38 - - res_graph = vermouth.graph_utils.make_residue_graph(molecule) - for node in res_graph.nodes: - mol_nodes = res_graph.nodes[node]['graph'].nodes - block = vermouth.molecule.Block() - resname = res_graph.nodes[node]['resname'] - resid = res_graph.nodes[node]['resid'] - # assign secondary structure - for mol_node in mol_nodes: - molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid] - block.add_node(molecule.nodes[mol_node]['atomname'], - atype=molecule.nodes[mol_node]['atype']) - - ff.blocks[resname] = block - - - # create the system - molecule._force_field = ff - system = System() - system.molecules.append(molecule) - return system +from vermouth.tests.helper_functions import create_sys_all_attrs @pytest.mark.parametrize('secstruc, water_bias, idr_regions, expected', (( @@ -125,28 +56,28 @@ def test_assign_residue_water_bias(test_molecule, # bead sizes sizes = {0: 0.47, 3: 0.41, 5: 0.38, 6: 0.47} # the molecule atomtypes - atypes = {0: "P1", 1: "SN4a", 2: "SN4a", + atypes = {0: "P1", 1: "SN4a", 2: "SN4a", 3: "SP1", 4: "C1", 5: "TP1", 6: "P1", 7: "SN3a", 8: "SP4"} # the molecule resnames - resnames = {0: "A", 1: "A", 2: "A", + resnames = {0: "A", 1: "A", 2: "A", 3: "B", 4: "B", 5: "C", 6: "D", 7: "D", 8: "D"} - system = create_sys_all_attrs(test_molecule, - moltype="molecule_0", + system = create_sys_all_attrs(test_molecule, + moltype="molecule_0", secstruc=secstruc, - defaults={"chain": "A"}, + defaults={"chain": "A"}, attrs={"resname": resnames, "atype": atypes}) # generate the virtual sites VirtualSiteCreator().run_system(system) - processor = ComputeWaterBias(water_bias=water_bias, - auto_bias=True, + processor = ComputeWaterBias(water_bias=water_bias, + auto_bias=True, idr_regions=idr_regions) processor.run_system(system) for nb_params in system.gmx_topology_params['nonbond_params']: From 56c87bb654bb484a28e52cb9be02dab0f3441bec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Thu, 19 Oct 2023 13:43:51 +0200 Subject: [PATCH 46/95] move test_molecule to helper_functions --- vermouth/tests/helper_functions.py | 55 ++++++++++++++++++++++++ vermouth/tests/test_apply_rubber_band.py | 53 +---------------------- vermouth/tests/test_water_bias.py | 3 +- 3 files changed, 57 insertions(+), 54 deletions(-) diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 9af47620..061b0372 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -17,6 +17,8 @@ """ import operator import os +import pytest +import numpy as np import networkx as nx import networkx.algorithms.isomorphism as iso import vermouth @@ -148,3 +150,56 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): system = System() system.molecules.append(molecule) return system + +@pytest.fixture +def test_molecule(scope='function'): + """ + Molecule with the following connectivity and atom-naming: + + SC2: 2 8 + | | + SC1: 1 4 7 + | | | + BB: 0 - 3 - 5 - 6 + ------------- + resid: 1 2 3 4 column wise + """ + + force_field = vermouth.forcefield.ForceField("test") + molecule = vermouth.molecule.Molecule(force_field=force_field) + molecule.meta['test'] = True + # The node keys should not be in a sorted order as it would mask any issue + # due to the keys being accidentally sorted. + molecule.add_node(2, atomname='SC2', + position=np.array([0., 1.0, 0.0]), resid=1) + molecule.add_node(0, atomname='BB', + position=np.array([0., 0., 0.]), resid=1) + molecule.add_node(1, atomname='SC1', + position=np.array([0., 0.5, 0.0]), resid=1) + + molecule.add_node(3, atomname='BB', position=np.array( + [0.5, 0.0, 0.0]), resid=2) + molecule.add_node(4, atomname='SC1', position=np.array( + [0.5, 0.5, 0.0]), resid=2) + + molecule.add_node(5, atomname='BB', position=np.array( + [1.0, 0.0, 0.0]), resid=3) + + molecule.add_node(6, atomname='BB', position=np.array( + [1.5, 0.0, 0.0]), resid=4) + molecule.add_node(7, atomname='SC1', position=np.array( + [1.5, 0.5, 0.0]), resid=4) + molecule.add_node(8, atomname='SC2', position=np.array( + [1.5, 1.0, 0.0]), resid=4) + + molecule.add_edge(0, 1) + molecule.add_edge(0, 2) + molecule.add_edge(0, 3) + molecule.add_edge(3, 4) + molecule.add_edge(3, 5) + molecule.add_edge(5, 6) + molecule.add_edge(6, 7) + molecule.add_edge(7, 8) + + return molecule + diff --git a/vermouth/tests/test_apply_rubber_band.py b/vermouth/tests/test_apply_rubber_band.py index b7fa5cad..f752727a 100644 --- a/vermouth/tests/test_apply_rubber_band.py +++ b/vermouth/tests/test_apply_rubber_band.py @@ -26,6 +26,7 @@ make_same_region_criterion, are_connected, build_connectivity_matrix) +from vermouth.tests.helper_functions import test_molecule # pylint: disable=redefined-outer-name @@ -260,58 +261,6 @@ def test_make_same_region_criterion(regions, left, right, nodes, edges, chain, r same_region = make_same_region_criterion(regions) assert same_region(graph=graph, left=left, right=right) == outcome -@pytest.fixture -def test_molecule(scope='function'): - """ - Molecule with the following connectivity and atom-naming: - - SC2: 2 8 - | | - SC1: 1 4 7 - | | | - BB: 0 - 3 - 5 - 6 - ------------- - resid: 1 2 3 4 column wise - """ - - force_field = vermouth.forcefield.ForceField("test") - molecule = vermouth.molecule.Molecule(force_field=force_field) - molecule.meta['test'] = True - # The node keys should not be in a sorted order as it would mask any issue - # due to the keys being accidentally sorted. - molecule.add_node(2, atomname='SC2', - position=np.array([0., 1.0, 0.0]), resid=1) - molecule.add_node(0, atomname='BB', - position=np.array([0., 0., 0.]), resid=1) - molecule.add_node(1, atomname='SC1', - position=np.array([0., 0.5, 0.0]), resid=1) - - molecule.add_node(3, atomname='BB', position=np.array( - [0.5, 0.0, 0.0]), resid=2) - molecule.add_node(4, atomname='SC1', position=np.array( - [0.5, 0.5, 0.0]), resid=2) - - molecule.add_node(5, atomname='BB', position=np.array( - [1.0, 0.0, 0.0]), resid=3) - - molecule.add_node(6, atomname='BB', position=np.array( - [1.5, 0.0, 0.0]), resid=4) - molecule.add_node(7, atomname='SC1', position=np.array( - [1.5, 0.5, 0.0]), resid=4) - molecule.add_node(8, atomname='SC2', position=np.array( - [1.5, 1.0, 0.0]), resid=4) - - molecule.add_edge(0, 1) - molecule.add_edge(0, 2) - molecule.add_edge(0, 3) - molecule.add_edge(3, 4) - molecule.add_edge(3, 5) - molecule.add_edge(5, 6) - molecule.add_edge(6, 7) - molecule.add_edge(7, 8) - - return molecule - @pytest.mark.parametrize('chain_attribute, atom_names, res_min_dist, outcome', (({0: 'A', 1: 'A', 2: 'A', diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index 1810457f..a83df021 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -18,8 +18,7 @@ import pytest from vermouth.rcsu.go_vs_includes import VirtualSiteCreator from vermouth.processors.water_bias import ComputeWaterBias -from vermouth.tests.test_apply_rubber_band import test_molecule -from vermouth.tests.helper_functions import create_sys_all_attrs +from vermouth.tests.helper_functions import create_sys_all_attrs, test_molecule @pytest.mark.parametrize('secstruc, water_bias, idr_regions, expected', (( From 0056f7fec33a6abbcda9743b3f71fe77a9be15a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Thu, 19 Oct 2023 13:56:12 +0200 Subject: [PATCH 47/95] More fixes --- vermouth/rcsu/go_pipeline.py | 2 -- vermouth/rcsu/go_structure_bias.py | 2 +- vermouth/tests/gmx/test_topology.py | 6 +++--- vermouth/tests/rcsu/test_go_utils.py | 2 +- 4 files changed, 5 insertions(+), 7 deletions(-) diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 557e542c..f31eb716 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -38,8 +38,6 @@ def prepare_run(self, system, moltype): # with the proper Go-model for multimers vermouth.MergeAllMolecules().run_system(system) molecule = system.molecules[0] -# res_graph = vermouth.graph_utils.make_residue_graph(molecule) -# molecule.res_graph = res_graph molecule.meta['moltype'] = moltype def run_system(self, system, **kwargs): diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index de95eeb4..07f15d42 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -94,7 +94,7 @@ def __init__(self, self.res_graph = None self.system = None self.__chain_id_to_resnode = {} - self.magic_number = 1.12246204830 + self.magic_number = 2**(1/6) # do not overwrite when subclassing def _chain_id_to_resnode(self, chain, resid): diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index f15c8575..4009d80b 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -87,7 +87,7 @@ def test_atomtypes(tmp_path, dummy_molecule, atomtypes, expected, C6C12): DeferredFileWriter().write() with open(str(outpath)) as infile: - for line, ref_line in zip(infile.readlines(), expected): + for line, ref_line in zip(infile, expected): assert line == ref_line @@ -147,7 +147,7 @@ def test_nonbond_params(tmp_path, nbparams, expected, C6C12): DeferredFileWriter().write() with open(str(outpath)) as infile: - for line, ref_line in zip(infile.readlines(), expected): + for line, ref_line in zip(infile, expected): assert line == ref_line def test_toplevel_topology(tmp_path, dummy_molecule): @@ -199,7 +199,7 @@ def test_toplevel_topology(tmp_path, dummy_molecule): """ ref_lines = textwrap.dedent(reference).splitlines() with open(str(outpath)) as infile: - for line, ref_line in zip(infile.readlines(), ref_lines): + for line, ref_line in zip(infile, ref_lines): print('l', line.strip()) print('lr', ref_line.strip()) assert line.strip() == ref_line diff --git a/vermouth/tests/rcsu/test_go_utils.py b/vermouth/tests/rcsu/test_go_utils.py index 00eb887e..7d13bace 100644 --- a/vermouth/tests/rcsu/test_go_utils.py +++ b/vermouth/tests/rcsu/test_go_utils.py @@ -43,7 +43,7 @@ def test_get_bead_size(atype, size): # two regions false ([(101, 120), (180, 210)], 15, False), )) -def test_get_bead_size(regions, resid, result): +def test_in_region(regions, resid, result): assert result == _in_resid_region(resid, regions) From 7a85e44fc905a8066f0f111b4ce157dc96eb3109 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Fri, 20 Oct 2023 16:00:17 +0200 Subject: [PATCH 48/95] Keep only symmetrical go contacts. --- vermouth/rcsu/go_structure_bias.py | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 07f15d42..da3c972e 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -151,6 +151,8 @@ def contact_selector(self, molecule): """ # distance_matrix of elegible pairs as tuple(node, node, dist) contact_matrix = [] + # distance_matrix of elegible symmetrical pairs as tuple(node, node, dist) + symmetrical_matrix = [] # find all pairs of residues that are within bonded distance of # self.res_dist connected_pairs = dict(nx.all_pairs_shortest_path_length(self.res_graph, @@ -184,15 +186,21 @@ def contact_selector(self, molecule): resid=resIDB, chain=chainB, prefix=self.moltype)) + # Check if symmetric contact has already been processed before + # and if so, we append the contact to the final symmetric contact matrix + # and add the exclusions. Else, we add to the full valid contact_matrix + # and continue searching. if (atype_b, atype_a, dist) in contact_matrix: - continue - # generate backbone backbone exclusions - # perhaps one day can be it's own function - excl = Interaction(atoms=(bb_node_A, bb_node_B), parameters=[], meta={"group": "Go model exclusion"}) - molecule.interactions['exclusions'].append(excl) - - contact_matrix.append((atype_a, atype_b, dist)) - return contact_matrix + # generate backbone backbone exclusions + # perhaps one day can be it's own function + excl = Interaction(atoms=(bb_node_A, bb_node_B), + parameters=[], meta={"group": "Go model exclusion"}) + molecule.interactions['exclusions'].append(excl) + symmetrical_matrix.append((atype_a, atype_b, dist)) + else: + contact_matrix.append((atype_a, atype_b, dist)) + + return symmetrical_matrix def compute_go_interaction(self, contacts): """ From 7adc157545fb98bda06d7143a975271712a2d1e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=ADs=20Borges=20Ara=C3=BAjo?= <42938615+Lp0lp@users.noreply.github.com> Date: Fri, 20 Oct 2023 16:34:48 +0200 Subject: [PATCH 49/95] Fix go_struct_bias tests & add some more. --- vermouth/tests/rcsu/test_go_structure_bias.py | 46 ++++++++++++++----- 1 file changed, 35 insertions(+), 11 deletions(-) diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 260779ec..973c97c9 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -37,46 +37,70 @@ def test_compute_go_interaction(test_molecule): assert nb_params.epsilon == 2.1 @pytest.mark.parametrize('cmap, cshort, clong, rdist, expected',( - # single contact good + # single assymetric contact bad ([(1, 'A', 4, 'A')], 0.3, 2.0, 0, - [("mol_0_1", "mol_0_4", 1.5)]), - # add symmetric contact good + []), + # single symmetric contact good ([(1, 'A', 4, 'A'), (4, 'A', 1, 'A')], 0.3, 2.0, 0, - [("mol_0_1", "mol_0_4", 1.5)]), - # single contact bad -> cshort + [("mol_0_4", "mol_0_1", 1.5)]), + # single symmetric contact bad -> cshort + ([(3, 'A', 1, 'A'),(1, 'A', 3, 'A')], + 1.5, + 2.0, + 0, + []), + # single symmetric contact bad -> clong + ([(4, 'A', 1, 'A'), (1, 'A', 4, 'A')], + 0.5, + 0.8, + 0, + []), + # single symmetric contact bad -> rdist + ([(4, 'A', 1, 'A'), (1, 'A', 4, 'A')], + 0.3, + 2.0, + 5, + []), + # single contact bad -> cshort & assym ([(1, 'A', 3, 'A')], 1.5, 2.0, 0, []), - # single contact bad -> clong + # single contact bad -> clong & assym ([(1, 'A', 4, 'A')], 0.5, 0.8, 0, []), - # single contact bad -> rdist + # single contact bad -> rdist & assym ([(1, 'A', 4, 'A')], 0.3, 2.0, 5, []), - # two contacts good - ([(1, 'A', 3, 'A'), (1, 'A', 4, 'A')], + # two symmetric contacts good + ([(3, 'A', 1, 'A'), (4, 'A', 1, 'A'),(1, 'A', 3, 'A'), (1, 'A', 4, 'A')], 0.3, 2.0, 1, [("mol_0_1", "mol_0_3", 1.0), ("mol_0_1", "mol_0_4", 1.5), ]), - # one good one bad rdist - ([(1, 'A', 4, 'A'), (1, 'A', 2, 'A')], + # one symmetric contacts good, one assymetric contact bad + ([(3, 'A', 1, 'A'), (4, 'A', 1, 'A'),(1, 'A', 3, 'A')], + 0.3, + 2.0, + 1, + [("mol_0_1", "mol_0_3", 1.0)]), + # one good one bad rdist + ([(4, 'A', 1, 'A'), (2, 'A', 1, 'A'), (1, 'A', 4, 'A'), (1, 'A', 2, 'A')], 0.3, 2.0, 2, From 6e361d25afdb727a08d75952ce47518173f50547 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 23 Oct 2023 10:46:52 +0200 Subject: [PATCH 50/95] use _old_resid in water bias for identifying ID regions --- vermouth/processors/water_bias.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index ff8e68d8..6caf889c 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -82,10 +82,11 @@ def assign_residue_water_bias(self, molecule, res_graph): """ for res_node in res_graph.nodes: resid = res_graph.nodes[res_node]['resid'] + _old_resid = res_graph.nodes[res_node]['_old_resid'] chain = res_graph.nodes[res_node]['chain'] resname = res_graph.nodes[res_node]['resname'] - if _in_resid_region(resid, self.idr_regions): + if _in_resid_region(_old_resid, self.idr_regions): eps = self.water_bias.get('idr', 0.0) elif self.auto_bias: sec_struc = res_graph.nodes[res_node]['cgsecstruct'] From 7f001958ec344df2a4384e8a44662b306744eebb Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 23 Oct 2023 10:47:17 +0200 Subject: [PATCH 51/95] add nx to go_pipeline --- vermouth/rcsu/go_pipeline.py | 1 + 1 file changed, 1 insertion(+) diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index f30bba10..82c892f0 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -14,6 +14,7 @@ """ Wrapper of Processors defining the GoPipline. """ +import networkx as nx import inspect import vermouth from ..processors.processor import Processor From 82df1183bc06e86f8c2c75ad925124a193af6969 Mon Sep 17 00:00:00 2001 From: Fabian Grunewald Date: Mon, 23 Oct 2023 10:48:09 +0200 Subject: [PATCH 52/95] use _old_resid in structure bias for finding the atomtype --- vermouth/rcsu/go_structure_bias.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index de95eeb4..db8d8b9b 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -177,11 +177,11 @@ def contact_selector(self, molecule): # find the go virtual-sites for this residue # probably can be done smarter but mehhhh atype_a = next(get_go_type_from_attributes(self.res_graph.nodes[resA]['graph'], - resid=resIDA, + _old_resid=resIDA, chain=chainA, prefix=self.moltype)) atype_b = next(get_go_type_from_attributes(self.res_graph.nodes[resB]['graph'], - resid=resIDB, + _old_resid=resIDB, chain=chainB, prefix=self.moltype)) if (atype_b, atype_a, dist) in contact_matrix: From 28359a083cdf206cee600fe2b7df32400f8cd89c Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 27 Oct 2023 14:50:22 +0200 Subject: [PATCH 53/95] test self interaction nb params --- vermouth/tests/gmx/test_topology.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index 4009d80b..6400eb2e 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -108,6 +108,13 @@ def test_atomtypes(tmp_path, dummy_molecule, atomtypes, expected, C6C12): ["[ nonbond_params ]\n", "A B 1 0.43000000 2.30000000 \n", "A C 1 0.47000000 2.50000000 \n"], False), + # self interaction + ( + [{"atoms": ("A",), "sigma": 0.43, "epsilon": 2.3, "meta": {}}, + {"atoms": ("A", "C"), "sigma": 0.47, "epsilon": 2.5, "meta": {}}], + ["[ nonbond_params ]\n", + "A A 1 0.43000000 2.30000000 \n", + "A C 1 0.47000000 2.50000000 \n"], False), ( [{"atoms": ("A", "B"), "sigma": 0.43, "epsilon": 2.3, "meta": {"comment": ["comment"]}}], ["[ nonbond_params ]\n", From 3182111d62394ba254967defaa0d5530f34aebdb Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Wed, 1 Nov 2023 13:26:00 +0100 Subject: [PATCH 54/95] add tests for high level errors in water generatoin --- vermouth/tests/test_water_bias.py | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index a83df021..6a93e54e 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -16,6 +16,7 @@ Test for the water bias processor. """ import pytest +import vermouth from vermouth.rcsu.go_vs_includes import VirtualSiteCreator from vermouth.processors.water_bias import ComputeWaterBias from vermouth.tests.helper_functions import create_sys_all_attrs, test_molecule @@ -89,3 +90,32 @@ def test_assign_residue_water_bias(test_molecule, water_sig = sizes[bb_node] assert water_eps == nb_params.epsilon assert water_sig == nb_params.sigma + +def test_no_moltype_error(test_molecule): + """ + Test that various high level IOErrors are + properly raised. + """ + # set up processor + processor = ComputeWaterBias(water_bias={"C": 3.1}, + auto_bias=True, + idr_regions=None) + # no moltype set + system = vermouth.System() + system.molecules.append(test_molecule) + with pytest.raises(ValueError): + processor.run_system(system) + +def test_no_moltype_error(test_molecule): + """ + Test that various high level IOErrors are + properly raised. + """ + # set up processor + processor = ComputeWaterBias(water_bias={"C": 3.1}, + auto_bias=True, + idr_regions=None) + test_molecule.meta['moltype'] = "random" + # no system + with pytest.raises(IOError): + processor.run_molecule(test_molecule) From 24662f897145bc0fc557a3b1887a7a433f3f17e2 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Wed, 1 Nov 2023 13:56:57 +0100 Subject: [PATCH 55/95] remove unneccesary post_section_lines feature --- vermouth/rcsu/go_vs_includes.py | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 92bb6528..4ff8df73 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -45,8 +45,7 @@ class VirtualSiteCreator(Processor): Assign molecule type names to the molecules in a system. :func:`add_virtual_sites` """ - def __init__(self, sections=()): - self.sections = sections + def __init__(self): self.system = None def run_molecule(self, molecule): @@ -59,13 +58,6 @@ def run_molecule(self, molecule): self.add_virtual_sites(molecule, prefix=moltype) - includes = molecule.meta.get('post_section_lines', {}) - for section in self.sections: - section_includes = includes.get(section, []) - section_includes.append('#include "{moltype}_{section}_VirtGoSites.itp"' - .format(moltype=moltype, section=section)) - includes[section] = section_includes - molecule.meta['post_section_lines'] = includes return molecule def run_system(self, system): From 2f48e61c1ede7f74085d51b5708d1cf84293ebff Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Wed, 1 Nov 2023 14:20:44 +0100 Subject: [PATCH 56/95] radd calls to super for run_system --- vermouth/processors/water_bias.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 6caf889c..be985bd1 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -145,8 +145,7 @@ def run_system(self, system): ---------- system: :class:`vermouth.System` """ - if self.idr_regions or self.auto_bias: - self.system = system - for molecule in system.molecules: - self.run_molecule(molecule) - return system + if not (self.idr_regions or self.auto_bias): + return system + self.system = system + super().run_system(system) From 2b5853cedc019864ddfeb7061765961ee9e65025 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Wed, 1 Nov 2023 14:20:55 +0100 Subject: [PATCH 57/95] radd calls to super for run_system --- vermouth/rcsu/go_structure_bias.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 294d8b6d..1c72517b 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -250,5 +250,4 @@ def run_system(self, system): The system to process. Is modified in-place. """ self.system = system - for molecule in system.molecules: - self.run_molecule(molecule) + super().run_system(system) From 01483d47124a56a521b349941a747060f3028d0a Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Fri, 3 Nov 2023 09:58:11 +0100 Subject: [PATCH 58/95] Apply suggestions from code review Co-authored-by: Peter C Kroon --- bin/martinize2 | 2 +- vermouth/gmx/topology.py | 2 +- vermouth/processors/water_bias.py | 8 ++++---- vermouth/rcsu/go_vs_includes.py | 3 +-- 4 files changed, 7 insertions(+), 8 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index d6e521b3..0c8cfd6b 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -608,7 +608,7 @@ def entry(): nargs='+', help=("Intrinsically disordered regions specified by resid." "These parts are biased differently when applying a water bias." - "format: :, :..." + "format: : :..." ), ) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index e4d98750..146f2dd3 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -25,7 +25,7 @@ def _group_by_conditionals(interactions): ) return interaction_grouped -def convert_sigma_epsilon(sigma, epsilon): +def sigma_epsilon_to_C6_C12(sigma, epsilon): """ Convert the LJ potential from sigma epsilon form to C6 C12 form. diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index be985bd1..90e0a5cb 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -22,8 +22,8 @@ class ComputeWaterBias(Processor): Processor which computes the water bias for the Martini Go and Martini IDP model. - The water bias streght is defined per secondary - structure element in `water_bias` and assinged if + The water bias strength is defined per secondary + structure element in `water_bias` and assigned if `auto_bias` is set to True. Using the `idr_regions` argument the water_bias can be changed for intrinsically disordered regions (IDRs). The IDR @@ -57,7 +57,7 @@ def __init__(self, regions defining the IDRs prefix: str prefix of the Go virtual-site atomtypes - system: :class:vermouth.System + system: :class:`vermouth.System` the system of the molecules is used for storing the nonbonded parameters """ @@ -71,7 +71,7 @@ def assign_residue_water_bias(self, molecule, res_graph): Assign the residue water bias for all residues with a secondary structure element or that are defined by the region selector. Region selectors - superceed the auto assignement. + supercede the auto assignment. Parameters ---------- diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 4ff8df73..21c6e7f6 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -63,8 +63,7 @@ def run_molecule(self, molecule): def run_system(self, system): self.system = system LOGGER.info("Adding Virtual Sites to backbone beads.", type="step") - for molecule in system.molecules: - self.run_molecule(molecule) + super().run_system(system) def add_virtual_sites(self, molecule, prefix, backbone='BB', atomname='CA', charge=0): """ From 23323a343fb5d3084012f88b6c72b09680cf8109 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 10:31:15 +0100 Subject: [PATCH 59/95] properly implement renaming of convert_sigma_to_epsilon --- vermouth/gmx/topology.py | 4 ++-- vermouth/tests/gmx/test_topology.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 146f2dd3..21e919f9 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -58,7 +58,7 @@ def write_atomtypes(system, itp_path, C6C12=False): mass = atomtype.molecule.nodes[atomtype.node]['mass'] if C6C12: - nb1, nb2 = convert_sigma_epsilon(atomtype.sigma, atomtype.epsilon) + nb1, nb2 = sigma_epsilon_to_C6_C12(atomtype.sigma, atomtype.epsilon) else: nb1, nb2 = atomtype.sigma, atomtype.epsilon @@ -96,7 +96,7 @@ def write_nonbond_params(system, itp_path, C6C12=False): a2 = nb_params.atoms[0] if C6C12: - nb1, nb2 = convert_sigma_epsilon(nb_params.sigma, nb_params.epsilon) + nb1, nb2 = sigma_epsilon_to_C6_C12(nb_params.sigma, nb_params.epsilon) else: nb1, nb2 = nb_params.sigma, nb_params.epsilon diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index 6400eb2e..516bb075 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -20,7 +20,7 @@ import pytest import vermouth from vermouth.file_writer import DeferredFileWriter -from vermouth.gmx.topology import (convert_sigma_epsilon, +from vermouth.gmx.topology import (sigma_epsilon_to_C6_C12, write_atomtypes, write_nonbond_params, write_gmx_topology, From e5357178a664bf683bfbd77c4a2b45ceadc88f85 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 10:45:57 +0100 Subject: [PATCH 60/95] add test for go utilitz error --- vermouth/rcsu/go_utils.py | 7 ++++--- vermouth/tests/rcsu/test_go_utils.py | 7 +++++++ 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index 83335169..464daf89 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -44,9 +44,10 @@ def get_go_type_from_attributes(molecule, prefix, **kwargs): attrs = molecule.nodes[node] if attributes_match(attrs, kwargs) and attrs['atype'].startswith(prefix): yield attrs['atype'] - resid = kwargs['resid'] - chain = kwargs['chain'] - raise IOError(f"Could not find GoVs with resid {resid} in chain {chain}.") + else: + resid = kwargs['resid'] + chain = kwargs['chain'] + raise ValueError(f"Could not find GoVs with resid {resid} in chain {chain}.") def _in_resid_region(resid, regions): """ diff --git a/vermouth/tests/rcsu/test_go_utils.py b/vermouth/tests/rcsu/test_go_utils.py index 7d13bace..bda0527e 100644 --- a/vermouth/tests/rcsu/test_go_utils.py +++ b/vermouth/tests/rcsu/test_go_utils.py @@ -54,3 +54,10 @@ def test_get_go_type_from_attributes(mol): mol.add_node(vs_node, atype="prefix_0", chain="A", resid=5) found_atype = next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) assert found_atype == "prefix_0" + +@hypothesis.settings(suppress_health_check=[hypothesis.HealthCheck.too_slow]) +@hypothesis.given(random_molecule()) +def test_error_get_go_type_from_attributes(mol): + vs_node = len(mol.nodes) + with pytest.raises(ValueError): + next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) From 54ba9d9a47fdcde8f5ae1a90502a8a9069c73cac Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 10:58:37 +0100 Subject: [PATCH 61/95] more tests --- vermouth/tests/test_vs_generation.py | 53 ++++++++++++++++++++++++++++ vermouth/tests/test_water_bias.py | 2 +- 2 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 vermouth/tests/test_vs_generation.py diff --git a/vermouth/tests/test_vs_generation.py b/vermouth/tests/test_vs_generation.py new file mode 100644 index 00000000..793fcc73 --- /dev/null +++ b/vermouth/tests/test_vs_generation.py @@ -0,0 +1,53 @@ +# Copyright 2022 University of Groningen +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Test for the virtual side creator. +""" +import pytest +import vermouth +from vermouth.rcsu.go_vs_includes import VirtualSiteCreator +from vermouth.tests.helper_functions import test_molecule + +def test_no_moltype_error(test_molecule): + """ + Test that various high level IOErrors are + properly raised. + """ + # set up processor + processor = VirtualSiteCreator() + # no moltype set + system = vermouth.System() + system.molecules.append(test_molecule) + with pytest.raises(ValueError): + processor.run_system(system) + +def test_no_system_error(test_molecule): + """ + Test that various high level IOErrors are + properly raised. + """ + # set up processor + processor = VirtualSiteCreator() + test_molecule.meta['moltype'] = "random" + # no system + with pytest.raises(IOError): + processor.run_molecule(test_molecule) + +def test_return_no_nodes(): + mol = vermouth.Molecule() + processor = VirtualSiteCreator() + mol.meta['moltype'] = "random" + system = vermouth.System() + system.molecules.append(mol) + assert processor.run_system(system) is None diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index 6a93e54e..c6097249 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -106,7 +106,7 @@ def test_no_moltype_error(test_molecule): with pytest.raises(ValueError): processor.run_system(system) -def test_no_moltype_error(test_molecule): +def test_no_system_error(test_molecule): """ Test that various high level IOErrors are properly raised. From f66d202b350446c23b5df5e6e814805c485d9af6 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 11:16:04 +0100 Subject: [PATCH 62/95] more tests water bias --- vermouth/tests/test_water_bias.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index c6097249..a5b3901f 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -29,6 +29,12 @@ [], {0: "H", 3: "H", 5: "H", 6: "H"} ), + # test skip unassigned node + ({1: None, 2: "H", 3: "H", 4: "H"}, + {"H": 2.1}, + [], + {5: "H", 6: "H"} + ), # only auto-bias two sec struct ({1: "H", 2: "H", 3: "C", 4: "C"}, {"H": 2.1, "C": 3.1}, @@ -119,3 +125,13 @@ def test_no_system_error(test_molecule): # no system with pytest.raises(IOError): processor.run_molecule(test_molecule) + +def test_clean_return(test_molecule): + # set up processor + processor = ComputeWaterBias(water_bias={"C": 3.1}, + auto_bias=None, + idr_regions=None) + test_molecule.meta['moltype'] = "random" + system = vermouth.System() + system.molecules.append(test_molecule) + assert processor.run_system(system) == system From 7d0727e8a540e82db13ba24b1cabc46b8a1946c0 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 11:26:11 +0100 Subject: [PATCH 63/95] fix docstring --- vermouth/gmx/topology.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 21e919f9..9d850ecb 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -119,12 +119,12 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), Parameters ---------- - system: :class:vermouth.System + system: vermouth.system.System top_path: pathlib.Path path for topology file itp_paths: list[pathlib.Path] list of paths for writing the topology parameters - like atomtypes. + like atomtypes. C6C12: bool write non-bonded interaction parameters using LJ C6C12 form From e3cf4ada8743d50f0dc7add6404f59b938e9d67a Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 11:27:39 +0100 Subject: [PATCH 64/95] loop over lines from buffer when reading contact map --- vermouth/rcsu/contact_map.py | 38 +++++++++++++++++------------------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index f0e303f5..ca593f26 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -33,25 +33,23 @@ def read_go_map(file_path): contact as chain id, res id, chain id, res id """ with open(file_path, "r", encoding='UTF-8') as _file: - lines = _file.readlines() - - contacts = [] - for line in lines: - tokens = line.strip().split() - if len(tokens) == 0: - continue - - if tokens[0] == "R" and len(tokens) == 18: - # this is a bad place to filter but follows - # the old script - if tokens[11] == "1": - # this is a OV contact we take it - contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) - if tokens[11] == "0" and tokens[14] == "1": - # this is a rCSU contact we take it - contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) - - if len(contacts) == 0: - raise IOError("You contact map is empty. Are you sure it has the right formatting?") + contacts = [] + for line in _file: + tokens = line.strip().split() + if len(tokens) == 0: + continue + + if tokens[0] == "R" and len(tokens) == 18: + # this is a bad place to filter but follows + # the old script + if tokens[11] == "1": + # this is a OV contact we take it + contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) + if tokens[11] == "0" and tokens[14] == "1": + # this is a rCSU contact we take it + contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) + + if len(contacts) == 0: + raise IOError("You contact map is empty. Are you sure it has the right formatting?") return contacts From a1c52baf6819a6edd8c64de000dbc8d28558841c Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 11:57:34 +0100 Subject: [PATCH 65/95] address some comments --- vermouth/rcsu/go_structure_bias.py | 12 ++++-------- vermouth/rcsu/go_utils.py | 2 +- vermouth/rcsu/go_vs_includes.py | 4 ++-- vermouth/tests/rcsu/test_go_utils.py | 2 +- 4 files changed, 8 insertions(+), 12 deletions(-) diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 1c72517b..67f786f5 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -62,9 +62,9 @@ def __init__(self, list of contacts defined as by the chain identifier and residue index cutoff_short: float - distances smaller than this are ignored + distances in nm smaller than this are ignored cutoff_long: float - distances larger than this are ignored + distances in nm larger than this are ignored go_eps: float epsilon value of the structural bias in kJ/mol @@ -94,7 +94,7 @@ def __init__(self, self.res_graph = None self.system = None self.__chain_id_to_resnode = {} - self.magic_number = 2**(1/6) + self.conversion_factor = 2**(1/6) # do not overwrite when subclassing def _chain_id_to_resnode(self, chain, resid): @@ -176,8 +176,6 @@ def contact_selector(self, molecule): # verify that the distance between BB-beads satisfies the # cut-off criteria if self.cutoff_long > dist > self.cutoff_short: - # find the go virtual-sites for this residue - # probably can be done smarter but mehhhh atype_a = next(get_go_type_from_attributes(self.res_graph.nodes[resA]['graph'], _old_resid=resIDA, chain=chainA, @@ -220,9 +218,7 @@ def compute_go_interaction(self, contacts): """ go_inters = {} for atype_a, atype_b, dist in contacts: - # compute the LJ sigma paramter for this contact - # 1.12246204830 is a magic number by Sebastian - sigma = dist / self.magic_number + sigma = dist / self.conversion_factor # find the go virtual-sites for this residue # probably can be done smarter but mehhhh contact_bias = NonbondParam(atoms=(atype_a, atype_b), diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index 464daf89..7a12095f 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -47,7 +47,7 @@ def get_go_type_from_attributes(molecule, prefix, **kwargs): else: resid = kwargs['resid'] chain = kwargs['chain'] - raise ValueError(f"Could not find GoVs with resid {resid} in chain {chain}.") + raise KeyError(f"Could not find GoVs with resid {resid} in chain {chain}.") def _in_resid_region(resid, regions): """ diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 21c6e7f6..2331242e 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -26,8 +26,8 @@ class VirtualSiteCreator(Processor): """ - Create virtual-sites for the Martini Go model implementation. - This processor also updates the gmx + Create virtual-sites for the Martini Go model implementation or + the specific water biasing options. See :mod:`vermouth.processors.go_vs_includes` for more details. diff --git a/vermouth/tests/rcsu/test_go_utils.py b/vermouth/tests/rcsu/test_go_utils.py index bda0527e..2d08b2c5 100644 --- a/vermouth/tests/rcsu/test_go_utils.py +++ b/vermouth/tests/rcsu/test_go_utils.py @@ -59,5 +59,5 @@ def test_get_go_type_from_attributes(mol): @hypothesis.given(random_molecule()) def test_error_get_go_type_from_attributes(mol): vs_node = len(mol.nodes) - with pytest.raises(ValueError): + with pytest.raises(KeyError): next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) From bd785f40e541794a4f64e964059c412fba561cfa Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Fri, 3 Nov 2023 14:20:50 +0100 Subject: [PATCH 66/95] fix docstring --- vermouth/processors/water_bias.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 90e0a5cb..a412845c 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -57,7 +57,7 @@ def __init__(self, regions defining the IDRs prefix: str prefix of the Go virtual-site atomtypes - system: :class:`vermouth.System` + system: vermouth.system.System the system of the molecules is used for storing the nonbonded parameters """ From cb223e5602aeb31bbfc9a8b5ec0de10068185f24 Mon Sep 17 00:00:00 2001 From: Borges Luis Date: Thu, 23 Nov 2023 17:04:08 +0100 Subject: [PATCH 67/95] Added go suport in tests. First GO integ test. --- .../tier-1/lysozyme_GO/README | 11 + .../tier-1/lysozyme_GO/aa.pdb | 1549 +++++++++++++++ .../tier-1/lysozyme_GO/map.map | 1275 +++++++++++++ .../tier-1/lysozyme_GO/martinize2/cg.pdb | 616 ++++++ .../tier-1/lysozyme_GO/martinize2/citation | 1 + .../tier-1/lysozyme_GO/martinize2/command | 9 + .../lysozyme_GO/martinize2/go_atomtypes.itp | 130 ++ .../lysozyme_GO/martinize2/go_nbparams.itp | 260 +++ .../lysozyme_GO/martinize2/molecule_0.itp | 1669 +++++++++++++++++ .../tier-1/lysozyme_GO/martinize2/topol.top | 12 + vermouth/tests/helper_functions.py | 25 + .../integration_tests/test_integration.py | 75 +- 12 files changed, 5610 insertions(+), 22 deletions(-) create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation create mode 100755 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README new file mode 100644 index 00000000..dc9a10d5 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README @@ -0,0 +1,11 @@ +### DETAILS: + +# Original PDB CODE: 3LZT +# Structure from X-ray crystallography experiment. +# Select atoms with occupancy higuer than 0.5 + +### TEST: + +# -ff martini 30 open beta +# -scfix and GO +# adding specific cys bridge as CONECT records diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb new file mode 100644 index 00000000..39371e9a --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/aa.pdb @@ -0,0 +1,1549 @@ +HEADER HYDROLASE(O-GLYCOSYL) 10-JAN-92 1HEL +TITLE STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING MUTATIONS WITHIN +TITLE 2 THE CORE OF CHICKEN EGG WHITE LYSOZYME +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: HEN EGG WHITE LYSOZYME; +COMPND 3 CHAIN: A; +COMPND 4 EC: 3.2.1.17; +COMPND 5 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; +SOURCE 3 ORGANISM_COMMON: CHICKEN; +SOURCE 4 ORGANISM_TAXID: 9031; +SOURCE 5 ORGAN: EGG +KEYWDS HYDROLASE(O-GLYCOSYL) +EXPDTA X-RAY DIFFRACTION +AUTHOR K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +REVDAT 3 16-NOV-11 1HEL 1 VERSN HETATM +REVDAT 2 24-FEB-09 1HEL 1 VERSN +REVDAT 1 31-OCT-93 1HEL 0 +JRNL AUTH K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +JRNL TITL STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING +JRNL TITL 2 MUTATIONS WITHIN THE CORE OF CHICKEN EGG WHITE LYSOZYME. +JRNL REF J.BIOL.CHEM. V. 267 10842 1992 +JRNL REFN ISSN 0021-9258 +JRNL PMID 1587860 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH B.A.MALCOLM,K.P.WILSON,B.W.MATTHEWS,J.F.KIRSCH,A.C.WILSON +REMARK 1 TITL ANCESTRAL LYSOZYMES RECONSTRUCTED, NEUTRALITY TESTED, AND +REMARK 1 TITL 2 THERMOSTABILITY LINKED TO HYDROCARBON PACKING +REMARK 1 REF NATURE V. 344 86 1990 +REMARK 1 REFN ISSN 0028-0836 +REMARK 2 +REMARK 2 RESOLUTION. 1.70 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : TNT +REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL +REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL +REMARK 3 COMPLETENESS FOR RANGE (%) : NULL +REMARK 3 NUMBER OF REFLECTIONS : NULL +REMARK 3 +REMARK 3 USING DATA ABOVE SIGMA CUTOFF. +REMARK 3 CROSS-VALIDATION METHOD : NULL +REMARK 3 FREE R VALUE TEST SET SELECTION : NULL +REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 +REMARK 3 R VALUE (WORKING SET) : NULL +REMARK 3 FREE R VALUE : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT : NULL +REMARK 3 +REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. +REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL +REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE (NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL +REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL +REMARK 3 +REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. +REMARK 3 PROTEIN ATOMS : 1001 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 185 +REMARK 3 +REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL +REMARK 3 +REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT +REMARK 3 BOND LENGTHS (A) : 0.019 ; NULL ; NULL +REMARK 3 BOND ANGLES (DEGREES) : 2.400 ; NULL ; NULL +REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL +REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL +REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL +REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL +REMARK 3 +REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL +REMARK 3 +REMARK 3 BULK SOLVENT MODELING. +REMARK 3 METHOD USED : NULL +REMARK 3 KSOL : NULL +REMARK 3 BSOL : NULL +REMARK 3 +REMARK 3 RESTRAINT LIBRARIES. +REMARK 3 STEREOCHEMISTRY : NULL +REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 1HEL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : NULL +REMARK 200 TEMPERATURE (KELVIN) : NULL +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : NULL +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : NULL +REMARK 200 RADIATION SOURCE : NULL +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : NULL +REMARK 200 DETECTOR MANUFACTURER : NULL +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL +REMARK 200 RESOLUTION RANGE HIGH (A) : NULL +REMARK 200 RESOLUTION RANGE LOW (A) : NULL +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: NULL +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 40.52 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X,-Y,Z+1/2 +REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 +REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 +REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 +REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 +REMARK 290 7555 Y,X,-Z +REMARK 290 8555 -Y,-X,-Z+1/2 +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.95000 +REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.42500 +REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.47500 +REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.42500 +REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.47500 +REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.95000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 375 +REMARK 375 SPECIAL POSITION +REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS +REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL +REMARK 375 POSITIONS. +REMARK 375 +REMARK 375 ATOM RES CSSEQI +REMARK 375 HOH A 318 LIES ON A SPECIAL POSITION. +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC +REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 +REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A +REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 +REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE +REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. +REMARK 500 +REMARK 500 DISTANCE CUTOFF: +REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS +REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE +REMARK 500 O HOH A 275 O HOH A 275 8555 0.35 +REMARK 500 O HOH A 203 O HOH A 203 7556 1.38 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: COVALENT BOND ANGLES +REMARK 500 +REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES +REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE +REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) +REMARK 500 +REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 +REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 +REMARK 500 +REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 +REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES +REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 8.7 DEGREES +REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES +REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 52 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES +REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES +REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES +REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES +REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: TORSION ANGLES +REMARK 500 +REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: +REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) +REMARK 500 +REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- +REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 +REMARK 500 +REMARK 500 M RES CSSEQI PSI PHI +REMARK 500 ARG A 68 19.50 -141.12 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 525 +REMARK 525 SOLVENT +REMARK 525 +REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT +REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST +REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT +REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE +REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; +REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE +REMARK 525 NUMBER; I=INSERTION CODE): +REMARK 525 +REMARK 525 M RES CSSEQI +REMARK 525 HOH A 188 DISTANCE = 6.89 ANGSTROMS +REMARK 525 HOH A 189 DISTANCE = 6.32 ANGSTROMS +REMARK 525 HOH A 190 DISTANCE = 5.68 ANGSTROMS +REMARK 525 HOH A 228 DISTANCE = 6.51 ANGSTROMS +REMARK 525 HOH A 230 DISTANCE = 5.30 ANGSTROMS +REMARK 525 HOH A 243 DISTANCE = 5.19 ANGSTROMS +REMARK 525 HOH A 249 DISTANCE = 6.99 ANGSTROMS +REMARK 525 HOH A 258 DISTANCE = 6.92 ANGSTROMS +REMARK 525 HOH A 268 DISTANCE = 8.36 ANGSTROMS +REMARK 525 HOH A 278 DISTANCE = 6.81 ANGSTROMS +REMARK 525 HOH A 304 DISTANCE = 7.48 ANGSTROMS +REMARK 525 HOH A 305 DISTANCE = 6.21 ANGSTROMS +REMARK 525 HOH A 308 DISTANCE = 19.71 ANGSTROMS +DBREF 1HEL A 1 129 UNP P00698 LYSC_CHICK 19 147 +SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS +SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY +SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN +SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP +SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN +SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE +SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER +SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY +SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY +SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU +FORMUL 2 HOH *185(H2 O) +HELIX 1 H1 GLY A 4 GLY A 16 1 13 +HELIX 2 H2 LEU A 25 PHE A 34 1 10 +HELIX 3 H3 PRO A 79 LEU A 84 5 6 +HELIX 4 H4 ILE A 88 SER A 100 1 13 +HELIX 5 H5 GLY A 104 TRP A 108 5 5 +HELIX 6 H6 VAL A 109 ARG A 114 1 6 +HELIX 7 H7 VAL A 120 ILE A 124 5 5 +SHEET 1 S1 3 ALA A 42 ASN A 46 0 +SHEET 2 S1 3 GLY A 49 GLY A 54 -1 O SER A 50 N ASN A 46 +SHEET 3 S1 3 LEU A 56 SER A 60 -1 O SER A 60 N THR A 51 +SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.99 +SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.11 +SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.00 +SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.10 +CRYST1 79.100 79.100 37.900 90.00 90.00 90.00 P 43 21 2 8 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.012642 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.012642 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.026385 0.00000 +ATOM 1 N LYS A 1 3.294 10.164 10.266 1.00 11.18 N +ATOM 2 CA LYS A 1 2.388 10.533 9.168 1.00 9.68 C +ATOM 3 C LYS A 1 2.438 12.049 8.889 1.00 14.00 C +ATOM 4 O LYS A 1 2.406 12.898 9.815 1.00 14.00 O +ATOM 5 CB LYS A 1 0.949 10.101 9.559 1.00 13.29 C +ATOM 6 CG LYS A 1 -0.050 10.621 8.573 1.00 13.52 C +ATOM 7 CD LYS A 1 -1.425 10.081 8.720 1.00 22.15 C +ATOM 8 CE LYS A 1 -2.370 10.773 7.722 1.00 20.23 C +ATOM 9 NZ LYS A 1 -3.776 10.439 7.933 1.00 68.72 N +ATOM 10 N VAL A 2 2.552 12.428 7.626 1.00 10.17 N +ATOM 11 CA VAL A 2 2.524 13.840 7.282 1.00 10.02 C +ATOM 12 C VAL A 2 1.120 14.180 6.770 1.00 27.84 C +ATOM 13 O VAL A 2 0.737 13.798 5.675 1.00 22.87 O +ATOM 14 CB VAL A 2 3.529 14.264 6.240 1.00 9.00 C +ATOM 15 CG1 VAL A 2 3.313 15.765 5.983 1.00 11.37 C +ATOM 16 CG2 VAL A 2 4.928 14.016 6.810 1.00 10.57 C +ATOM 17 N PHE A 3 0.333 14.851 7.573 1.00 16.35 N +ATOM 18 CA PHE A 3 -1.021 15.173 7.169 1.00 15.34 C +ATOM 19 C PHE A 3 -1.097 16.285 6.126 1.00 14.79 C +ATOM 20 O PHE A 3 -0.261 17.203 6.054 1.00 14.99 O +ATOM 21 CB PHE A 3 -1.867 15.710 8.361 1.00 14.03 C +ATOM 22 CG PHE A 3 -2.412 14.638 9.295 1.00 16.41 C +ATOM 23 CD1 PHE A 3 -1.575 14.049 10.240 1.00 14.44 C +ATOM 24 CD2 PHE A 3 -3.757 14.285 9.274 1.00 18.12 C +ATOM 25 CE1 PHE A 3 -2.065 13.116 11.135 1.00 11.11 C +ATOM 26 CE2 PHE A 3 -4.263 13.332 10.178 1.00 32.24 C +ATOM 27 CZ PHE A 3 -3.413 12.758 11.132 1.00 14.31 C +ATOM 28 N GLY A 4 -2.229 16.228 5.393 1.00 15.47 N +ATOM 29 CA GLY A 4 -2.645 17.273 4.511 1.00 13.97 C +ATOM 30 C GLY A 4 -3.456 18.261 5.350 1.00 10.95 C +ATOM 31 O GLY A 4 -4.070 17.876 6.282 1.00 16.45 O +ATOM 32 N ARG A 5 -3.414 19.518 5.009 1.00 14.28 N +ATOM 33 CA ARG A 5 -4.106 20.560 5.674 1.00 11.63 C +ATOM 34 C ARG A 5 -5.540 20.226 5.992 1.00 21.37 C +ATOM 35 O ARG A 5 -5.963 20.258 7.138 1.00 9.74 O +ATOM 36 CB ARG A 5 -3.952 21.857 4.900 1.00 13.31 C +ATOM 37 CG ARG A 5 -4.508 23.053 5.610 1.00 13.02 C +ATOM 38 CD ARG A 5 -4.414 24.335 4.775 1.00 19.72 C +ATOM 39 NE ARG A 5 -5.013 24.223 3.447 1.00 23.52 N +ATOM 40 CZ ARG A 5 -6.287 24.522 3.048 1.00 40.17 C +ATOM 41 NH1 ARG A 5 -7.248 25.009 3.841 1.00 17.54 N +ATOM 42 NH2 ARG A 5 -6.619 24.303 1.767 1.00 33.21 N +ATOM 43 N CYS A 6 -6.327 19.866 4.967 1.00 15.04 N +ATOM 44 CA CYS A 6 -7.767 19.572 5.189 1.00 12.93 C +ATOM 45 C CYS A 6 -7.997 18.269 5.916 1.00 5.10 C +ATOM 46 O CYS A 6 -8.992 18.125 6.630 1.00 13.60 O +ATOM 47 CB CYS A 6 -8.607 19.637 3.859 1.00 16.72 C +ATOM 48 SG CYS A 6 -8.669 21.273 3.104 1.00 16.68 S +ATOM 49 N GLU A 7 -7.142 17.274 5.653 1.00 7.34 N +ATOM 50 CA GLU A 7 -7.309 15.981 6.323 1.00 10.86 C +ATOM 51 C GLU A 7 -7.129 16.181 7.848 1.00 17.71 C +ATOM 52 O GLU A 7 -7.835 15.638 8.657 1.00 14.19 O +ATOM 53 CB GLU A 7 -6.187 15.048 5.880 1.00 16.19 C +ATOM 54 CG GLU A 7 -6.206 13.614 6.496 1.00 16.67 C +ATOM 55 CD GLU A 7 -4.952 12.864 6.030 1.00 32.91 C +ATOM 56 OE1 GLU A 7 -4.003 13.411 5.480 1.00 18.18 O +ATOM 57 OE2 GLU A 7 -4.992 11.578 6.219 1.00 28.07 O +ATOM 58 N LEU A 8 -6.148 16.987 8.221 1.00 14.04 N +ATOM 59 CA LEU A 8 -5.919 17.285 9.637 1.00 8.65 C +ATOM 60 C LEU A 8 -7.068 18.103 10.254 1.00 10.08 C +ATOM 61 O LEU A 8 -7.500 17.827 11.353 1.00 15.66 O +ATOM 62 CB LEU A 8 -4.607 18.084 9.809 1.00 14.88 C +ATOM 63 CG LEU A 8 -4.384 18.432 11.299 1.00 12.61 C +ATOM 64 CD1 LEU A 8 -4.110 17.104 12.053 1.00 12.51 C +ATOM 65 CD2 LEU A 8 -3.147 19.299 11.372 1.00 13.98 C +ATOM 66 N ALA A 9 -7.524 19.122 9.561 1.00 11.92 N +ATOM 67 CA ALA A 9 -8.664 19.896 9.982 1.00 10.97 C +ATOM 68 C ALA A 9 -9.841 18.971 10.304 1.00 15.73 C +ATOM 69 O ALA A 9 -10.469 19.046 11.359 1.00 13.41 O +ATOM 70 CB ALA A 9 -9.039 21.012 8.954 1.00 8.88 C +ATOM 71 N ALA A 10 -10.124 18.049 9.425 1.00 12.11 N +ATOM 72 CA ALA A 10 -11.262 17.129 9.595 1.00 12.19 C +ATOM 73 C ALA A 10 -11.034 16.206 10.780 1.00 18.02 C +ATOM 74 O ALA A 10 -11.932 15.902 11.522 1.00 17.70 O +ATOM 75 CB ALA A 10 -11.457 16.297 8.313 1.00 14.75 C +ATOM 76 N ALA A 11 -9.815 15.771 10.988 1.00 14.94 N +ATOM 77 CA ALA A 11 -9.544 14.908 12.136 1.00 12.19 C +ATOM 78 C ALA A 11 -9.651 15.641 13.494 1.00 7.51 C +ATOM 79 O ALA A 11 -10.088 15.066 14.457 1.00 12.99 O +ATOM 80 CB ALA A 11 -8.153 14.250 12.041 1.00 15.76 C +ATOM 81 N MET A 12 -9.107 16.884 13.529 1.00 10.71 N +ATOM 82 CA MET A 12 -9.160 17.683 14.710 1.00 12.27 C +ATOM 83 C MET A 12 -10.599 17.988 15.028 1.00 16.76 C +ATOM 84 O MET A 12 -10.964 17.966 16.195 1.00 17.43 O +ATOM 85 CB MET A 12 -8.385 18.996 14.563 1.00 6.96 C +ATOM 86 CG MET A 12 -6.872 18.717 14.593 1.00 7.53 C +ATOM 87 SD MET A 12 -5.971 20.286 14.351 1.00 16.25 S +ATOM 88 CE MET A 12 -4.392 19.972 15.137 1.00 11.48 C +ATOM 89 N LYS A 13 -11.421 18.239 13.985 1.00 11.66 N +ATOM 90 CA LYS A 13 -12.844 18.554 14.146 1.00 12.77 C +ATOM 91 C LYS A 13 -13.552 17.402 14.762 1.00 17.21 C +ATOM 92 O LYS A 13 -14.278 17.533 15.704 1.00 15.75 O +ATOM 93 CB LYS A 13 -13.505 18.908 12.852 1.00 14.38 C +ATOM 94 CG LYS A 13 -14.874 19.457 13.096 1.00 16.88 C +ATOM 95 CD LYS A 13 -15.519 20.062 11.867 1.00 19.73 C +ATOM 96 CE LYS A 13 -17.062 20.060 11.971 1.00 41.06 C +ATOM 97 NZ LYS A 13 -17.725 20.836 10.899 1.00 61.80 N +ATOM 98 N ARG A 14 -13.273 16.240 14.220 1.00 21.68 N +ATOM 99 CA ARG A 14 -13.878 15.021 14.667 1.00 17.17 C +ATOM 100 C ARG A 14 -13.480 14.746 16.099 1.00 27.88 C +ATOM 101 O ARG A 14 -14.217 14.129 16.823 1.00 17.70 O +ATOM 102 CB ARG A 14 -13.448 13.876 13.756 1.00 23.48 C +ATOM 103 CG ARG A 14 -14.102 12.553 14.162 1.00 51.76 C +ATOM 104 CD ARG A 14 -13.875 11.424 13.160 1.00 52.15 C +ATOM 105 NE ARG A 14 -12.616 10.730 13.354 1.00 61.79 N +ATOM 106 CZ ARG A 14 -12.406 9.681 14.156 1.00 47.00 C +ATOM 107 NH1 ARG A 14 -13.357 9.121 14.898 1.00 35.04 N +ATOM 108 NH2 ARG A 14 -11.177 9.169 14.196 1.00 55.70 N +ATOM 109 N HIS A 15 -12.300 15.219 16.498 1.00 20.13 N +ATOM 110 CA HIS A 15 -11.791 15.016 17.846 1.00 14.58 C +ATOM 111 C HIS A 15 -12.221 16.074 18.888 1.00 18.83 C +ATOM 112 O HIS A 15 -11.689 16.060 19.970 1.00 22.76 O +ATOM 113 CB HIS A 15 -10.268 14.799 17.851 1.00 23.09 C +ATOM 114 CG HIS A 15 -9.906 13.364 17.563 1.00 21.53 C +ATOM 115 ND1 HIS A 15 -9.721 12.896 16.256 1.00 28.28 N +ATOM 116 CD2 HIS A 15 -9.723 12.308 18.413 1.00 30.99 C +ATOM 117 CE1 HIS A 15 -9.422 11.580 16.350 1.00 20.50 C +ATOM 118 NE2 HIS A 15 -9.412 11.213 17.627 1.00 42.34 N +ATOM 119 N GLY A 16 -13.146 16.952 18.551 1.00 14.90 N +ATOM 120 CA GLY A 16 -13.687 17.956 19.401 1.00 16.84 C +ATOM 121 C GLY A 16 -12.871 19.227 19.554 1.00 23.06 C +ATOM 122 O GLY A 16 -13.121 20.016 20.460 1.00 19.24 O +ATOM 123 N LEU A 17 -11.922 19.491 18.685 1.00 14.25 N +ATOM 124 CA LEU A 17 -11.134 20.695 18.826 1.00 10.83 C +ATOM 125 C LEU A 17 -11.728 21.961 18.295 1.00 16.61 C +ATOM 126 O LEU A 17 -11.276 23.016 18.657 1.00 18.63 O +ATOM 127 CB LEU A 17 -9.749 20.538 18.218 1.00 14.80 C +ATOM 128 CG LEU A 17 -8.792 19.745 19.031 1.00 19.84 C +ATOM 129 CD1 LEU A 17 -7.483 19.876 18.293 1.00 22.16 C +ATOM 130 CD2 LEU A 17 -8.675 20.282 20.474 1.00 15.82 C +ATOM 131 N ASP A 18 -12.704 21.930 17.405 1.00 18.32 N +ATOM 132 CA ASP A 18 -13.261 23.178 16.884 1.00 18.68 C +ATOM 133 C ASP A 18 -13.986 23.912 17.979 1.00 19.05 C +ATOM 134 O ASP A 18 -14.952 23.375 18.512 1.00 21.74 O +ATOM 135 CB ASP A 18 -14.275 23.002 15.717 1.00 25.90 C +ATOM 136 CG ASP A 18 -14.712 24.288 15.010 1.00 37.66 C +ATOM 137 OD1 ASP A 18 -14.134 25.393 15.038 1.00 26.98 O +ATOM 138 OD2 ASP A 18 -15.751 24.055 14.248 1.00 63.41 O +ATOM 139 N ASN A 19 -13.542 25.130 18.229 1.00 12.22 N +ATOM 140 CA ASN A 19 -14.046 26.010 19.253 1.00 9.99 C +ATOM 141 C ASN A 19 -13.851 25.507 20.671 1.00 15.97 C +ATOM 142 O ASN A 19 -14.534 25.975 21.595 1.00 18.10 O +ATOM 143 CB ASN A 19 -15.518 26.259 19.032 1.00 20.32 C +ATOM 144 CG ASN A 19 -15.706 27.052 17.774 1.00 40.03 C +ATOM 145 OD1 ASN A 19 -15.227 28.183 17.693 1.00 57.25 O +ATOM 146 ND2 ASN A 19 -16.402 26.456 16.811 1.00 40.09 N +ATOM 147 N TYR A 20 -12.956 24.552 20.827 1.00 12.49 N +ATOM 148 CA TYR A 20 -12.652 24.027 22.106 1.00 8.91 C +ATOM 149 C TYR A 20 -12.037 25.159 22.929 1.00 19.06 C +ATOM 150 O TYR A 20 -10.978 25.687 22.602 1.00 16.99 O +ATOM 151 CB TYR A 20 -11.717 22.810 22.005 1.00 17.23 C +ATOM 152 CG TYR A 20 -11.532 22.151 23.355 1.00 13.76 C +ATOM 153 CD1 TYR A 20 -12.444 21.206 23.832 1.00 17.40 C +ATOM 154 CD2 TYR A 20 -10.475 22.556 24.184 1.00 24.53 C +ATOM 155 CE1 TYR A 20 -12.311 20.657 25.111 1.00 20.84 C +ATOM 156 CE2 TYR A 20 -10.331 22.023 25.461 1.00 16.26 C +ATOM 157 CZ TYR A 20 -11.259 21.078 25.922 1.00 35.41 C +ATOM 158 OH TYR A 20 -11.104 20.560 27.183 1.00 29.68 O +ATOM 159 N ARG A 21 -12.721 25.593 23.977 1.00 19.00 N +ATOM 160 CA ARG A 21 -12.250 26.715 24.791 1.00 15.05 C +ATOM 161 C ARG A 21 -12.264 27.987 24.017 1.00 8.63 C +ATOM 162 O ARG A 21 -11.450 28.877 24.295 1.00 13.69 O +ATOM 163 CB ARG A 21 -10.847 26.601 25.387 1.00 18.33 C +ATOM 164 CG ARG A 21 -10.694 25.514 26.442 1.00 27.37 C +ATOM 165 CD ARG A 21 -11.577 25.864 27.598 1.00 40.81 C +ATOM 166 NE ARG A 21 -11.597 24.902 28.676 1.00 57.85 N +ATOM 167 CZ ARG A 21 -11.253 25.330 29.884 1.00 97.15 C +ATOM 168 NH1 ARG A 21 -10.859 26.593 30.049 1.00 63.15 N +ATOM 169 NH2 ARG A 21 -11.283 24.508 30.937 1.00 68.08 N +ATOM 170 N GLY A 22 -13.173 28.076 23.045 1.00 11.97 N +ATOM 171 CA GLY A 22 -13.290 29.312 22.253 1.00 13.56 C +ATOM 172 C GLY A 22 -12.276 29.499 21.125 1.00 15.57 C +ATOM 173 O GLY A 22 -12.274 30.537 20.508 1.00 15.13 O +ATOM 174 N TYR A 23 -11.414 28.511 20.863 1.00 17.25 N +ATOM 175 CA TYR A 23 -10.419 28.584 19.787 1.00 12.17 C +ATOM 176 C TYR A 23 -10.964 27.832 18.564 1.00 7.69 C +ATOM 177 O TYR A 23 -11.097 26.573 18.581 1.00 8.57 O +ATOM 178 CB TYR A 23 -9.059 27.910 20.217 1.00 11.16 C +ATOM 179 CG TYR A 23 -8.358 28.702 21.299 1.00 14.01 C +ATOM 180 CD1 TYR A 23 -7.560 29.766 20.910 1.00 10.23 C +ATOM 181 CD2 TYR A 23 -8.534 28.427 22.652 1.00 6.77 C +ATOM 182 CE1 TYR A 23 -6.879 30.557 21.846 1.00 9.23 C +ATOM 183 CE2 TYR A 23 -7.907 29.219 23.612 1.00 10.96 C +ATOM 184 CZ TYR A 23 -7.061 30.276 23.207 1.00 12.99 C +ATOM 185 OH TYR A 23 -6.411 31.069 24.111 1.00 13.78 O +ATOM 186 N SER A 24 -11.219 28.590 17.517 1.00 12.88 N +ATOM 187 CA SER A 24 -11.730 28.032 16.253 1.00 14.99 C +ATOM 188 C SER A 24 -10.726 27.075 15.616 1.00 20.42 C +ATOM 189 O SER A 24 -9.487 27.191 15.841 1.00 9.73 O +ATOM 190 CB SER A 24 -12.060 29.179 15.305 1.00 9.90 C +ATOM 191 OG SER A 24 -10.830 29.750 14.853 1.00 17.68 O +ATOM 192 N LEU A 25 -11.267 26.110 14.822 1.00 16.10 N +ATOM 193 CA LEU A 25 -10.460 25.111 14.092 1.00 11.40 C +ATOM 194 C LEU A 25 -9.205 25.683 13.438 1.00 11.44 C +ATOM 195 O LEU A 25 -8.145 25.073 13.536 1.00 10.56 O +ATOM 196 CB LEU A 25 -11.293 24.412 12.993 1.00 13.62 C +ATOM 197 CG LEU A 25 -10.826 23.089 12.491 1.00 16.00 C +ATOM 198 CD1 LEU A 25 -10.359 22.212 13.644 1.00 15.17 C +ATOM 199 CD2 LEU A 25 -12.018 22.437 11.805 1.00 15.75 C +ATOM 200 N GLY A 26 -9.311 26.836 12.758 1.00 10.18 N +ATOM 201 CA GLY A 26 -8.169 27.388 12.084 1.00 7.13 C +ATOM 202 C GLY A 26 -6.984 27.643 12.997 1.00 9.12 C +ATOM 203 O GLY A 26 -5.854 27.610 12.555 1.00 12.61 O +ATOM 204 N ASN A 27 -7.232 27.928 14.280 1.00 10.01 N +ATOM 205 CA ASN A 27 -6.132 28.159 15.255 1.00 10.13 C +ATOM 206 C ASN A 27 -5.317 26.889 15.464 1.00 2.57 C +ATOM 207 O ASN A 27 -4.057 26.899 15.477 1.00 7.08 O +ATOM 208 CB ASN A 27 -6.688 28.636 16.631 1.00 9.13 C +ATOM 209 CG ASN A 27 -7.131 30.092 16.624 1.00 4.84 C +ATOM 210 OD1 ASN A 27 -6.292 30.979 16.582 1.00 9.37 O +ATOM 211 ND2 ASN A 27 -8.466 30.324 16.587 1.00 8.00 N +ATOM 212 N TRP A 28 -6.033 25.791 15.639 1.00 5.40 N +ATOM 213 CA TRP A 28 -5.402 24.497 15.879 1.00 5.45 C +ATOM 214 C TRP A 28 -4.584 24.047 14.657 1.00 6.38 C +ATOM 215 O TRP A 28 -3.510 23.501 14.767 1.00 7.31 O +ATOM 216 CB TRP A 28 -6.482 23.490 16.237 1.00 7.31 C +ATOM 217 CG TRP A 28 -7.149 23.849 17.539 1.00 7.66 C +ATOM 218 CD1 TRP A 28 -8.351 24.415 17.748 1.00 11.80 C +ATOM 219 CD2 TRP A 28 -6.540 23.691 18.841 1.00 9.47 C +ATOM 220 NE1 TRP A 28 -8.575 24.567 19.117 1.00 11.48 N +ATOM 221 CE2 TRP A 28 -7.475 24.139 19.807 1.00 9.56 C +ATOM 222 CE3 TRP A 28 -5.321 23.121 19.249 1.00 10.24 C +ATOM 223 CZ2 TRP A 28 -7.187 24.066 21.210 1.00 11.03 C +ATOM 224 CZ3 TRP A 28 -5.059 23.060 20.609 1.00 20.66 C +ATOM 225 CH2 TRP A 28 -5.985 23.551 21.560 1.00 9.06 C +ATOM 226 N VAL A 29 -5.166 24.262 13.469 1.00 3.89 N +ATOM 227 CA VAL A 29 -4.458 23.870 12.217 1.00 5.65 C +ATOM 228 C VAL A 29 -3.242 24.746 11.972 1.00 2.99 C +ATOM 229 O VAL A 29 -2.170 24.273 11.571 1.00 7.90 O +ATOM 230 CB VAL A 29 -5.456 23.881 11.020 1.00 7.66 C +ATOM 231 CG1 VAL A 29 -4.630 23.646 9.743 1.00 13.23 C +ATOM 232 CG2 VAL A 29 -6.516 22.751 11.149 1.00 6.73 C +ATOM 233 N CYS A 30 -3.372 26.060 12.262 1.00 2.63 N +ATOM 234 CA CYS A 30 -2.281 26.976 12.125 1.00 7.05 C +ATOM 235 C CYS A 30 -1.151 26.582 13.072 1.00 10.47 C +ATOM 236 O CYS A 30 0.054 26.552 12.766 1.00 4.93 O +ATOM 237 CB CYS A 30 -2.756 28.428 12.303 1.00 2.61 C +ATOM 238 SG CYS A 30 -1.467 29.667 12.134 1.00 10.20 S +ATOM 239 N ALA A 31 -1.521 26.283 14.306 1.00 9.82 N +ATOM 240 CA ALA A 31 -0.491 25.884 15.276 1.00 15.61 C +ATOM 241 C ALA A 31 0.235 24.607 14.849 1.00 5.07 C +ATOM 242 O ALA A 31 1.464 24.554 14.987 1.00 9.27 O +ATOM 243 CB ALA A 31 -1.089 25.781 16.704 1.00 7.85 C +ATOM 244 N ALA A 32 -0.483 23.609 14.315 1.00 7.79 N +ATOM 245 CA ALA A 32 0.162 22.357 13.855 1.00 8.61 C +ATOM 246 C ALA A 32 1.085 22.594 12.673 1.00 7.90 C +ATOM 247 O ALA A 32 2.197 22.050 12.585 1.00 9.35 O +ATOM 248 CB ALA A 32 -0.823 21.268 13.540 1.00 10.83 C +ATOM 249 N LYS A 33 0.653 23.463 11.786 1.00 7.35 N +ATOM 250 CA LYS A 33 1.542 23.795 10.635 1.00 6.50 C +ATOM 251 C LYS A 33 2.867 24.333 11.097 1.00 6.89 C +ATOM 252 O LYS A 33 3.936 23.889 10.727 1.00 10.45 O +ATOM 253 CB LYS A 33 0.863 24.886 9.776 1.00 10.32 C +ATOM 254 CG LYS A 33 1.793 25.437 8.676 1.00 13.52 C +ATOM 255 CD LYS A 33 1.927 24.485 7.491 1.00 19.87 C +ATOM 256 CE LYS A 33 3.138 24.764 6.621 1.00 27.04 C +ATOM 257 NZ LYS A 33 3.217 23.793 5.511 1.00 45.44 N +ATOM 258 N PHE A 34 2.807 25.345 11.961 1.00 9.24 N +ATOM 259 CA PHE A 34 4.029 25.958 12.436 1.00 8.96 C +ATOM 260 C PHE A 34 4.846 25.192 13.455 1.00 16.48 C +ATOM 261 O PHE A 34 6.039 25.360 13.540 1.00 14.96 O +ATOM 262 CB PHE A 34 3.856 27.469 12.721 1.00 9.21 C +ATOM 263 CG PHE A 34 3.417 28.201 11.426 1.00 11.78 C +ATOM 264 CD1 PHE A 34 4.231 28.189 10.282 1.00 11.49 C +ATOM 265 CD2 PHE A 34 2.212 28.933 11.385 1.00 12.86 C +ATOM 266 CE1 PHE A 34 3.830 28.854 9.136 1.00 12.74 C +ATOM 267 CE2 PHE A 34 1.803 29.618 10.224 1.00 13.38 C +ATOM 268 CZ PHE A 34 2.627 29.554 9.090 1.00 13.39 C +ATOM 269 N GLU A 35 4.201 24.324 14.225 1.00 9.90 N +ATOM 270 CA GLU A 35 4.889 23.543 15.263 1.00 11.92 C +ATOM 271 C GLU A 35 5.641 22.352 14.706 1.00 13.79 C +ATOM 272 O GLU A 35 6.781 22.129 15.054 1.00 8.23 O +ATOM 273 CB GLU A 35 3.839 23.026 16.259 1.00 6.00 C +ATOM 274 CG GLU A 35 3.409 24.107 17.322 1.00 11.89 C +ATOM 275 CD GLU A 35 4.516 24.690 18.200 1.00 12.03 C +ATOM 276 OE1 GLU A 35 5.640 24.296 18.226 1.00 12.97 O +ATOM 277 OE2 GLU A 35 4.167 25.730 18.876 1.00 13.03 O +ATOM 278 N SER A 36 4.983 21.591 13.819 1.00 8.49 N +ATOM 279 CA SER A 36 5.541 20.369 13.283 1.00 8.82 C +ATOM 280 C SER A 36 5.483 20.189 11.756 1.00 10.13 C +ATOM 281 O SER A 36 5.800 19.070 11.251 1.00 14.88 O +ATOM 282 CB SER A 36 4.684 19.256 13.831 1.00 7.77 C +ATOM 283 OG SER A 36 3.330 19.336 13.297 1.00 8.30 O +ATOM 284 N ASN A 37 4.975 21.223 11.050 1.00 11.55 N +ATOM 285 CA ASN A 37 4.752 21.103 9.605 1.00 8.89 C +ATOM 286 C ASN A 37 3.825 19.918 9.321 1.00 14.33 C +ATOM 287 O ASN A 37 3.972 19.215 8.320 1.00 14.19 O +ATOM 288 CB ASN A 37 6.061 21.002 8.788 1.00 20.93 C +ATOM 289 CG ASN A 37 5.851 21.458 7.334 1.00 25.83 C +ATOM 290 OD1 ASN A 37 5.061 22.365 7.057 1.00 26.84 O +ATOM 291 ND2 ASN A 37 6.474 20.759 6.397 1.00 52.87 N +ATOM 292 N PHE A 38 2.864 19.696 10.220 1.00 7.19 N +ATOM 293 CA PHE A 38 1.862 18.625 10.075 1.00 11.76 C +ATOM 294 C PHE A 38 2.411 17.214 10.168 1.00 10.63 C +ATOM 295 O PHE A 38 1.747 16.276 9.742 1.00 9.49 O +ATOM 296 CB PHE A 38 1.092 18.696 8.696 1.00 8.56 C +ATOM 297 CG PHE A 38 0.280 19.956 8.505 1.00 13.59 C +ATOM 298 CD1 PHE A 38 -0.367 20.558 9.597 1.00 8.45 C +ATOM 299 CD2 PHE A 38 0.112 20.532 7.255 1.00 17.61 C +ATOM 300 CE1 PHE A 38 -1.146 21.685 9.432 1.00 11.53 C +ATOM 301 CE2 PHE A 38 -0.664 21.687 7.081 1.00 17.65 C +ATOM 302 CZ PHE A 38 -1.316 22.268 8.162 1.00 13.17 C +ATOM 303 N ASN A 39 3.667 17.073 10.600 1.00 8.40 N +ATOM 304 CA ASN A 39 4.271 15.737 10.699 1.00 6.01 C +ATOM 305 C ASN A 39 4.101 15.211 12.158 1.00 6.81 C +ATOM 306 O ASN A 39 4.597 15.858 13.147 1.00 11.41 O +ATOM 307 CB ASN A 39 5.776 15.925 10.373 1.00 6.39 C +ATOM 308 CG ASN A 39 6.552 14.636 10.450 1.00 6.34 C +ATOM 309 OD1 ASN A 39 5.992 13.541 10.684 1.00 10.75 O +ATOM 310 ND2 ASN A 39 7.832 14.764 10.100 1.00 13.88 N +ATOM 311 N THR A 40 3.430 14.054 12.314 1.00 8.05 N +ATOM 312 CA THR A 40 3.222 13.509 13.676 1.00 10.13 C +ATOM 313 C THR A 40 4.525 13.041 14.358 1.00 8.64 C +ATOM 314 O THR A 40 4.546 12.831 15.542 1.00 12.11 O +ATOM 315 CB THR A 40 2.279 12.302 13.663 1.00 12.49 C +ATOM 316 OG1 THR A 40 2.862 11.250 12.880 1.00 10.89 O +ATOM 317 CG2 THR A 40 0.843 12.666 13.219 1.00 9.90 C +ATOM 318 N GLN A 41 5.594 12.819 13.559 1.00 6.61 N +ATOM 319 CA GLN A 41 6.860 12.308 14.019 1.00 3.67 C +ATOM 320 C GLN A 41 7.861 13.372 14.433 1.00 4.66 C +ATOM 321 O GLN A 41 8.986 13.051 14.864 1.00 8.80 O +ATOM 322 CB GLN A 41 7.463 11.344 12.979 1.00 9.30 C +ATOM 323 CG GLN A 41 6.598 10.100 12.797 1.00 12.21 C +ATOM 324 CD GLN A 41 7.402 8.999 12.104 1.00 22.47 C +ATOM 325 OE1 GLN A 41 8.254 8.393 12.763 1.00 16.54 O +ATOM 326 NE2 GLN A 41 7.257 8.847 10.744 1.00 13.11 N +ATOM 327 N ALA A 42 7.460 14.657 14.305 1.00 6.51 N +ATOM 328 CA ALA A 42 8.376 15.748 14.672 1.00 8.14 C +ATOM 329 C ALA A 42 8.824 15.710 16.237 1.00 11.70 C +ATOM 330 O ALA A 42 8.005 15.547 17.165 1.00 5.54 O +ATOM 331 CB ALA A 42 7.744 17.108 14.349 1.00 8.97 C +ATOM 332 N THR A 43 10.132 15.865 16.445 1.00 7.08 N +ATOM 333 CA THR A 43 10.705 15.992 17.773 1.00 10.42 C +ATOM 334 C THR A 43 11.694 17.112 17.692 1.00 11.09 C +ATOM 335 O THR A 43 12.280 17.411 16.646 1.00 12.80 O +ATOM 336 CB THR A 43 11.362 14.748 18.354 1.00 13.93 C +ATOM 337 OG1 THR A 43 12.360 14.429 17.435 1.00 11.09 O +ATOM 338 CG2 THR A 43 10.420 13.567 18.530 1.00 7.58 C +ATOM 339 N ASN A 44 11.894 17.801 18.808 1.00 10.77 N +ATOM 340 CA ASN A 44 12.828 18.909 18.863 1.00 6.02 C +ATOM 341 C ASN A 44 13.258 19.036 20.281 1.00 16.51 C +ATOM 342 O ASN A 44 12.426 19.127 21.185 1.00 11.61 O +ATOM 343 CB ASN A 44 12.171 20.225 18.473 1.00 13.37 C +ATOM 344 CG ASN A 44 11.932 20.272 16.966 1.00 55.95 C +ATOM 345 OD1 ASN A 44 12.883 20.299 16.146 1.00 30.16 O +ATOM 346 ND2 ASN A 44 10.659 20.233 16.594 1.00 20.67 N +ATOM 347 N ARG A 45 14.545 19.035 20.479 1.00 13.41 N +ATOM 348 CA ARG A 45 15.061 19.112 21.827 1.00 12.01 C +ATOM 349 C ARG A 45 15.250 20.555 22.252 1.00 20.93 C +ATOM 350 O ARG A 45 15.601 21.418 21.435 1.00 20.22 O +ATOM 351 CB ARG A 45 16.408 18.438 21.953 1.00 19.70 C +ATOM 352 CG ARG A 45 16.935 18.714 23.338 1.00 35.82 C +ATOM 353 CD ARG A 45 16.730 17.468 24.141 1.00 27.63 C +ATOM 354 NE ARG A 45 17.249 16.408 23.330 1.00 67.37 N +ATOM 355 CZ ARG A 45 18.249 15.588 23.641 1.00 91.84 C +ATOM 356 NH1 ARG A 45 18.868 15.589 24.830 1.00 36.08 N +ATOM 357 NH2 ARG A 45 18.624 14.698 22.716 1.00 64.26 N +ATOM 358 N ASN A 46 15.056 20.796 23.543 1.00 12.63 N +ATOM 359 CA ASN A 46 15.247 22.135 24.062 1.00 12.92 C +ATOM 360 C ASN A 46 16.508 22.245 24.900 1.00 8.11 C +ATOM 361 O ASN A 46 17.149 21.253 25.274 1.00 15.77 O +ATOM 362 CB ASN A 46 13.989 22.699 24.735 1.00 11.70 C +ATOM 363 CG ASN A 46 12.659 22.418 24.007 1.00 21.14 C +ATOM 364 OD1 ASN A 46 11.762 21.669 24.459 1.00 23.29 O +ATOM 365 ND2 ASN A 46 12.508 23.062 22.886 1.00 24.99 N +ATOM 366 N THR A 47 16.906 23.489 25.146 1.00 23.92 N +ATOM 367 CA THR A 47 18.108 23.768 25.931 1.00 39.90 C +ATOM 368 C THR A 47 17.996 23.269 27.358 1.00 25.44 C +ATOM 369 O THR A 47 18.958 22.798 27.923 1.00 34.24 O +ATOM 370 CB THR A 47 18.506 25.250 25.905 1.00 47.42 C +ATOM 371 OG1 THR A 47 17.376 26.053 26.142 1.00 38.53 O +ATOM 372 CG2 THR A 47 19.115 25.572 24.552 1.00 58.08 C +ATOM 373 N ASP A 48 16.797 23.339 27.935 1.00 20.62 N +ATOM 374 CA ASP A 48 16.626 22.832 29.261 1.00 9.90 C +ATOM 375 C ASP A 48 16.700 21.306 29.306 1.00 19.23 C +ATOM 376 O ASP A 48 16.586 20.723 30.361 1.00 22.36 O +ATOM 377 CB ASP A 48 15.349 23.377 29.887 1.00 14.78 C +ATOM 378 CG ASP A 48 14.119 22.821 29.267 1.00 19.04 C +ATOM 379 OD1 ASP A 48 14.160 21.981 28.422 1.00 28.31 O +ATOM 380 OD2 ASP A 48 13.002 23.315 29.717 1.00 28.61 O +ATOM 381 N GLY A 49 16.883 20.637 28.166 1.00 17.28 N +ATOM 382 CA GLY A 49 16.950 19.205 28.182 1.00 10.24 C +ATOM 383 C GLY A 49 15.608 18.534 27.977 1.00 14.24 C +ATOM 384 O GLY A 49 15.499 17.291 27.852 1.00 13.58 O +ATOM 385 N SER A 50 14.564 19.331 27.973 1.00 9.07 N +ATOM 386 CA SER A 50 13.311 18.716 27.712 1.00 7.32 C +ATOM 387 C SER A 50 13.217 18.531 26.131 1.00 11.52 C +ATOM 388 O SER A 50 14.085 19.016 25.374 1.00 13.96 O +ATOM 389 CB SER A 50 12.113 19.490 28.182 1.00 4.67 C +ATOM 390 OG SER A 50 12.074 20.716 27.461 1.00 9.76 O +ATOM 391 N THR A 51 12.150 17.857 25.646 1.00 11.43 N +ATOM 392 CA THR A 51 11.958 17.610 24.179 1.00 9.12 C +ATOM 393 C THR A 51 10.485 17.806 23.917 1.00 16.87 C +ATOM 394 O THR A 51 9.677 17.499 24.825 1.00 8.33 O +ATOM 395 CB THR A 51 12.363 16.177 23.757 1.00 5.49 C +ATOM 396 OG1 THR A 51 13.711 15.986 24.120 1.00 6.88 O +ATOM 397 CG2 THR A 51 12.234 15.930 22.227 1.00 7.94 C +ATOM 398 N ASP A 52 10.158 18.354 22.701 1.00 9.46 N +ATOM 399 CA ASP A 52 8.767 18.608 22.181 1.00 5.88 C +ATOM 400 C ASP A 52 8.451 17.463 21.198 1.00 5.87 C +ATOM 401 O ASP A 52 9.311 17.033 20.476 1.00 5.53 O +ATOM 402 CB ASP A 52 8.717 19.972 21.485 1.00 6.73 C +ATOM 403 CG ASP A 52 9.014 21.046 22.449 1.00 17.46 C +ATOM 404 OD1 ASP A 52 8.778 20.978 23.593 1.00 16.69 O +ATOM 405 OD2 ASP A 52 9.531 22.065 21.923 1.00 28.92 O +ATOM 406 N TYR A 53 7.279 16.908 21.280 1.00 7.33 N +ATOM 407 CA TYR A 53 6.899 15.745 20.548 1.00 9.37 C +ATOM 408 C TYR A 53 5.580 15.922 19.790 1.00 13.52 C +ATOM 409 O TYR A 53 4.554 16.399 20.326 1.00 7.94 O +ATOM 410 CB TYR A 53 6.630 14.562 21.517 1.00 7.91 C +ATOM 411 CG TYR A 53 7.865 14.099 22.242 1.00 6.82 C +ATOM 412 CD1 TYR A 53 8.335 14.742 23.399 1.00 8.88 C +ATOM 413 CD2 TYR A 53 8.618 13.027 21.749 1.00 6.30 C +ATOM 414 CE1 TYR A 53 9.548 14.382 24.006 1.00 1.83 C +ATOM 415 CE2 TYR A 53 9.846 12.646 22.351 1.00 10.07 C +ATOM 416 CZ TYR A 53 10.229 13.264 23.534 1.00 8.70 C +ATOM 417 OH TYR A 53 11.374 12.889 24.151 1.00 12.40 O +ATOM 418 N GLY A 54 5.598 15.446 18.516 1.00 11.04 N +ATOM 419 CA GLY A 54 4.390 15.347 17.710 1.00 7.71 C +ATOM 420 C GLY A 54 3.939 16.599 17.020 1.00 3.67 C +ATOM 421 O GLY A 54 4.535 17.621 17.017 1.00 8.49 O +ATOM 422 N ILE A 55 2.748 16.458 16.496 1.00 11.91 N +ATOM 423 CA ILE A 55 2.096 17.435 15.686 1.00 7.88 C +ATOM 424 C ILE A 55 1.893 18.749 16.386 1.00 10.21 C +ATOM 425 O ILE A 55 1.904 19.805 15.761 1.00 9.17 O +ATOM 426 CB ILE A 55 0.838 16.805 15.068 1.00 19.48 C +ATOM 427 CG1 ILE A 55 0.390 17.438 13.734 1.00 15.27 C +ATOM 428 CG2 ILE A 55 -0.262 16.528 16.106 1.00 16.63 C +ATOM 429 CD1 ILE A 55 -0.353 16.483 12.846 1.00 21.60 C +ATOM 430 N LEU A 56 1.765 18.677 17.706 1.00 9.90 N +ATOM 431 CA LEU A 56 1.584 19.877 18.488 1.00 7.23 C +ATOM 432 C LEU A 56 2.735 20.173 19.390 1.00 18.66 C +ATOM 433 O LEU A 56 2.660 21.074 20.200 1.00 10.73 O +ATOM 434 CB LEU A 56 0.216 19.957 19.205 1.00 11.28 C +ATOM 435 CG LEU A 56 -0.990 20.157 18.283 1.00 12.31 C +ATOM 436 CD1 LEU A 56 -2.255 19.795 19.036 1.00 11.09 C +ATOM 437 CD2 LEU A 56 -1.074 21.607 17.850 1.00 11.43 C +ATOM 438 N GLN A 57 3.804 19.441 19.202 1.00 7.01 N +ATOM 439 CA GLN A 57 5.029 19.733 19.898 1.00 9.13 C +ATOM 440 C GLN A 57 4.883 19.918 21.451 1.00 11.13 C +ATOM 441 O GLN A 57 5.272 20.968 22.020 1.00 12.02 O +ATOM 442 CB GLN A 57 5.767 20.937 19.263 1.00 10.29 C +ATOM 443 CG GLN A 57 6.362 20.658 17.863 1.00 6.27 C +ATOM 444 CD GLN A 57 7.544 19.747 17.936 1.00 2.25 C +ATOM 445 OE1 GLN A 57 8.676 20.257 18.147 1.00 7.47 O +ATOM 446 NE2 GLN A 57 7.279 18.413 17.746 1.00 7.69 N +ATOM 447 N ILE A 58 4.303 18.898 22.061 1.00 9.58 N +ATOM 448 CA ILE A 58 4.031 18.814 23.487 1.00 12.88 C +ATOM 449 C ILE A 58 5.301 18.482 24.282 1.00 14.09 C +ATOM 450 O ILE A 58 6.055 17.583 23.982 1.00 10.65 O +ATOM 451 CB ILE A 58 2.839 17.923 23.711 1.00 12.15 C +ATOM 452 CG1 ILE A 58 1.599 18.614 23.110 1.00 12.61 C +ATOM 453 CG2 ILE A 58 2.704 17.544 25.215 1.00 12.37 C +ATOM 454 CD1 ILE A 58 0.329 17.770 23.138 1.00 17.22 C +ATOM 455 N ASN A 59 5.556 19.297 25.282 1.00 11.07 N +ATOM 456 CA ASN A 59 6.797 19.305 26.034 1.00 6.68 C +ATOM 457 C ASN A 59 6.893 18.239 27.099 1.00 8.46 C +ATOM 458 O ASN A 59 5.904 18.002 27.761 1.00 12.15 O +ATOM 459 CB ASN A 59 7.045 20.721 26.565 1.00 7.94 C +ATOM 460 CG ASN A 59 8.434 20.839 27.178 1.00 12.92 C +ATOM 461 OD1 ASN A 59 8.578 20.809 28.411 1.00 30.15 O +ATOM 462 ND2 ASN A 59 9.469 20.939 26.342 1.00 15.71 N +ATOM 463 N SER A 60 8.096 17.590 27.218 1.00 8.63 N +ATOM 464 CA SER A 60 8.333 16.496 28.162 1.00 11.30 C +ATOM 465 C SER A 60 8.586 17.015 29.647 1.00 7.42 C +ATOM 466 O SER A 60 8.559 16.218 30.620 1.00 18.39 O +ATOM 467 CB SER A 60 9.448 15.619 27.698 1.00 9.31 C +ATOM 468 OG SER A 60 10.642 16.390 27.790 1.00 9.01 O +ATOM 469 N ARG A 61 8.806 18.347 29.787 1.00 11.96 N +ATOM 470 CA ARG A 61 8.981 18.933 31.125 1.00 18.58 C +ATOM 471 C ARG A 61 7.701 18.806 31.935 1.00 21.66 C +ATOM 472 O ARG A 61 7.730 18.363 33.063 1.00 24.43 O +ATOM 473 CB ARG A 61 9.507 20.347 31.068 1.00 19.81 C +ATOM 474 CG ARG A 61 9.259 21.125 32.338 1.00 40.52 C +ATOM 475 CD ARG A 61 10.511 21.648 33.063 1.00 30.90 C +ATOM 476 NE ARG A 61 11.777 21.523 32.353 1.00 58.97 N +ATOM 477 CZ ARG A 61 12.722 20.587 32.539 1.00 70.61 C +ATOM 478 NH1 ARG A 61 12.610 19.570 33.413 1.00 68.85 N +ATOM 479 NH2 ARG A 61 13.829 20.673 31.795 1.00 56.33 N +ATOM 480 N TRP A 62 6.542 19.071 31.329 1.00 12.69 N +ATOM 481 CA TRP A 62 5.279 18.955 32.026 1.00 10.92 C +ATOM 482 C TRP A 62 4.281 17.916 31.682 1.00 19.26 C +ATOM 483 O TRP A 62 3.526 17.478 32.563 1.00 19.01 O +ATOM 484 CB TRP A 62 4.455 20.234 31.875 1.00 14.48 C +ATOM 485 CG TRP A 62 5.346 21.376 31.920 1.00 34.77 C +ATOM 486 CD1 TRP A 62 5.937 21.965 30.857 1.00 48.56 C +ATOM 487 CD2 TRP A 62 5.859 21.980 33.091 1.00 34.03 C +ATOM 488 NE1 TRP A 62 6.753 22.970 31.303 1.00 60.61 N +ATOM 489 CE2 TRP A 62 6.730 22.995 32.671 1.00 37.59 C +ATOM 490 CE3 TRP A 62 5.619 21.790 34.443 1.00 44.85 C +ATOM 491 CZ2 TRP A 62 7.373 23.823 33.582 1.00 74.91 C +ATOM 492 CZ3 TRP A 62 6.254 22.606 35.347 1.00 49.52 C +ATOM 493 CH2 TRP A 62 7.122 23.609 34.923 1.00 52.73 C +ATOM 494 N TRP A 63 4.152 17.600 30.385 1.00 11.21 N +ATOM 495 CA TRP A 63 3.036 16.858 29.848 1.00 9.63 C +ATOM 496 C TRP A 63 3.155 15.396 29.592 1.00 4.89 C +ATOM 497 O TRP A 63 2.183 14.725 29.581 1.00 11.10 O +ATOM 498 CB TRP A 63 2.652 17.635 28.566 1.00 6.50 C +ATOM 499 CG TRP A 63 2.429 19.101 28.874 1.00 5.59 C +ATOM 500 CD1 TRP A 63 3.223 20.140 28.615 1.00 15.86 C +ATOM 501 CD2 TRP A 63 1.364 19.632 29.695 1.00 11.68 C +ATOM 502 NE1 TRP A 63 2.675 21.309 29.075 1.00 15.89 N +ATOM 503 CE2 TRP A 63 1.567 21.028 29.780 1.00 12.27 C +ATOM 504 CE3 TRP A 63 0.230 19.055 30.324 1.00 14.52 C +ATOM 505 CZ2 TRP A 63 0.682 21.862 30.488 1.00 10.75 C +ATOM 506 CZ3 TRP A 63 -0.678 19.891 30.985 1.00 10.21 C +ATOM 507 CH2 TRP A 63 -0.421 21.271 31.057 1.00 13.33 C +ATOM 508 N CYS A 64 4.324 14.905 29.353 1.00 8.53 N +ATOM 509 CA CYS A 64 4.448 13.469 29.032 1.00 14.18 C +ATOM 510 C CYS A 64 5.785 12.968 29.569 1.00 8.75 C +ATOM 511 O CYS A 64 6.694 13.742 29.793 1.00 11.88 O +ATOM 512 CB CYS A 64 4.366 13.241 27.432 1.00 12.87 C +ATOM 513 SG CYS A 64 5.695 14.086 26.427 1.00 9.81 S +ATOM 514 N ASN A 65 5.913 11.651 29.720 1.00 9.55 N +ATOM 515 CA ASN A 65 7.127 11.114 30.200 1.00 16.84 C +ATOM 516 C ASN A 65 7.999 10.547 29.073 1.00 4.97 C +ATOM 517 O ASN A 65 7.529 9.623 28.435 1.00 10.83 O +ATOM 518 CB ASN A 65 6.809 9.953 31.188 1.00 9.17 C +ATOM 519 CG ASN A 65 8.120 9.322 31.715 1.00 22.59 C +ATOM 520 OD1 ASN A 65 9.033 10.017 32.182 1.00 21.36 O +ATOM 521 ND2 ASN A 65 8.276 8.015 31.524 1.00 36.98 N +ATOM 522 N ASP A 66 9.254 10.993 28.982 1.00 7.66 N +ATOM 523 CA ASP A 66 10.153 10.434 27.995 1.00 14.97 C +ATOM 524 C ASP A 66 11.354 9.742 28.601 1.00 23.09 C +ATOM 525 O ASP A 66 12.237 9.341 27.867 1.00 9.43 O +ATOM 526 CB ASP A 66 10.641 11.448 26.948 1.00 13.58 C +ATOM 527 CG ASP A 66 11.480 12.554 27.535 1.00 11.41 C +ATOM 528 OD1 ASP A 66 11.787 12.613 28.717 1.00 18.43 O +ATOM 529 OD2 ASP A 66 11.850 13.432 26.659 1.00 10.72 O +ATOM 530 N GLY A 67 11.395 9.644 29.920 1.00 14.60 N +ATOM 531 CA GLY A 67 12.449 8.941 30.665 1.00 9.04 C +ATOM 532 C GLY A 67 13.738 9.677 30.697 1.00 13.04 C +ATOM 533 O GLY A 67 14.726 9.165 31.164 1.00 23.22 O +ATOM 534 N ARG A 68 13.787 10.891 30.194 1.00 8.50 N +ATOM 535 CA ARG A 68 15.089 11.512 30.237 1.00 11.50 C +ATOM 536 C ARG A 68 15.046 12.949 30.560 1.00 11.49 C +ATOM 537 O ARG A 68 15.995 13.645 30.281 1.00 17.90 O +ATOM 538 CB ARG A 68 15.872 11.277 28.959 1.00 18.67 C +ATOM 539 CG ARG A 68 15.218 11.867 27.707 1.00 21.19 C +ATOM 540 CD ARG A 68 16.251 12.103 26.592 1.00 19.51 C +ATOM 541 NE ARG A 68 15.790 12.984 25.527 1.00 20.38 N +ATOM 542 CZ ARG A 68 16.264 12.978 24.248 1.00 29.94 C +ATOM 543 NH1 ARG A 68 17.253 12.102 23.926 1.00 13.00 N +ATOM 544 NH2 ARG A 68 15.787 13.865 23.293 1.00 13.47 N +ATOM 545 N THR A 69 13.937 13.376 31.145 1.00 12.12 N +ATOM 546 CA THR A 69 13.674 14.782 31.586 1.00 17.22 C +ATOM 547 C THR A 69 13.372 14.770 33.144 1.00 15.41 C +ATOM 548 O THR A 69 12.260 14.526 33.618 1.00 19.26 O +ATOM 549 CB THR A 69 12.464 15.410 30.798 1.00 12.81 C +ATOM 550 OG1 THR A 69 12.589 15.107 29.412 1.00 17.25 O +ATOM 551 CG2 THR A 69 12.392 16.932 30.990 1.00 8.98 C +ATOM 552 N PRO A 70 14.431 14.960 33.874 1.00 30.00 N +ATOM 553 CA PRO A 70 14.563 14.964 35.315 1.00 31.13 C +ATOM 554 C PRO A 70 13.654 16.003 35.904 1.00 43.01 C +ATOM 555 O PRO A 70 13.699 17.188 35.594 1.00 37.19 O +ATOM 556 CB PRO A 70 16.056 15.221 35.541 1.00 43.11 C +ATOM 557 CG PRO A 70 16.728 15.203 34.148 1.00 49.23 C +ATOM 558 CD PRO A 70 15.635 15.319 33.119 1.00 44.60 C +ATOM 559 N GLY A 71 12.698 15.573 36.672 1.00 29.79 N +ATOM 560 CA GLY A 71 11.785 16.609 37.130 1.00 38.84 C +ATOM 561 C GLY A 71 10.547 16.728 36.220 1.00 34.52 C +ATOM 562 O GLY A 71 9.750 17.644 36.328 1.00 53.49 O +ATOM 563 N SER A 72 10.339 15.797 35.324 1.00 30.26 N +ATOM 564 CA SER A 72 9.157 15.860 34.502 1.00 32.28 C +ATOM 565 C SER A 72 7.906 15.615 35.374 1.00 22.29 C +ATOM 566 O SER A 72 7.914 14.715 36.197 1.00 26.48 O +ATOM 567 CB SER A 72 9.249 14.700 33.473 1.00 31.83 C +ATOM 568 OG SER A 72 8.038 14.552 32.612 1.00 33.11 O +ATOM 569 N ARG A 73 6.801 16.311 35.113 1.00 20.31 N +ATOM 570 CA ARG A 73 5.550 16.055 35.819 1.00 12.77 C +ATOM 571 C ARG A 73 4.564 15.081 35.174 1.00 35.87 C +ATOM 572 O ARG A 73 3.662 14.597 35.845 1.00 50.20 O +ATOM 573 CB ARG A 73 4.830 17.322 36.128 1.00 19.66 C +ATOM 574 CG ARG A 73 5.605 18.165 37.124 1.00 35.18 C +ATOM 575 CD ARG A 73 4.864 19.471 37.396 1.00 86.10 C +ATOM 576 NE ARG A 73 4.736 19.744 38.823 1.00 80.19 N +ATOM 577 CZ ARG A 73 4.227 20.854 39.398 1.00 81.09 C +ATOM 578 NH1 ARG A 73 3.742 21.891 38.705 1.00 81.15 N +ATOM 579 NH2 ARG A 73 4.215 20.930 40.739 1.00 71.03 N +ATOM 580 N ASN A 74 4.668 14.781 33.896 1.00 18.76 N +ATOM 581 CA ASN A 74 3.715 13.833 33.313 1.00 10.40 C +ATOM 582 C ASN A 74 2.194 14.147 33.501 1.00 8.97 C +ATOM 583 O ASN A 74 1.355 13.278 33.697 1.00 15.29 O +ATOM 584 CB ASN A 74 4.053 12.334 33.426 1.00 16.10 C +ATOM 585 CG ASN A 74 3.479 11.413 32.309 1.00 15.75 C +ATOM 586 OD1 ASN A 74 2.928 11.864 31.297 1.00 22.77 O +ATOM 587 ND2 ASN A 74 3.593 10.101 32.490 1.00 17.62 N +ATOM 588 N LEU A 75 1.851 15.405 33.334 1.00 13.92 N +ATOM 589 CA LEU A 75 0.471 15.774 33.458 1.00 16.58 C +ATOM 590 C LEU A 75 -0.505 15.089 32.565 1.00 21.84 C +ATOM 591 O LEU A 75 -1.654 14.976 32.957 1.00 22.99 O +ATOM 592 CB LEU A 75 0.245 17.277 33.466 1.00 17.10 C +ATOM 593 CG LEU A 75 0.919 17.845 34.715 1.00 30.53 C +ATOM 594 CD1 LEU A 75 0.889 19.358 34.725 1.00 35.25 C +ATOM 595 CD2 LEU A 75 0.238 17.306 35.969 1.00 21.06 C +ATOM 596 N CYS A 76 -0.146 14.663 31.359 1.00 18.42 N +ATOM 597 CA CYS A 76 -1.153 13.970 30.513 1.00 10.67 C +ATOM 598 C CYS A 76 -1.137 12.463 30.738 1.00 12.68 C +ATOM 599 O CYS A 76 -1.935 11.725 30.131 1.00 17.21 O +ATOM 600 CB CYS A 76 -1.094 14.295 28.984 1.00 9.97 C +ATOM 601 SG CYS A 76 -1.329 16.050 28.713 1.00 13.70 S +ATOM 602 N ASN A 77 -0.194 12.038 31.586 1.00 14.93 N +ATOM 603 CA ASN A 77 -0.117 10.607 31.926 1.00 19.18 C +ATOM 604 C ASN A 77 0.099 9.697 30.747 1.00 21.40 C +ATOM 605 O ASN A 77 -0.626 8.715 30.538 1.00 17.53 O +ATOM 606 CB ASN A 77 -1.421 10.174 32.620 1.00 36.06 C +ATOM 607 CG ASN A 77 -1.361 8.783 33.215 1.00 80.95 C +ATOM 608 OD1 ASN A 77 -2.358 8.042 33.188 1.00 78.33 O +ATOM 609 ND2 ASN A 77 -0.186 8.412 33.715 1.00 38.97 N +ATOM 610 N ILE A 78 1.114 10.006 29.979 1.00 14.33 N +ATOM 611 CA ILE A 78 1.373 9.191 28.838 1.00 11.33 C +ATOM 612 C ILE A 78 2.873 9.258 28.499 1.00 13.41 C +ATOM 613 O ILE A 78 3.568 10.265 28.718 1.00 12.78 O +ATOM 614 CB ILE A 78 0.764 9.855 27.598 1.00 15.98 C +ATOM 615 CG1 ILE A 78 0.764 11.376 27.743 1.00 20.19 C +ATOM 616 CG2 ILE A 78 -0.461 9.195 26.985 1.00 25.51 C +ATOM 617 CD1 ILE A 78 0.735 12.094 26.406 1.00 31.88 C +ATOM 618 N PRO A 79 3.343 8.210 27.843 1.00 14.97 N +ATOM 619 CA PRO A 79 4.715 8.229 27.362 1.00 12.65 C +ATOM 620 C PRO A 79 4.738 9.234 26.187 1.00 10.18 C +ATOM 621 O PRO A 79 3.762 9.304 25.359 1.00 11.71 O +ATOM 622 CB PRO A 79 4.962 6.830 26.843 1.00 11.25 C +ATOM 623 CG PRO A 79 3.631 6.096 26.844 1.00 17.21 C +ATOM 624 CD PRO A 79 2.621 6.951 27.581 1.00 9.85 C +ATOM 625 N CYS A 80 5.798 10.020 26.078 1.00 11.09 N +ATOM 626 CA CYS A 80 5.870 11.003 24.969 1.00 5.24 C +ATOM 627 C CYS A 80 5.782 10.359 23.546 1.00 8.89 C +ATOM 628 O CYS A 80 5.284 10.950 22.568 1.00 11.52 O +ATOM 629 CB CYS A 80 7.126 11.894 25.061 1.00 7.40 C +ATOM 630 SG CYS A 80 7.251 12.847 26.592 1.00 9.47 S +ATOM 631 N SER A 81 6.259 9.115 23.442 1.00 9.85 N +ATOM 632 CA SER A 81 6.242 8.432 22.154 1.00 7.67 C +ATOM 633 C SER A 81 4.815 8.223 21.687 1.00 15.55 C +ATOM 634 O SER A 81 4.554 8.156 20.510 1.00 15.82 O +ATOM 635 CB SER A 81 6.995 7.111 22.234 1.00 15.31 C +ATOM 636 OG SER A 81 6.295 6.245 23.119 1.00 17.97 O +ATOM 637 N ALA A 82 3.857 8.169 22.598 1.00 11.39 N +ATOM 638 CA ALA A 82 2.452 8.033 22.185 1.00 14.65 C +ATOM 639 C ALA A 82 2.000 9.216 21.325 1.00 20.26 C +ATOM 640 O ALA A 82 1.033 9.113 20.571 1.00 22.13 O +ATOM 641 CB ALA A 82 1.481 8.009 23.384 1.00 17.51 C +ATOM 642 N LEU A 83 2.659 10.349 21.528 1.00 9.56 N +ATOM 643 CA LEU A 83 2.329 11.589 20.867 1.00 12.01 C +ATOM 644 C LEU A 83 2.834 11.627 19.385 1.00 18.14 C +ATOM 645 O LEU A 83 2.626 12.620 18.685 1.00 12.31 O +ATOM 646 CB LEU A 83 2.986 12.761 21.651 1.00 15.90 C +ATOM 647 CG LEU A 83 2.370 12.966 23.055 1.00 9.43 C +ATOM 648 CD1 LEU A 83 3.076 14.069 23.849 1.00 12.61 C +ATOM 649 CD2 LEU A 83 0.843 13.174 22.965 1.00 15.37 C +ATOM 650 N LEU A 84 3.542 10.556 18.940 1.00 13.34 N +ATOM 651 CA LEU A 84 4.131 10.512 17.618 1.00 11.55 C +ATOM 652 C LEU A 84 3.361 9.657 16.630 1.00 16.60 C +ATOM 653 O LEU A 84 3.704 9.570 15.475 1.00 22.63 O +ATOM 654 CB LEU A 84 5.630 10.044 17.645 1.00 7.92 C +ATOM 655 CG LEU A 84 6.546 10.859 18.552 1.00 18.00 C +ATOM 656 CD1 LEU A 84 7.978 10.414 18.359 1.00 17.76 C +ATOM 657 CD2 LEU A 84 6.513 12.306 18.116 1.00 8.41 C +ATOM 658 N SER A 85 2.332 9.023 17.096 1.00 15.68 N +ATOM 659 CA SER A 85 1.485 8.148 16.333 1.00 22.63 C +ATOM 660 C SER A 85 0.792 8.827 15.194 1.00 14.76 C +ATOM 661 O SER A 85 0.519 10.007 15.280 1.00 16.99 O +ATOM 662 CB SER A 85 0.376 7.776 17.295 1.00 16.59 C +ATOM 663 OG SER A 85 -0.373 6.761 16.741 1.00 23.89 O +ATOM 664 N SER A 86 0.371 8.039 14.186 1.00 19.04 N +ATOM 665 CA SER A 86 -0.430 8.505 13.025 1.00 17.09 C +ATOM 666 C SER A 86 -1.827 8.884 13.487 1.00 21.77 C +ATOM 667 O SER A 86 -2.481 9.696 12.857 1.00 24.42 O +ATOM 668 CB SER A 86 -0.584 7.358 12.026 1.00 21.75 C +ATOM 669 OG SER A 86 0.687 7.146 11.467 1.00 50.53 O +ATOM 670 N ASP A 87 -2.288 8.227 14.575 1.00 13.55 N +ATOM 671 CA ASP A 87 -3.611 8.483 15.195 1.00 14.83 C +ATOM 672 C ASP A 87 -3.426 9.673 16.162 1.00 16.43 C +ATOM 673 O ASP A 87 -2.640 9.585 17.147 1.00 17.32 O +ATOM 674 CB ASP A 87 -4.025 7.244 15.987 1.00 17.38 C +ATOM 675 CG ASP A 87 -5.365 7.435 16.676 1.00 36.42 C +ATOM 676 OD1 ASP A 87 -5.875 8.512 16.868 1.00 21.05 O +ATOM 677 OD2 ASP A 87 -5.952 6.315 17.005 1.00 56.25 O +ATOM 678 N ILE A 88 -4.037 10.803 15.879 1.00 12.05 N +ATOM 679 CA ILE A 88 -3.749 11.974 16.722 1.00 17.85 C +ATOM 680 C ILE A 88 -4.490 12.067 18.055 1.00 12.40 C +ATOM 681 O ILE A 88 -4.393 13.081 18.780 1.00 11.64 O +ATOM 682 CB ILE A 88 -4.014 13.293 15.954 1.00 16.92 C +ATOM 683 CG1 ILE A 88 -5.565 13.392 15.634 1.00 15.36 C +ATOM 684 CG2 ILE A 88 -3.104 13.384 14.694 1.00 18.11 C +ATOM 685 CD1 ILE A 88 -6.065 14.738 15.196 1.00 20.80 C +ATOM 686 N THR A 89 -5.257 11.069 18.381 1.00 13.72 N +ATOM 687 CA THR A 89 -6.058 11.103 19.584 1.00 12.45 C +ATOM 688 C THR A 89 -5.326 11.520 20.907 1.00 8.02 C +ATOM 689 O THR A 89 -5.777 12.403 21.614 1.00 14.43 O +ATOM 690 CB THR A 89 -6.717 9.735 19.716 1.00 18.11 C +ATOM 691 OG1 THR A 89 -7.492 9.539 18.564 1.00 18.36 O +ATOM 692 CG2 THR A 89 -7.642 9.724 20.953 1.00 16.37 C +ATOM 693 N ALA A 90 -4.186 10.900 21.216 1.00 10.40 N +ATOM 694 CA ALA A 90 -3.483 11.250 22.444 1.00 14.23 C +ATOM 695 C ALA A 90 -2.971 12.685 22.412 1.00 17.47 C +ATOM 696 O ALA A 90 -2.981 13.344 23.413 1.00 10.92 O +ATOM 697 CB ALA A 90 -2.331 10.290 22.751 1.00 15.55 C +ATOM 698 N SER A 91 -2.504 13.185 21.257 1.00 8.67 N +ATOM 699 CA SER A 91 -2.032 14.567 21.163 1.00 7.03 C +ATOM 700 C SER A 91 -3.155 15.522 21.418 1.00 6.83 C +ATOM 701 O SER A 91 -3.033 16.547 22.059 1.00 13.20 O +ATOM 702 CB SER A 91 -1.445 14.870 19.783 1.00 7.71 C +ATOM 703 OG SER A 91 -0.111 14.402 19.670 1.00 11.50 O +ATOM 704 N VAL A 92 -4.289 15.234 20.839 1.00 9.57 N +ATOM 705 CA VAL A 92 -5.449 16.101 21.004 1.00 7.79 C +ATOM 706 C VAL A 92 -5.938 16.148 22.488 1.00 10.65 C +ATOM 707 O VAL A 92 -6.254 17.195 23.018 1.00 12.26 O +ATOM 708 CB VAL A 92 -6.523 15.597 19.994 1.00 23.58 C +ATOM 709 CG1 VAL A 92 -7.936 16.117 20.303 1.00 19.93 C +ATOM 710 CG2 VAL A 92 -6.110 15.987 18.555 1.00 17.17 C +ATOM 711 N ASN A 93 -6.047 14.973 23.140 1.00 10.03 N +ATOM 712 CA ASN A 93 -6.511 14.862 24.536 1.00 24.44 C +ATOM 713 C ASN A 93 -5.602 15.647 25.472 1.00 10.79 C +ATOM 714 O ASN A 93 -6.049 16.390 26.310 1.00 15.54 O +ATOM 715 CB ASN A 93 -6.580 13.395 24.989 1.00 13.16 C +ATOM 716 CG ASN A 93 -7.781 12.668 24.406 1.00 15.37 C +ATOM 717 OD1 ASN A 93 -7.842 11.422 24.426 1.00 35.75 O +ATOM 718 ND2 ASN A 93 -8.682 13.436 23.835 1.00 16.65 N +ATOM 719 N CYS A 94 -4.284 15.477 25.249 1.00 10.49 N +ATOM 720 CA CYS A 94 -3.267 16.178 25.984 1.00 7.62 C +ATOM 721 C CYS A 94 -3.353 17.649 25.690 1.00 17.58 C +ATOM 722 O CYS A 94 -3.298 18.462 26.598 1.00 9.76 O +ATOM 723 CB CYS A 94 -1.875 15.620 25.709 1.00 5.33 C +ATOM 724 SG CYS A 94 -0.613 16.312 26.762 1.00 13.87 S +ATOM 725 N ALA A 95 -3.546 18.041 24.407 1.00 7.01 N +ATOM 726 CA ALA A 95 -3.656 19.481 24.142 1.00 8.80 C +ATOM 727 C ALA A 95 -4.864 20.156 24.849 1.00 8.68 C +ATOM 728 O ALA A 95 -4.867 21.353 25.215 1.00 11.44 O +ATOM 729 CB ALA A 95 -3.774 19.698 22.627 1.00 6.34 C +ATOM 730 N LYS A 96 -5.932 19.405 24.966 1.00 9.62 N +ATOM 731 CA LYS A 96 -7.108 19.927 25.596 1.00 9.41 C +ATOM 732 C LYS A 96 -6.804 20.229 27.091 1.00 11.43 C +ATOM 733 O LYS A 96 -7.271 21.199 27.627 1.00 15.34 O +ATOM 734 CB LYS A 96 -8.195 18.868 25.472 1.00 12.74 C +ATOM 735 CG LYS A 96 -8.927 18.820 24.137 1.00 9.62 C +ATOM 736 CD LYS A 96 -9.976 17.699 24.147 1.00 14.08 C +ATOM 737 CE LYS A 96 -10.973 17.784 22.960 1.00 16.34 C +ATOM 738 NZ LYS A 96 -11.641 16.485 22.720 1.00 20.55 N +ATOM 739 N LYS A 97 -5.944 19.447 27.750 1.00 13.54 N +ATOM 740 CA LYS A 97 -5.538 19.706 29.158 1.00 14.41 C +ATOM 741 C LYS A 97 -4.672 20.981 29.209 1.00 13.37 C +ATOM 742 O LYS A 97 -4.809 21.878 30.014 1.00 13.38 O +ATOM 743 CB LYS A 97 -4.710 18.544 29.689 1.00 10.77 C +ATOM 744 CG LYS A 97 -5.493 17.342 30.140 1.00 32.04 C +ATOM 745 CD LYS A 97 -6.434 17.637 31.297 1.00 45.76 C +ATOM 746 CE LYS A 97 -7.073 16.369 31.886 1.00 70.47 C +ATOM 747 NZ LYS A 97 -8.523 16.232 31.620 1.00 59.21 N +ATOM 748 N ILE A 98 -3.760 21.072 28.264 1.00 12.65 N +ATOM 749 CA ILE A 98 -2.856 22.204 28.161 1.00 10.78 C +ATOM 750 C ILE A 98 -3.607 23.536 27.991 1.00 8.94 C +ATOM 751 O ILE A 98 -3.322 24.532 28.701 1.00 12.98 O +ATOM 752 CB ILE A 98 -1.778 22.026 27.022 1.00 17.91 C +ATOM 753 CG1 ILE A 98 -0.899 20.798 27.234 1.00 15.21 C +ATOM 754 CG2 ILE A 98 -0.932 23.292 26.811 1.00 10.73 C +ATOM 755 CD1 ILE A 98 -0.035 20.440 26.059 1.00 5.59 C +ATOM 756 N VAL A 99 -4.497 23.570 26.973 1.00 12.61 N +ATOM 757 CA VAL A 99 -5.194 24.822 26.643 1.00 14.92 C +ATOM 758 C VAL A 99 -6.158 25.244 27.757 1.00 17.60 C +ATOM 759 O VAL A 99 -6.529 26.431 27.844 1.00 21.46 O +ATOM 760 CB VAL A 99 -5.863 24.788 25.223 1.00 7.93 C +ATOM 761 CG1 VAL A 99 -7.102 23.930 25.230 1.00 13.13 C +ATOM 762 CG2 VAL A 99 -6.203 26.159 24.648 1.00 14.05 C +ATOM 763 N SER A 100 -6.529 24.274 28.623 1.00 14.94 N +ATOM 764 CA SER A 100 -7.469 24.559 29.728 1.00 23.99 C +ATOM 765 C SER A 100 -6.810 25.233 30.952 1.00 23.57 C +ATOM 766 O SER A 100 -7.460 25.872 31.759 1.00 30.51 O +ATOM 767 CB SER A 100 -8.109 23.250 30.148 1.00 15.96 C +ATOM 768 OG SER A 100 -9.019 22.837 29.120 1.00 33.46 O +ATOM 769 N ASP A 101 -5.495 25.061 30.981 1.00 27.50 N +ATOM 770 CA ASP A 101 -4.485 25.414 31.955 1.00 38.61 C +ATOM 771 C ASP A 101 -4.239 26.879 32.265 1.00 31.46 C +ATOM 772 O ASP A 101 -3.422 27.194 33.137 1.00 49.53 O +ATOM 773 CB ASP A 101 -3.173 24.648 31.624 1.00 32.62 C +ATOM 774 CG ASP A 101 -2.133 24.566 32.715 1.00 66.21 C +ATOM 775 OD1 ASP A 101 -2.482 23.821 33.747 1.00 53.53 O +ATOM 776 OD2 ASP A 101 -1.045 25.095 32.609 1.00 62.33 O +ATOM 777 N GLY A 102 -4.876 27.820 31.617 1.00 31.57 N +ATOM 778 CA GLY A 102 -4.525 29.170 32.093 1.00 42.83 C +ATOM 779 C GLY A 102 -4.082 30.192 31.049 1.00 56.99 C +ATOM 780 O GLY A 102 -4.713 31.264 30.990 1.00 31.68 O +ATOM 781 N ASN A 103 -2.979 29.915 30.284 1.00 23.55 N +ATOM 782 CA ASN A 103 -2.573 30.864 29.246 1.00 11.97 C +ATOM 783 C ASN A 103 -3.176 30.497 27.876 1.00 9.86 C +ATOM 784 O ASN A 103 -2.905 31.106 26.860 1.00 13.84 O +ATOM 785 CB ASN A 103 -1.070 31.114 29.177 1.00 17.92 C +ATOM 786 CG ASN A 103 -0.638 31.476 30.587 1.00 65.73 C +ATOM 787 OD1 ASN A 103 0.384 30.993 31.105 1.00 74.71 O +ATOM 788 ND2 ASN A 103 -1.509 32.224 31.271 1.00 54.30 N +ATOM 789 N GLY A 104 -4.070 29.522 27.865 1.00 10.94 N +ATOM 790 CA GLY A 104 -4.733 29.138 26.601 1.00 18.78 C +ATOM 791 C GLY A 104 -3.725 28.668 25.570 1.00 8.28 C +ATOM 792 O GLY A 104 -2.766 27.947 25.892 1.00 12.01 O +ATOM 793 N MET A 105 -3.906 29.119 24.313 1.00 13.56 N +ATOM 794 CA MET A 105 -3.014 28.684 23.198 1.00 9.18 C +ATOM 795 C MET A 105 -1.637 29.372 23.232 1.00 8.69 C +ATOM 796 O MET A 105 -0.727 29.013 22.506 1.00 9.67 O +ATOM 797 CB MET A 105 -3.739 28.882 21.838 1.00 3.51 C +ATOM 798 CG MET A 105 -4.790 27.788 21.646 1.00 9.82 C +ATOM 799 SD MET A 105 -5.184 27.455 19.852 1.00 12.90 S +ATOM 800 CE MET A 105 -3.617 26.757 19.326 1.00 6.80 C +ATOM 801 N ASN A 106 -1.509 30.373 24.105 1.00 7.08 N +ATOM 802 CA ASN A 106 -0.270 31.037 24.269 1.00 4.32 C +ATOM 803 C ASN A 106 0.809 30.046 24.765 1.00 8.04 C +ATOM 804 O ASN A 106 2.030 30.336 24.608 1.00 11.37 O +ATOM 805 CB ASN A 106 -0.396 32.190 25.241 1.00 12.62 C +ATOM 806 CG ASN A 106 -1.239 33.309 24.682 1.00 16.51 C +ATOM 807 OD1 ASN A 106 -0.864 33.972 23.658 1.00 9.88 O +ATOM 808 ND2 ASN A 106 -2.372 33.492 25.355 1.00 15.30 N +ATOM 809 N ALA A 107 0.360 28.870 25.250 1.00 8.10 N +ATOM 810 CA ALA A 107 1.308 27.840 25.625 1.00 10.48 C +ATOM 811 C ALA A 107 2.113 27.450 24.395 1.00 16.77 C +ATOM 812 O ALA A 107 3.191 26.948 24.511 1.00 16.10 O +ATOM 813 CB ALA A 107 0.585 26.599 26.143 1.00 11.40 C +ATOM 814 N TRP A 108 1.577 27.639 23.205 1.00 10.51 N +ATOM 815 CA TRP A 108 2.303 27.285 21.966 1.00 9.27 C +ATOM 816 C TRP A 108 2.970 28.504 21.404 1.00 9.11 C +ATOM 817 O TRP A 108 2.312 29.428 20.865 1.00 9.30 O +ATOM 818 CB TRP A 108 1.398 26.569 20.912 1.00 4.39 C +ATOM 819 CG TRP A 108 1.005 25.176 21.256 1.00 2.06 C +ATOM 820 CD1 TRP A 108 1.760 24.069 21.021 1.00 10.56 C +ATOM 821 CD2 TRP A 108 -0.146 24.722 21.926 1.00 4.61 C +ATOM 822 NE1 TRP A 108 1.131 22.972 21.471 1.00 11.23 N +ATOM 823 CE2 TRP A 108 -0.048 23.321 22.045 1.00 11.25 C +ATOM 824 CE3 TRP A 108 -1.256 25.348 22.436 1.00 8.16 C +ATOM 825 CZ2 TRP A 108 -1.038 22.520 22.626 1.00 7.13 C +ATOM 826 CZ3 TRP A 108 -2.220 24.549 23.074 1.00 13.29 C +ATOM 827 CH2 TRP A 108 -2.156 23.123 23.101 1.00 8.74 C +ATOM 828 N VAL A 109 4.320 28.523 21.508 1.00 10.59 N +ATOM 829 CA VAL A 109 5.046 29.672 21.044 1.00 10.72 C +ATOM 830 C VAL A 109 4.800 30.025 19.545 1.00 7.07 C +ATOM 831 O VAL A 109 4.617 31.199 19.228 1.00 12.32 O +ATOM 832 CB VAL A 109 6.549 29.491 21.342 1.00 15.75 C +ATOM 833 CG1 VAL A 109 7.068 28.242 20.605 1.00 38.18 C +ATOM 834 CG2 VAL A 109 7.327 30.751 20.898 1.00 17.01 C +ATOM 835 N ALA A 110 4.761 28.998 18.662 1.00 7.28 N +ATOM 836 CA ALA A 110 4.506 29.281 17.232 1.00 14.92 C +ATOM 837 C ALA A 110 3.122 29.845 17.031 1.00 12.74 C +ATOM 838 O ALA A 110 2.902 30.659 16.125 1.00 13.19 O +ATOM 839 CB ALA A 110 4.783 28.117 16.262 1.00 12.16 C +ATOM 840 N TRP A 111 2.190 29.398 17.892 1.00 7.58 N +ATOM 841 CA TRP A 111 0.821 29.901 17.789 1.00 5.91 C +ATOM 842 C TRP A 111 0.815 31.399 18.100 1.00 9.06 C +ATOM 843 O TRP A 111 0.249 32.308 17.369 1.00 6.22 O +ATOM 844 CB TRP A 111 -0.240 29.136 18.618 1.00 6.54 C +ATOM 845 CG TRP A 111 -1.589 29.763 18.461 1.00 9.13 C +ATOM 846 CD1 TRP A 111 -2.510 29.517 17.447 1.00 5.89 C +ATOM 847 CD2 TRP A 111 -2.190 30.781 19.295 1.00 10.48 C +ATOM 848 NE1 TRP A 111 -3.642 30.322 17.597 1.00 5.88 N +ATOM 849 CE2 TRP A 111 -3.471 31.090 18.728 1.00 5.72 C +ATOM 850 CE3 TRP A 111 -1.805 31.432 20.511 1.00 4.95 C +ATOM 851 CZ2 TRP A 111 -4.306 32.057 19.314 1.00 13.37 C +ATOM 852 CZ3 TRP A 111 -2.658 32.382 21.061 1.00 6.90 C +ATOM 853 CH2 TRP A 111 -3.906 32.666 20.489 1.00 4.12 C +ATOM 854 N ARG A 112 1.497 31.701 19.218 1.00 7.90 N +ATOM 855 CA ARG A 112 1.527 33.107 19.659 1.00 11.81 C +ATOM 856 C ARG A 112 2.221 34.013 18.630 1.00 9.34 C +ATOM 857 O ARG A 112 1.746 35.118 18.330 1.00 9.72 O +ATOM 858 CB ARG A 112 2.215 33.175 21.040 1.00 18.21 C +ATOM 859 CG ARG A 112 2.053 34.513 21.722 1.00 52.15 C +ATOM 860 CD ARG A 112 2.813 34.593 23.056 1.00 27.12 C +ATOM 861 NE ARG A 112 3.479 33.351 23.413 1.00 52.40 N +ATOM 862 CZ ARG A 112 4.785 33.247 23.639 1.00 49.41 C +ATOM 863 NH1 ARG A 112 5.612 34.286 23.535 1.00 53.98 N +ATOM 864 NH2 ARG A 112 5.274 32.058 23.981 1.00 51.24 N +ATOM 865 N ASN A 113 3.331 33.501 18.078 1.00 8.96 N +ATOM 866 CA ASN A 113 4.132 34.283 17.152 1.00 15.60 C +ATOM 867 C ASN A 113 3.657 34.303 15.695 1.00 17.72 C +ATOM 868 O ASN A 113 3.919 35.261 14.974 1.00 16.73 O +ATOM 869 CB ASN A 113 5.657 33.938 17.244 1.00 8.06 C +ATOM 870 CG ASN A 113 6.192 34.297 18.636 1.00 11.97 C +ATOM 871 OD1 ASN A 113 5.714 35.228 19.278 1.00 19.44 O +ATOM 872 ND2 ASN A 113 7.179 33.595 19.091 1.00 9.04 N +ATOM 873 N ARG A 114 2.964 33.273 15.287 1.00 7.06 N +ATOM 874 CA ARG A 114 2.604 33.129 13.873 1.00 11.57 C +ATOM 875 C ARG A 114 1.171 33.002 13.552 1.00 19.78 C +ATOM 876 O ARG A 114 0.827 33.118 12.375 1.00 14.27 O +ATOM 877 CB ARG A 114 3.309 31.830 13.395 1.00 8.51 C +ATOM 878 CG ARG A 114 4.766 31.877 13.898 1.00 21.43 C +ATOM 879 CD ARG A 114 5.833 31.132 13.125 1.00 27.54 C +ATOM 880 NE ARG A 114 5.898 31.278 11.660 1.00 16.59 N +ATOM 881 CZ ARG A 114 6.631 30.413 10.970 1.00 12.23 C +ATOM 882 NH1 ARG A 114 7.271 29.439 11.649 1.00 11.43 N +ATOM 883 NH2 ARG A 114 6.744 30.477 9.659 1.00 12.83 N +ATOM 884 N CYS A 115 0.351 32.723 14.572 1.00 5.86 N +ATOM 885 CA CYS A 115 -1.055 32.487 14.333 1.00 8.05 C +ATOM 886 C CYS A 115 -1.937 33.541 14.914 1.00 18.18 C +ATOM 887 O CYS A 115 -2.914 34.024 14.264 1.00 11.36 O +ATOM 888 CB CYS A 115 -1.488 31.114 14.872 1.00 7.31 C +ATOM 889 SG CYS A 115 -0.553 29.849 14.022 1.00 10.81 S +ATOM 890 N LYS A 116 -1.630 33.796 16.196 1.00 10.46 N +ATOM 891 CA LYS A 116 -2.372 34.723 16.976 1.00 9.75 C +ATOM 892 C LYS A 116 -2.562 36.032 16.228 1.00 9.63 C +ATOM 893 O LYS A 116 -1.583 36.599 15.729 1.00 13.85 O +ATOM 894 CB LYS A 116 -1.716 34.948 18.335 1.00 12.72 C +ATOM 895 CG LYS A 116 -2.557 35.791 19.284 1.00 7.87 C +ATOM 896 CD LYS A 116 -1.809 35.938 20.635 1.00 15.62 C +ATOM 897 CE LYS A 116 -2.607 36.597 21.773 1.00 17.04 C +ATOM 898 NZ LYS A 116 -1.889 36.524 23.073 1.00 11.32 N +ATOM 899 N GLY A 117 -3.862 36.462 16.131 1.00 9.19 N +ATOM 900 CA GLY A 117 -4.213 37.737 15.493 1.00 22.87 C +ATOM 901 C GLY A 117 -4.091 37.759 13.972 1.00 33.97 C +ATOM 902 O GLY A 117 -4.044 38.799 13.371 1.00 28.79 O +ATOM 903 N THR A 118 -4.019 36.612 13.340 1.00 15.57 N +ATOM 904 CA THR A 118 -3.940 36.537 11.885 1.00 20.24 C +ATOM 905 C THR A 118 -5.285 35.977 11.407 1.00 18.25 C +ATOM 906 O THR A 118 -6.080 35.563 12.249 1.00 18.09 O +ATOM 907 CB THR A 118 -2.747 35.680 11.439 1.00 13.62 C +ATOM 908 OG1 THR A 118 -3.060 34.321 11.639 1.00 12.88 O +ATOM 909 CG2 THR A 118 -1.455 36.072 12.193 1.00 12.89 C +ATOM 910 N ASP A 119 -5.573 35.973 10.102 1.00 20.97 N +ATOM 911 CA ASP A 119 -6.848 35.408 9.620 1.00 17.43 C +ATOM 912 C ASP A 119 -6.693 33.892 9.567 1.00 19.50 C +ATOM 913 O ASP A 119 -6.430 33.280 8.509 1.00 24.87 O +ATOM 914 CB ASP A 119 -7.228 35.933 8.234 1.00 27.62 C +ATOM 915 CG ASP A 119 -8.359 35.154 7.625 1.00 57.62 C +ATOM 916 OD1 ASP A 119 -9.168 34.529 8.288 1.00 36.72 O +ATOM 917 OD2 ASP A 119 -8.349 35.190 6.315 1.00 41.26 O +ATOM 918 N VAL A 120 -6.836 33.291 10.750 1.00 20.10 N +ATOM 919 CA VAL A 120 -6.637 31.835 10.895 1.00 24.77 C +ATOM 920 C VAL A 120 -7.664 31.011 10.149 1.00 16.15 C +ATOM 921 O VAL A 120 -7.486 29.777 9.914 1.00 13.85 O +ATOM 922 CB VAL A 120 -6.476 31.372 12.367 1.00 15.61 C +ATOM 923 CG1 VAL A 120 -5.271 32.055 13.060 1.00 17.17 C +ATOM 924 CG2 VAL A 120 -7.761 31.691 13.097 1.00 18.96 C +ATOM 925 N GLN A 121 -8.761 31.679 9.776 1.00 18.05 N +ATOM 926 CA GLN A 121 -9.808 30.981 9.039 1.00 20.34 C +ATOM 927 C GLN A 121 -9.285 30.499 7.694 1.00 14.19 C +ATOM 928 O GLN A 121 -9.831 29.566 7.093 1.00 15.61 O +ATOM 929 CB GLN A 121 -10.896 31.993 8.746 1.00 39.58 C +ATOM 930 CG GLN A 121 -12.076 31.743 9.628 1.00 39.30 C +ATOM 931 CD GLN A 121 -13.286 31.887 8.785 1.00 58.93 C +ATOM 932 OE1 GLN A 121 -13.734 30.908 8.174 1.00 64.91 O +ATOM 933 NE2 GLN A 121 -13.757 33.131 8.683 1.00 55.29 N +ATOM 934 N ALA A 122 -8.222 31.161 7.229 1.00 14.53 N +ATOM 935 CA ALA A 122 -7.588 30.777 5.964 1.00 13.31 C +ATOM 936 C ALA A 122 -7.152 29.312 5.955 1.00 18.32 C +ATOM 937 O ALA A 122 -7.123 28.622 4.924 1.00 14.96 O +ATOM 938 CB ALA A 122 -6.378 31.657 5.724 1.00 18.92 C +ATOM 939 N TRP A 123 -6.792 28.829 7.138 1.00 14.16 N +ATOM 940 CA TRP A 123 -6.304 27.460 7.305 1.00 21.27 C +ATOM 941 C TRP A 123 -7.326 26.369 7.031 1.00 12.05 C +ATOM 942 O TRP A 123 -6.976 25.209 6.736 1.00 15.94 O +ATOM 943 CB TRP A 123 -5.545 27.274 8.649 1.00 14.43 C +ATOM 944 CG TRP A 123 -4.302 28.098 8.663 1.00 16.32 C +ATOM 945 CD1 TRP A 123 -4.115 29.310 9.238 1.00 16.23 C +ATOM 946 CD2 TRP A 123 -3.066 27.733 8.045 1.00 6.26 C +ATOM 947 NE1 TRP A 123 -2.826 29.737 8.996 1.00 13.70 N +ATOM 948 CE2 TRP A 123 -2.184 28.799 8.248 1.00 10.20 C +ATOM 949 CE3 TRP A 123 -2.680 26.618 7.323 1.00 14.76 C +ATOM 950 CZ2 TRP A 123 -0.873 28.742 7.761 1.00 21.80 C +ATOM 951 CZ3 TRP A 123 -1.413 26.574 6.804 1.00 21.47 C +ATOM 952 CH2 TRP A 123 -0.520 27.623 7.023 1.00 22.40 C +ATOM 953 N ILE A 124 -8.590 26.696 7.126 1.00 10.36 N +ATOM 954 CA ILE A 124 -9.573 25.659 6.831 1.00 14.89 C +ATOM 955 C ILE A 124 -10.353 25.927 5.530 1.00 16.52 C +ATOM 956 O ILE A 124 -11.277 25.213 5.172 1.00 16.40 O +ATOM 957 CB ILE A 124 -10.480 25.421 8.019 1.00 15.33 C +ATOM 958 CG1 ILE A 124 -11.016 26.778 8.456 1.00 15.55 C +ATOM 959 CG2 ILE A 124 -9.624 24.846 9.164 1.00 15.50 C +ATOM 960 CD1 ILE A 124 -12.489 26.742 8.908 1.00 32.95 C +ATOM 961 N ARG A 125 -9.977 27.003 4.848 1.00 17.59 N +ATOM 962 CA ARG A 125 -10.598 27.366 3.586 1.00 26.87 C +ATOM 963 C ARG A 125 -10.424 26.259 2.569 1.00 18.05 C +ATOM 964 O ARG A 125 -9.339 25.658 2.433 1.00 24.03 O +ATOM 965 CB ARG A 125 -10.123 28.708 3.068 1.00 29.23 C +ATOM 966 CG ARG A 125 -10.586 29.089 1.669 1.00 46.98 C +ATOM 967 CD ARG A 125 -10.321 30.571 1.370 1.00 51.79 C +ATOM 968 NE ARG A 125 -8.921 30.857 1.669 1.00 80.40 N +ATOM 969 CZ ARG A 125 -7.924 30.424 0.892 1.00 80.57 C +ATOM 970 NH1 ARG A 125 -8.167 29.752 -0.234 1.00 50.97 N +ATOM 971 NH2 ARG A 125 -6.657 30.677 1.239 1.00 73.99 N +ATOM 972 N GLY A 126 -11.581 25.957 1.917 1.00 23.54 N +ATOM 973 CA GLY A 126 -11.741 24.959 0.858 1.00 15.85 C +ATOM 974 C GLY A 126 -11.903 23.570 1.356 1.00 22.07 C +ATOM 975 O GLY A 126 -11.988 22.638 0.564 1.00 33.97 O +ATOM 976 N CYS A 127 -11.912 23.409 2.685 1.00 12.41 N +ATOM 977 CA CYS A 127 -12.009 22.059 3.164 1.00 10.52 C +ATOM 978 C CYS A 127 -13.442 21.578 3.291 1.00 13.96 C +ATOM 979 O CYS A 127 -14.383 22.316 3.676 1.00 19.22 O +ATOM 980 CB CYS A 127 -11.259 21.795 4.516 1.00 16.08 C +ATOM 981 SG CYS A 127 -9.562 22.365 4.503 1.00 17.92 S +ATOM 982 N ARG A 128 -13.609 20.299 3.023 1.00 19.23 N +ATOM 983 CA ARG A 128 -14.929 19.757 3.200 1.00 29.52 C +ATOM 984 C ARG A 128 -15.116 19.387 4.645 1.00 19.23 C +ATOM 985 O ARG A 128 -14.626 18.345 5.078 1.00 29.24 O +ATOM 986 CB ARG A 128 -15.159 18.511 2.363 1.00 35.15 C +ATOM 987 CG ARG A 128 -16.602 18.043 2.481 1.00 32.92 C +ATOM 988 CD ARG A 128 -16.961 17.187 1.277 1.00 38.70 C +ATOM 989 NE ARG A 128 -15.779 16.498 0.721 1.00 50.55 N +ATOM 990 CZ ARG A 128 -15.503 16.208 -0.581 1.00 55.70 C +ATOM 991 NH1 ARG A 128 -16.293 16.551 -1.610 1.00 46.94 N +ATOM 992 NH2 ARG A 128 -14.377 15.541 -0.856 1.00 48.25 N +ATOM 993 N LEU A 129 -15.775 20.226 5.404 1.00 22.75 N +ATOM 994 CA LEU A 129 -15.976 19.869 6.811 1.00 33.38 C +ATOM 995 C LEU A 129 -17.449 19.906 7.141 1.00 72.70 C +ATOM 996 O LEU A 129 -18.191 20.465 6.277 1.00 49.87 O +ATOM 997 CB LEU A 129 -15.235 20.742 7.845 1.00 23.67 C +ATOM 998 CG LEU A 129 -13.711 20.917 7.641 1.00 28.34 C +ATOM 999 CD1 LEU A 129 -13.308 22.315 8.150 1.00 36.38 C +ATOM 1000 CD2 LEU A 129 -12.970 19.868 8.434 1.00 43.93 C +ATOM 1001 OXT LEU A 129 -17.769 19.416 8.251 1.00 70.56 O +TER 1002 LEU A 129 +HETATM 1003 O HOH A 131 10.467 23.310 29.307 1.00 39.80 O +HETATM 1004 O HOH A 132 -1.176 15.339 1.263 1.00 49.26 O +HETATM 1005 O HOH A 133 -2.951 23.272 0.888 1.00 44.65 O +HETATM 1006 O HOH A 134 1.217 11.752 36.245 1.00 47.43 O +HETATM 1007 O HOH A 135 -5.565 19.565 2.145 1.00 30.47 O +HETATM 1008 O HOH A 136 -8.561 15.857 2.186 1.00 67.45 O +HETATM 1009 O HOH A 137 -11.371 18.534 1.797 1.00 29.55 O +HETATM 1010 O HOH A 138 -5.769 17.371 2.752 1.00 20.51 O +HETATM 1011 O HOH A 139 -1.154 20.600 3.261 1.00 38.26 O +HETATM 1012 O HOH A 140 -14.391 27.317 2.971 1.00 41.99 O +HETATM 1013 O HOH A 141 9.925 21.314 4.349 1.00 72.67 O +HETATM 1014 O HOH A 142 -3.255 29.381 4.245 1.00 58.91 O +HETATM 1015 O HOH A 143 -1.469 12.396 4.494 1.00 45.35 O +HETATM 1016 O HOH A 144 1.369 18.410 4.770 1.00 33.99 O +HETATM 1017 O HOH A 145 -13.995 24.766 5.080 1.00 22.81 O +HETATM 1018 O HOH A 146 -11.877 17.908 5.201 1.00 33.63 O +HETATM 1019 O HOH A 147 3.579 19.755 5.269 1.00 28.71 O +HETATM 1020 O HOH A 148 -0.938 23.757 3.720 1.00 71.21 O +HETATM 1021 O HOH A 149 2.851 10.418 5.675 1.00 22.01 O +HETATM 1022 O HOH A 150 6.153 10.387 6.792 1.00 23.16 O +HETATM 1023 O HOH A 151 -4.154 33.433 7.551 1.00 36.56 O +HETATM 1024 O HOH A 152 -2.892 31.523 5.422 1.00 70.64 O +HETATM 1025 O HOH A 153 8.184 17.799 8.234 1.00 52.27 O +HETATM 1026 O HOH A 154 7.851 28.286 8.261 1.00 20.33 O +HETATM 1027 O HOH A 155 -0.327 32.726 8.576 1.00 42.08 O +HETATM 1028 O HOH A 156 -7.096 11.131 8.405 1.00 40.02 O +HETATM 1029 O HOH A 157 -3.462 37.549 8.393 1.00 46.77 O +HETATM 1030 O HOH A 158 -8.809 13.307 8.142 1.00 30.47 O +HETATM 1031 O HOH A 159 -0.082 35.568 8.883 1.00 34.44 O +HETATM 1032 O HOH A 160 5.759 11.110 9.448 1.00 12.55 O +HETATM 1033 O HOH A 161 1.655 33.826 9.694 1.00 24.07 O +HETATM 1034 O HOH A 162 -2.547 32.477 9.746 1.00 26.29 O +HETATM 1035 O HOH A 163 4.474 33.152 9.881 1.00 17.58 O +HETATM 1036 O HOH A 164 3.338 7.494 10.654 1.00 33.32 O +HETATM 1037 O HOH A 165 8.193 18.034 10.710 1.00 21.87 O +HETATM 1038 O HOH A 166 7.329 25.034 11.046 1.00 35.50 O +HETATM 1039 O HOH A 167 -14.609 15.459 10.822 1.00 40.68 O +HETATM 1040 O HOH A 168 -10.475 34.131 10.612 1.00 52.70 O +HETATM 1041 O HOH A 169 2.254 4.105 11.205 1.00 64.88 O +HETATM 1042 O HOH A 170 8.719 22.583 10.964 1.00 48.95 O +HETATM 1043 O HOH A 171 -11.115 29.055 11.946 1.00 14.76 O +HETATM 1044 O HOH A 172 -13.874 27.050 11.990 1.00 53.84 O +HETATM 1045 O HOH A 173 -5.674 10.727 13.313 1.00 39.68 O +HETATM 1046 O HOH A 174 -11.999 31.072 12.630 1.00 63.32 O +HETATM 1047 O HOH A 175 -17.134 26.536 21.794 1.00 62.44 O +HETATM 1048 O HOH A 176 10.318 19.087 12.648 1.00 26.21 O +HETATM 1049 O HOH A 177 -6.214 5.635 13.140 1.00 68.62 O +HETATM 1050 O HOH A 178 4.038 7.633 13.524 1.00 23.33 O +HETATM 1051 O HOH A 179 -3.450 4.975 13.407 1.00 49.46 O +HETATM 1052 O HOH A 180 -7.339 10.569 14.831 1.00 42.40 O +HETATM 1053 O HOH A 181 7.627 28.588 14.215 1.00 19.60 O +HETATM 1054 O HOH A 182 1.193 5.002 14.601 1.00 41.13 O +HETATM 1055 O HOH A 183 -8.623 6.412 17.116 1.00 59.00 O +HETATM 1056 O HOH A 184 9.260 21.322 13.868 1.00 48.09 O +HETATM 1057 O HOH A 185 -16.033 21.080 23.763 1.00 60.47 O +HETATM 1058 O HOH A 186 11.590 13.479 14.940 1.00 13.69 O +HETATM 1059 O HOH A 187 -6.668 35.428 15.178 1.00 31.78 O +HETATM 1060 O HOH A 188 -4.892 -0.201 15.033 1.00 72.09 O +HETATM 1061 O HOH A 189 1.858 30.674 4.862 1.00 56.21 O +HETATM 1062 O HOH A 190 -10.895 36.814 14.982 1.00 35.20 O +HETATM 1063 O HOH A 191 0.992 36.275 15.433 1.00 18.46 O +HETATM 1064 O HOH A 192 4.392 4.463 15.873 1.00 37.98 O +HETATM 1065 O HOH A 193 -9.880 33.178 15.826 1.00 28.17 O +HETATM 1066 O HOH A 194 9.025 23.955 15.613 1.00 37.22 O +HETATM 1067 O HOH A 195 -7.206 38.395 16.256 1.00 55.89 O +HETATM 1068 O HOH A 196 -0.377 36.589 25.905 1.00 34.65 O +HETATM 1069 O HOH A 197 -14.982 19.034 22.737 1.00 64.15 O +HETATM 1070 O HOH A 198 -0.223 12.099 16.607 1.00 28.04 O +HETATM 1071 O HOH A 199 -6.317 33.838 16.796 1.00 22.79 O +HETATM 1072 O HOH A 200 8.078 31.375 16.915 1.00 10.01 O +HETATM 1073 O HOH A 201 1.489 13.820 17.020 1.00 21.39 O +HETATM 1074 O HOH A 202 9.131 28.844 17.354 1.00 52.49 O +HETATM 1075 O HOH A 203 14.994 15.102 18.263 1.00 53.36 O +HETATM 1076 O HOH A 204 15.333 22.227 18.703 1.00 50.97 O +HETATM 1077 O HOH A 205 16.093 18.390 18.034 1.00 33.35 O +HETATM 1078 O HOH A 206 3.768 6.469 18.636 1.00 38.13 O +HETATM 1079 O HOH A 207 -13.347 18.342 27.796 1.00 58.07 O +HETATM 1080 O HOH A 208 -14.200 9.443 18.914 1.00 81.98 O +HETATM 1081 O HOH A 209 9.257 22.574 18.988 1.00 22.39 O +HETATM 1082 O HOH A 210 4.907 37.823 19.024 1.00 41.16 O +HETATM 1083 O HOH A 211 -1.433 4.723 19.249 1.00 62.14 O +HETATM 1084 O HOH A 212 -1.071 11.315 19.089 1.00 15.91 O +HETATM 1085 O HOH A 213 -3.235 8.498 19.677 1.00 21.40 O +HETATM 1086 O HOH A 214 7.620 25.081 19.861 1.00 35.14 O +HETATM 1087 O HOH A 215 1.711 16.542 19.779 1.00 9.12 O +HETATM 1088 O HOH A 216 11.204 23.310 20.531 1.00 44.08 O +HETATM 1089 O HOH A 217 -0.792 7.051 20.523 1.00 25.44 O +HETATM 1090 O HOH A 219 -11.306 12.254 20.909 1.00 58.87 O +HETATM 1091 O HOH A 220 -15.497 22.071 20.968 1.00 42.59 O +HETATM 1092 O HOH A 221 -14.046 13.904 22.148 1.00 59.61 O +HETATM 1093 O HOH A 222 5.919 23.529 21.973 1.00 36.31 O +HETATM 1094 O HOH A 223 5.611 26.207 22.382 1.00 26.89 O +HETATM 1095 O HOH A 224 8.793 23.775 23.737 1.00 53.46 O +HETATM 1096 O HOH A 225 -14.958 24.195 25.086 1.00 26.18 O +HETATM 1097 O HOH A 226 -14.258 17.077 24.576 1.00 42.15 O +HETATM 1098 O HOH A 227 3.901 21.949 25.503 1.00 15.15 O +HETATM 1099 O HOH A 228 -17.138 15.370 26.017 1.00 64.87 O +HETATM 1100 O HOH A 229 1.041 39.543 25.118 1.00 75.63 O +HETATM 1101 O HOH A 230 -18.171 19.097 19.147 1.00 58.24 O +HETATM 1102 O HOH A 231 19.800 18.720 25.766 1.00 41.96 O +HETATM 1103 O HOH A 232 13.910 14.986 26.681 1.00 11.69 O +HETATM 1104 O HOH A 233 4.284 26.127 26.885 1.00 44.36 O +HETATM 1105 O HOH A 234 14.969 25.124 27.122 1.00 37.22 O +HETATM 1106 O HOH A 235 19.235 28.375 27.869 1.00 51.94 O +HETATM 1107 O HOH A 236 -8.227 15.787 27.736 1.00 28.71 O +HETATM 1108 O HOH A 237 11.129 29.398 26.784 1.00 53.97 O +HETATM 1109 O HOH A 238 -2.152 26.984 28.613 1.00 25.16 O +HETATM 1110 O HOH A 239 -12.126 14.584 29.332 1.00 70.39 O +HETATM 1111 O HOH A 240 -6.410 28.639 29.739 1.00 33.78 O +HETATM 1112 O HOH A 241 -9.363 18.929 29.236 1.00 54.93 O +HETATM 1113 O HOH A 242 7.290 6.035 29.744 1.00 44.70 O +HETATM 1114 O HOH A 243 0.532 4.323 25.856 1.00 66.97 O +HETATM 1115 O HOH A 244 -5.527 11.769 31.278 1.00 52.96 O +HETATM 1116 O HOH A 245 9.709 13.211 30.865 1.00 15.87 O +HETATM 1117 O HOH A 246 -5.539 14.098 29.938 1.00 63.37 O +HETATM 1118 O HOH A 247 2.285 7.164 31.744 1.00 42.72 O +HETATM 1119 O HOH A 249 2.557 37.778 32.502 1.00 60.66 O +HETATM 1120 O HOH A 250 11.653 11.933 32.683 1.00 24.19 O +HETATM 1121 O HOH A 251 -2.007 6.140 23.286 1.00 48.50 O +HETATM 1122 O HOH A 252 7.578 12.160 33.759 1.00 39.59 O +HETATM 1123 O HOH A 253 14.454 7.531 33.771 1.00 35.83 O +HETATM 1124 O HOH A 254 -3.513 31.619 34.652 1.00 56.09 O +HETATM 1125 O HOH A 255 13.552 10.709 34.982 1.00 58.90 O +HETATM 1126 O HOH A 256 -0.456 24.995 36.970 1.00 68.09 O +HETATM 1127 O HOH A 257 -2.238 9.934 2.797 1.00 67.44 O +HETATM 1128 O HOH A 258 -7.483 20.739 37.397 1.00 68.20 O +HETATM 1129 O HOH A 259 16.885 30.334 28.147 1.00 50.66 O +HETATM 1130 O HOH A 260 -2.189 19.144 1.123 1.00 56.23 O +HETATM 1131 O HOH A 263 5.554 35.805 21.621 1.00 47.47 O +HETATM 1132 O HOH A 264 0.167 38.321 22.074 1.00 63.57 O +HETATM 1133 O HOH A 265 2.643 23.311 24.222 1.00 37.06 O +HETATM 1134 O HOH A 266 -3.261 12.368 26.079 1.00 36.01 O +HETATM 1135 O HOH A 267 -8.163 28.523 28.227 1.00 31.53 O +HETATM 1136 O HOH A 268 11.314 34.308 29.649 1.00 69.35 O +HETATM 1137 O HOH A 269 -8.925 18.710 -0.425 1.00 67.80 O +HETATM 1138 O HOH A 270 1.106 7.975 2.503 1.00 57.87 O +HETATM 1139 O HOH A 271 3.658 14.557 2.346 1.00 58.10 O +HETATM 1140 O HOH A 272 5.462 18.910 4.058 1.00 56.45 O +HETATM 1141 O HOH A 273 -12.194 34.778 7.299 1.00 56.09 O +HETATM 1142 O HOH A 274 -1.696 6.065 8.495 1.00 68.76 O +HETATM 1143 O HOH A 275 -12.182 12.057 9.624 1.00 89.37 O +HETATM 1144 O HOH A 276 -17.165 32.342 9.988 1.00 67.99 O +HETATM 1145 O HOH A 277 -0.310 4.774 9.964 1.00 51.58 O +HETATM 1146 O HOH A 278 -18.106 6.723 19.155 1.00 64.11 O +HETATM 1147 O HOH A 279 -10.523 7.855 18.757 1.00 55.12 O +HETATM 1148 O HOH A 280 -5.786 9.627 24.788 1.00 56.60 O +HETATM 1149 O HOH A 281 4.973 30.366 26.631 1.00 56.27 O +HETATM 1150 O HOH A 282 -14.163 23.294 27.041 1.00 80.21 O +HETATM 1151 O HOH A 283 4.190 23.920 28.202 1.00 47.07 O +HETATM 1152 O HOH A 284 1.927 24.235 28.261 1.00 53.05 O +HETATM 1153 O HOH A 285 8.469 24.914 28.323 1.00 76.29 O +HETATM 1154 O HOH A 286 0.504 26.234 30.223 1.00 48.47 O +HETATM 1155 O HOH A 287 4.961 6.376 30.326 1.00 57.17 O +HETATM 1156 O HOH A 288 -9.395 28.233 30.605 1.00 55.86 O +HETATM 1157 O HOH A 289 -7.403 29.010 31.768 1.00 58.13 O +HETATM 1158 O HOH A 290 17.262 22.252 32.977 1.00 32.13 O +HETATM 1159 O HOH A 291 -13.958 24.749 32.936 1.00 40.16 O +HETATM 1160 O HOH A 292 11.050 6.576 33.893 1.00 53.38 O +HETATM 1161 O HOH A 293 -6.940 30.679 34.967 1.00 57.95 O +HETATM 1162 O HOH A 294 -7.751 19.631 32.932 1.00 55.95 O +HETATM 1163 O HOH A 295 -11.917 25.473 35.232 1.00 70.62 O +HETATM 1164 O HOH A 296 -0.614 22.162 37.001 1.00 49.79 O +HETATM 1165 O HOH A 297 -5.763 25.243 36.097 1.00 78.09 O +HETATM 1166 O HOH A 298 -0.024 14.493 36.828 1.00 63.91 O +HETATM 1167 O HOH A 299 0.443 17.296 2.028 1.00 52.55 O +HETATM 1168 O HOH A 300 1.738 27.507 3.463 1.00 74.82 O +HETATM 1169 O HOH A 301 3.836 11.760 3.259 1.00 57.42 O +HETATM 1170 O HOH A 302 -9.211 4.115 14.687 1.00 48.13 O +HETATM 1171 O HOH A 303 16.205 21.210 16.009 1.00 69.59 O +HETATM 1172 O HOH A 304 -14.845 6.428 21.717 1.00 61.77 O +HETATM 1173 O HOH A 305 -13.311 8.488 24.665 1.00 62.09 O +HETATM 1174 O HOH A 306 8.880 27.820 26.816 1.00 71.28 O +HETATM 1175 O HOH A 307 0.932 10.327 2.387 1.00 62.28 O +HETATM 1176 O HOH A 308 -32.793 6.518 16.878 1.00 55.27 O +HETATM 1177 O HOH A 309 -10.109 33.422 4.951 1.00 51.37 O +HETATM 1178 O HOH A 310 -6.930 35.720 3.927 1.00 68.08 O +HETATM 1179 O HOH A 311 -1.458 29.021 31.741 1.00 71.39 O +HETATM 1180 O HOH A 312 -7.776 27.408 33.976 1.00 51.50 O +HETATM 1181 O HOH A 313 2.002 13.196 3.708 1.00 54.99 O +HETATM 1182 O HOH A 314 7.005 28.792 27.719 1.00 69.52 O +HETATM 1183 O HOH A 315 -14.736 20.042 16.788 1.00 37.49 O +HETATM 1184 O HOH A 316 17.457 15.414 26.607 1.00 36.58 O +HETATM 1185 O HOH A 317 1.388 37.676 19.438 1.00 42.27 O +HETATM 1186 O HOH A 318 12.884 12.733 37.805 0.50 65.31 O +HETATM 1187 O HOH A 319 7.795 26.278 15.645 1.00 44.16 O +CONECT 48 981 +CONECT 238 889 +CONECT 513 630 +CONECT 601 724 +CONECT 630 513 +CONECT 724 601 +CONECT 889 238 +CONECT 981 48 +MASTER 294 0 0 7 3 0 0 6 1186 1 8 10 +END diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map new file mode 100644 index 00000000..3c638013 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/map.map @@ -0,0 +1,1275 @@ + CONTACT MAPS FROM PDB FILES + + This software is written by: + Rodrigo Azevedo Moreira da Silva + + Copyright (c) 2020 - IPPT-PAN + Institute of Fundamental Techonological Research + Polish Academy of Sciences + MIT LICENSE, check out LICENSE for more informations. + +Reading file: ../aa.pdb +pdb natoms: 1001 +pdb nresidues: 129 +Memory usage: 6.38 MB +UNMAPPED ATOM LEU OXT +Fibonacci grid: 610 +ALPHA: 1.24 +WATER_RADIUS: 2.80 + +Residue-Residue Contacts + +ID - atom identification +I1,I2 - serial residue id +AA - 3-letter code of aminoacid +C - chain +I(PDB) - residue number in PDB file +DCA - distance between CA +CMs - OV , CSU , oCSU , rCSU + (CSU does not take into account chemical properties of atoms) +rCSU - net contact from rCSU +Count - number of contacts between residues +MODEL - model number + + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model +============================================================================================ +R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 +R 2 1 LYS A 1 3 PHE A 3 6.0948 1 1 1 0 -13 106 0 +R 3 1 LYS A 1 7 GLU A 7 11.4807 1 1 1 1 121 225 0 +R 4 1 LYS A 1 38 PHE A 38 8.1596 1 1 0 0 -12 12 0 +R 5 1 LYS A 1 39 ASN A 39 5.7421 1 0 0 0 0 0 0 +R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 +R 7 1 LYS A 1 41 GLN A 41 6.8324 1 1 0 0 -112 118 0 +R 8 1 LYS A 1 86 SER A 86 5.1894 1 1 1 0 -53 161 0 +R 9 2 VAL A 2 1 LYS A 1 3.8094 1 1 0 0 -21 386 0 +R 10 2 VAL A 2 3 PHE A 3 3.7890 1 1 1 0 -32 413 0 +R 11 2 VAL A 2 4 GLY A 4 6.7958 0 1 1 1 10 14 0 +R 12 2 VAL A 2 7 GLU A 7 10.1090 0 1 0 0 -12 12 0 +R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 +R 14 2 VAL A 2 38 PHE A 38 5.5799 1 1 1 0 -20 27 0 +R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 +R 16 3 PHE A 3 1 LYS A 1 6.0948 1 1 1 0 -49 77 0 +R 17 3 PHE A 3 2 VAL A 2 3.7890 1 1 0 0 -25 380 0 +R 18 3 PHE A 3 4 GLY A 4 3.7566 1 1 1 0 -9 362 0 +R 19 3 PHE A 3 7 GLU A 7 6.3959 1 1 1 1 27 66 0 +R 20 3 PHE A 3 8 LEU A 8 5.8772 1 1 1 1 71 144 0 +R 21 3 PHE A 3 11 ALA A 11 9.8683 1 1 1 1 35 35 0 +R 22 3 PHE A 3 38 PHE A 38 5.3547 1 1 1 0 -112 144 0 +R 23 3 PHE A 3 40 THR A 40 7.9444 1 1 1 1 133 133 0 +R 24 3 PHE A 3 55 ILE A 55 9.3473 1 1 1 1 35 35 0 +R 25 3 PHE A 3 86 SER A 86 8.8941 1 1 0 0 -65 65 0 +R 26 3 PHE A 3 88 ILE A 88 10.4372 1 1 1 1 102 102 0 +R 27 4 GLY A 4 2 VAL A 2 6.7958 0 1 1 1 6 11 0 +R 28 4 GLY A 4 3 PHE A 3 3.7566 1 1 0 0 -1 353 0 +R 29 4 GLY A 4 5 ARG A 5 3.7804 1 1 1 1 24 382 0 +R 30 4 GLY A 4 6 CYS A 6 5.6551 1 1 0 0 0 9 0 +R 31 4 GLY A 4 7 GLU A 7 5.1677 1 1 1 1 39 78 0 +R 32 4 GLY A 4 8 LEU A 8 6.0824 1 1 1 1 97 105 0 +R 33 4 GLY A 4 38 PHE A 38 7.2869 0 1 0 0 0 2 0 +R 34 5 ARG A 5 3 PHE A 3 6.3853 0 1 1 1 10 10 0 +R 35 5 ARG A 5 4 GLY A 4 3.7804 1 1 0 0 0 324 0 +R 36 5 ARG A 5 6 CYS A 6 3.8229 1 1 1 1 16 405 0 +R 37 5 ARG A 5 7 GLU A 7 5.6256 1 0 0 0 0 0 0 +R 38 5 ARG A 5 8 LEU A 8 5.4514 1 1 0 0 -5 5 0 +R 39 5 ARG A 5 9 ALA A 9 6.3068 1 1 1 1 111 121 0 +R 40 5 ARG A 5 29 VAL A 29 7.3410 1 0 0 0 0 0 0 +R 41 5 ARG A 5 38 PHE A 38 7.6636 1 1 1 1 72 111 0 +R 42 5 ARG A 5 122 ALA A 122 10.7979 1 1 1 1 15 21 0 +R 43 5 ARG A 5 123 TRP A 123 7.4230 1 1 1 1 80 312 0 +R 44 5 ARG A 5 124 ILE A 124 7.5648 1 0 0 0 0 0 0 +R 45 5 ARG A 5 125 ARG A 125 9.6347 1 1 1 1 135 211 0 +R 46 5 ARG A 5 126 GLY A 126 10.0418 0 1 0 0 -1 13 0 +R 47 5 ARG A 5 127 CYS A 127 8.4264 1 1 0 0 0 21 0 +R 48 6 CYS A 6 4 GLY A 4 5.6551 1 1 0 0 0 2 0 +R 49 6 CYS A 6 5 ARG A 5 3.8229 1 1 0 0 -20 442 0 +R 50 6 CYS A 6 7 GLU A 7 3.7935 1 1 1 0 -3 369 0 +R 51 6 CYS A 6 8 LEU A 8 5.3320 1 0 0 0 0 0 0 +R 52 6 CYS A 6 9 ALA A 9 4.8870 1 0 0 0 0 0 0 +R 53 6 CYS A 6 10 ALA A 10 6.1316 1 1 1 1 85 131 0 +R 54 6 CYS A 6 126 GLY A 126 7.9731 0 1 0 0 0 12 0 +R 55 6 CYS A 6 127 CYS A 127 5.3179 1 1 1 1 23 264 0 +R 56 6 CYS A 6 128 ARG A 128 7.4354 0 1 0 0 -14 14 0 +R 57 7 GLU A 7 1 LYS A 1 11.4807 1 1 1 1 153 207 0 +R 58 7 GLU A 7 2 VAL A 2 10.1090 0 1 0 0 -7 7 0 +R 59 7 GLU A 7 3 PHE A 3 6.3959 1 1 1 1 29 30 0 +R 60 7 GLU A 7 4 GLY A 4 5.1677 1 1 1 1 95 139 0 +R 61 7 GLU A 7 5 ARG A 5 5.6256 1 0 0 0 0 0 0 +R 62 7 GLU A 7 6 CYS A 6 3.7935 1 1 1 0 -23 363 0 +R 63 7 GLU A 7 8 LEU A 8 3.8230 1 1 1 1 10 347 0 +R 64 7 GLU A 7 9 ALA A 9 5.5273 1 0 0 0 0 0 0 +R 65 7 GLU A 7 10 ALA A 10 5.2583 1 1 1 1 2 28 0 +R 66 7 GLU A 7 11 ALA A 11 6.3196 1 1 1 1 115 119 0 +R 67 8 LEU A 8 3 PHE A 3 5.8772 1 1 1 1 56 64 0 +R 68 8 LEU A 8 4 GLY A 4 6.0824 1 1 1 0 -47 63 0 +R 69 8 LEU A 8 5 ARG A 5 5.4514 1 1 0 0 -5 5 0 +R 70 8 LEU A 8 6 CYS A 6 5.3320 1 0 0 0 0 0 0 +R 71 8 LEU A 8 7 GLU A 7 3.8230 1 1 0 0 -20 356 0 +R 72 8 LEU A 8 9 ALA A 9 3.8041 1 1 1 1 10 355 0 +R 73 8 LEU A 8 10 ALA A 10 5.3454 1 0 0 0 0 0 0 +R 74 8 LEU A 8 11 ALA A 11 5.0036 1 0 0 0 0 0 0 +R 75 8 LEU A 8 12 MET A 12 6.0331 1 1 1 1 189 211 0 +R 76 8 LEU A 8 29 VAL A 29 7.2217 0 1 1 1 1 1 0 +R 77 8 LEU A 8 32 ALA A 32 8.9719 1 1 1 1 78 78 0 +R 78 8 LEU A 8 38 PHE A 38 7.9077 1 1 1 1 168 168 0 +R 79 8 LEU A 8 55 ILE A 55 10.0426 1 1 1 1 102 102 0 +R 80 8 LEU A 8 88 ILE A 88 9.1166 1 1 1 1 16 16 0 +R 81 9 ALA A 9 5 ARG A 5 6.3068 1 1 1 0 -49 77 0 +R 82 9 ALA A 9 6 CYS A 6 4.8870 1 1 0 0 -20 30 0 +R 83 9 ALA A 9 7 GLU A 7 5.5273 1 0 0 0 0 0 0 +R 84 9 ALA A 9 8 LEU A 8 3.8041 1 1 0 0 -13 342 0 +R 85 9 ALA A 9 10 ALA A 10 3.8152 1 1 1 1 4 325 0 +R 86 9 ALA A 9 11 ALA A 11 5.5040 1 0 0 0 0 0 0 +R 87 9 ALA A 9 12 MET A 12 5.2438 1 0 0 0 0 0 0 +R 88 9 ALA A 9 13 LYS A 13 6.0508 1 1 1 1 121 177 0 +R 89 9 ALA A 9 25 LEU A 25 6.8785 1 1 0 0 -1 1 0 +R 90 9 ALA A 9 29 VAL A 29 6.2031 1 1 1 1 65 103 0 +R 91 9 ALA A 9 124 ILE A 124 6.6308 1 1 1 1 91 91 0 +R 92 9 ALA A 9 129 LEU A 129 7.9700 1 1 1 1 31 31 0 +R 93 10 ALA A 10 6 CYS A 6 6.1316 1 1 1 0 -57 71 0 +R 94 10 ALA A 10 7 GLU A 7 5.2583 1 1 1 0 -14 35 0 +R 95 10 ALA A 10 8 LEU A 8 5.3454 1 0 0 0 0 0 0 +R 96 10 ALA A 10 9 ALA A 9 3.8152 1 1 0 0 -12 348 0 +R 97 10 ALA A 10 11 ALA A 11 3.7870 1 1 1 1 4 363 0 +R 98 10 ALA A 10 12 MET A 12 5.5577 1 0 0 0 0 0 0 +R 99 10 ALA A 10 13 LYS A 13 5.0244 1 1 0 0 -2 3 0 +R 100 10 ALA A 10 14 ARG A 14 6.0838 1 1 1 1 85 143 0 +R 101 10 ALA A 10 128 ARG A 128 7.8262 0 1 0 0 -37 37 0 +R 102 10 ALA A 10 129 LEU A 129 6.1221 1 1 1 1 42 83 0 +R 103 11 ALA A 11 3 PHE A 3 9.8683 1 1 1 1 49 49 0 +R 104 11 ALA A 11 7 GLU A 7 6.3196 1 1 1 0 -44 76 0 +R 105 11 ALA A 11 8 LEU A 8 5.0036 1 1 0 0 -13 13 0 +R 106 11 ALA A 11 9 ALA A 9 5.5040 1 0 0 0 0 0 0 +R 107 11 ALA A 11 10 ALA A 10 3.7870 1 1 0 0 -22 362 0 +R 108 11 ALA A 11 12 MET A 12 3.8044 1 1 1 1 4 329 0 +R 109 11 ALA A 11 13 LYS A 13 5.3126 1 0 0 0 0 0 0 +R 110 11 ALA A 11 14 ARG A 14 5.0202 1 1 0 0 -15 41 0 +R 111 11 ALA A 11 15 HIS A 15 6.1372 1 1 1 1 176 196 0 +R 112 11 ALA A 11 88 ILE A 88 7.9512 1 1 1 1 91 91 0 +R 113 12 MET A 12 8 LEU A 8 6.0331 1 1 1 1 81 189 0 +R 114 12 MET A 12 9 ALA A 9 5.2438 1 1 0 0 -12 12 0 +R 115 12 MET A 12 10 ALA A 10 5.5577 1 0 0 0 0 0 0 +R 116 12 MET A 12 11 ALA A 11 3.8044 1 1 0 0 -10 337 0 +R 117 12 MET A 12 13 LYS A 13 3.8273 1 1 1 0 0 351 0 +R 118 12 MET A 12 14 ARG A 14 5.4173 1 0 0 0 0 0 0 +R 119 12 MET A 12 15 HIS A 15 4.8856 1 1 1 1 55 59 0 +R 120 12 MET A 12 16 GLY A 16 6.5249 1 1 1 1 1 1 0 +R 121 12 MET A 12 17 LEU A 17 5.4690 1 1 1 1 162 162 0 +R 122 12 MET A 12 25 LEU A 25 7.5662 1 1 1 1 34 34 0 +R 123 12 MET A 12 28 TRP A 28 7.8689 1 1 1 0 -80 205 0 +R 124 12 MET A 12 29 VAL A 29 8.1611 1 1 0 0 0 12 0 +R 125 12 MET A 12 32 ALA A 32 10.4631 1 1 1 1 31 31 0 +R 126 12 MET A 12 55 ILE A 55 11.3010 0 1 1 1 3 3 0 +R 127 12 MET A 12 56 LEU A 56 11.5983 1 1 1 1 52 52 0 +R 128 12 MET A 12 88 ILE A 88 8.1191 1 1 1 1 12 26 0 +R 129 13 LYS A 13 9 ALA A 9 6.0508 1 1 1 0 -47 63 0 +R 130 13 LYS A 13 10 ALA A 10 5.0244 1 1 0 0 -13 13 0 +R 131 13 LYS A 13 11 ALA A 11 5.3126 1 0 0 0 0 0 0 +R 132 13 LYS A 13 12 MET A 12 3.8273 1 1 0 0 -22 349 0 +R 133 13 LYS A 13 14 ARG A 14 3.7179 1 1 1 1 4 358 0 +R 134 13 LYS A 13 15 HIS A 15 5.2265 1 0 0 0 0 0 0 +R 135 13 LYS A 13 16 GLY A 16 5.3557 1 1 1 1 71 90 0 +R 136 13 LYS A 13 18 ASP A 18 5.3900 1 1 1 1 51 92 0 +R 137 13 LYS A 13 25 LEU A 25 6.9771 1 1 1 1 52 74 0 +R 138 13 LYS A 13 129 LEU A 129 8.0834 1 1 1 1 59 161 0 +R 139 14 ARG A 14 10 ALA A 10 6.0838 1 1 1 0 -54 66 0 +R 140 14 ARG A 14 11 ALA A 11 5.0202 1 1 1 0 -14 33 0 +R 141 14 ARG A 14 12 MET A 12 5.4173 1 0 0 0 0 0 0 +R 142 14 ARG A 14 13 LYS A 13 3.7179 1 1 1 0 -16 374 0 +R 143 14 ARG A 14 15 HIS A 15 3.8028 1 1 1 0 -115 484 0 +R 144 14 ARG A 14 16 GLY A 16 5.5733 1 1 1 1 11 16 0 +R 145 14 ARG A 14 89 THR A 89 10.0339 0 1 1 1 12 12 0 +R 146 15 HIS A 15 11 ALA A 11 6.1372 1 1 1 1 67 117 0 +R 147 15 HIS A 15 12 MET A 12 4.8856 1 1 0 0 -6 6 0 +R 148 15 HIS A 15 13 LYS A 13 5.2265 1 0 0 0 0 0 0 +R 149 15 HIS A 15 14 ARG A 14 3.8028 1 1 1 0 -121 524 0 +R 150 15 HIS A 15 16 GLY A 16 3.8284 1 1 1 1 25 263 0 +R 151 15 HIS A 15 17 LEU A 17 5.8003 1 0 0 0 0 0 0 +R 152 15 HIS A 15 87 ASP A 87 10.7991 0 1 0 0 -1 1 0 +R 153 15 HIS A 15 88 ILE A 88 8.6713 1 1 1 1 35 53 0 +R 154 15 HIS A 15 89 THR A 89 7.1554 1 1 1 1 53 244 0 +R 155 15 HIS A 15 92 VAL A 92 7.1674 1 1 1 1 71 71 0 +R 156 15 HIS A 15 93 ASN A 93 8.5240 0 1 0 0 -5 5 0 +R 157 15 HIS A 15 96 LYS A 96 10.3010 1 1 1 1 191 193 0 +R 158 16 GLY A 16 12 MET A 12 6.5249 1 0 0 0 0 0 0 +R 159 16 GLY A 16 13 LYS A 13 5.3557 1 1 1 1 11 44 0 +R 160 16 GLY A 16 14 ARG A 14 5.5733 1 1 1 1 2 14 0 +R 161 16 GLY A 16 15 HIS A 15 3.8284 1 1 0 0 -32 379 0 +R 162 16 GLY A 16 17 LEU A 17 3.7882 1 1 1 1 23 340 0 +R 163 16 GLY A 16 18 ASP A 18 5.8126 1 1 1 0 -8 32 0 +R 164 16 GLY A 16 20 TYR A 20 6.7265 1 1 0 0 -129 130 0 +R 165 16 GLY A 16 96 LYS A 96 9.2491 1 1 0 0 0 24 0 +R 166 17 LEU A 17 12 MET A 12 5.4690 1 1 1 1 110 161 0 +R 167 17 LEU A 17 15 HIS A 15 5.8003 1 0 0 0 0 0 0 +R 168 17 LEU A 17 16 GLY A 16 3.7882 1 1 0 0 -18 366 0 +R 169 17 LEU A 17 18 ASP A 18 3.8027 1 1 1 1 12 357 0 +R 170 17 LEU A 17 19 ASN A 19 6.0755 1 1 1 1 30 30 0 +R 171 17 LEU A 17 20 TYR A 20 4.9158 1 1 1 1 43 43 0 +R 172 17 LEU A 17 28 TRP A 28 7.4830 1 1 1 1 217 217 0 +R 173 17 LEU A 17 92 VAL A 92 7.6268 1 1 1 1 89 89 0 +R 174 17 LEU A 17 96 LYS A 96 7.9140 1 1 1 1 155 155 0 +R 175 18 ASP A 18 13 LYS A 13 5.3900 1 1 1 1 2 165 0 +R 176 18 ASP A 18 16 GLY A 16 5.8126 1 1 0 0 -28 33 0 +R 177 18 ASP A 18 17 LEU A 17 3.8027 1 1 0 0 -35 354 0 +R 178 18 ASP A 18 19 ASN A 19 3.7747 1 1 1 1 115 510 0 +R 179 18 ASP A 18 20 TYR A 20 5.3255 1 1 1 1 5 6 0 +R 180 18 ASP A 18 24 SER A 24 5.1287 1 1 0 0 0 12 0 +R 181 18 ASP A 18 25 LEU A 25 4.4020 1 1 1 1 152 244 0 +R 182 19 ASN A 19 17 LEU A 17 6.0755 1 0 0 0 0 0 0 +R 183 19 ASN A 19 18 ASP A 18 3.7747 1 1 1 1 107 498 0 +R 184 19 ASN A 19 20 TYR A 20 3.7437 1 1 1 1 17 326 0 +R 185 19 ASN A 19 21 ARG A 21 5.8645 1 1 1 1 9 9 0 +R 186 19 ASN A 19 22 GLY A 22 4.5249 1 1 1 1 59 129 0 +R 187 19 ASN A 19 23 TYR A 23 4.4795 1 1 1 1 32 73 0 +R 188 19 ASN A 19 24 SER A 24 4.2956 1 1 1 1 9 109 0 +R 189 20 TYR A 20 16 GLY A 16 6.7265 1 1 0 0 -86 87 0 +R 190 20 TYR A 20 17 LEU A 17 4.9158 1 1 1 0 -66 84 0 +R 191 20 TYR A 20 18 ASP A 18 5.3255 1 1 0 0 0 9 0 +R 192 20 TYR A 20 19 ASN A 19 3.7437 1 1 0 0 -19 347 0 +R 193 20 TYR A 20 21 ARG A 21 3.8205 1 1 1 1 84 506 0 +R 194 20 TYR A 20 22 GLY A 22 5.3254 1 1 1 1 3 3 0 +R 195 20 TYR A 20 23 TYR A 23 5.5795 1 1 1 1 12 68 0 +R 196 20 TYR A 20 96 LYS A 96 7.7283 1 1 1 0 0 186 0 +R 197 20 TYR A 20 97 LYS A 97 10.9092 0 1 1 1 1 2 0 +R 198 20 TYR A 20 99 VAL A 99 8.7657 1 1 1 1 64 64 0 +R 199 20 TYR A 20 100 SER A 100 9.2326 1 1 1 1 87 87 0 +R 200 21 ARG A 21 19 ASN A 19 5.8645 1 1 1 1 10 10 0 +R 201 21 ARG A 21 20 TYR A 20 3.8205 1 1 1 1 40 461 0 +R 202 21 ARG A 21 22 GLY A 22 3.7772 1 1 1 1 13 344 0 +R 203 21 ARG A 21 23 TYR A 23 5.6467 1 1 1 0 -14 110 0 +R 204 21 ARG A 21 99 VAL A 99 7.5366 1 1 1 1 39 39 0 +R 205 21 ARG A 21 100 SER A 100 7.2028 1 1 1 1 180 220 0 +R 206 22 GLY A 22 19 ASN A 19 4.5249 1 1 1 1 6 85 0 +R 207 22 GLY A 22 20 TYR A 20 5.3254 1 0 0 0 0 0 0 +R 208 22 GLY A 22 21 ARG A 21 3.7772 1 1 0 0 -33 385 0 +R 209 22 GLY A 22 23 TYR A 23 3.8541 1 1 1 1 5 337 0 +R 210 22 GLY A 22 24 SER A 24 6.3302 1 1 1 1 23 31 0 +R 211 22 GLY A 22 27 ASN A 27 10.0766 0 1 1 1 5 5 0 +R 212 23 TYR A 23 19 ASN A 19 4.4795 1 1 1 1 110 110 0 +R 213 23 TYR A 23 20 TYR A 20 5.5795 1 1 0 0 -29 29 0 +R 214 23 TYR A 23 21 ARG A 21 5.6467 1 1 1 0 -120 126 0 +R 215 23 TYR A 23 22 GLY A 22 3.8541 1 1 0 0 -27 365 0 +R 216 23 TYR A 23 24 SER A 24 3.8095 1 1 1 1 20 358 0 +R 217 23 TYR A 23 25 LEU A 25 6.6706 1 0 0 0 0 0 0 +R 218 23 TYR A 23 27 ASN A 27 6.2528 1 1 0 0 -2 10 0 +R 219 23 TYR A 23 28 TRP A 28 7.5595 1 1 1 0 -54 94 0 +R 220 23 TYR A 23 99 VAL A 99 9.4052 1 1 1 1 96 96 0 +R 221 23 TYR A 23 103 ASN A 103 12.4992 0 1 1 1 16 16 0 +R 222 23 TYR A 23 104 GLY A 104 8.8920 1 1 0 0 0 47 0 +R 223 23 TYR A 23 105 MET A 105 8.1535 1 1 1 1 150 217 0 +R 224 23 TYR A 23 106 ASN A 106 11.3626 0 1 1 1 16 16 0 +R 225 23 TYR A 23 111 TRP A 111 11.4919 1 1 1 1 60 94 0 +R 226 24 SER A 24 18 ASP A 18 5.1287 1 1 0 0 0 35 0 +R 227 24 SER A 24 19 ASN A 19 4.2956 1 1 0 0 0 57 0 +R 228 24 SER A 24 22 GLY A 22 6.3302 1 1 1 1 7 14 0 +R 229 24 SER A 24 23 TYR A 23 3.8095 1 1 0 0 -10 366 0 +R 230 24 SER A 24 25 LEU A 25 3.8490 1 1 1 1 26 309 0 +R 231 24 SER A 24 26 GLY A 26 5.5205 1 1 1 1 31 37 0 +R 232 24 SER A 24 27 ASN A 27 5.6877 1 1 1 1 232 265 0 +R 233 24 SER A 24 28 TRP A 28 7.2581 1 1 0 0 -1 1 0 +R 234 24 SER A 24 120 VAL A 120 8.3132 1 1 0 0 -53 53 0 +R 235 24 SER A 24 121 GLN A 121 8.0270 0 1 0 0 -4 47 0 +R 236 25 LEU A 25 9 ALA A 9 6.8785 1 1 0 0 -75 75 0 +R 237 25 LEU A 25 12 MET A 12 7.5662 1 1 1 1 156 156 0 +R 238 25 LEU A 25 13 LYS A 13 6.9771 1 1 1 1 48 80 0 +R 239 25 LEU A 25 18 ASP A 18 4.4020 1 1 1 0 -33 86 0 +R 240 25 LEU A 25 23 TYR A 23 6.6706 1 1 1 1 3 3 0 +R 241 25 LEU A 25 24 SER A 24 3.8490 1 1 0 0 0 326 0 +R 242 25 LEU A 25 26 GLY A 26 3.8034 1 1 1 1 10 356 0 +R 243 25 LEU A 25 27 ASN A 27 5.4198 1 0 0 0 0 0 0 +R 244 25 LEU A 25 28 TRP A 28 5.3994 1 1 1 1 77 86 0 +R 245 25 LEU A 25 29 VAL A 29 6.4093 1 1 1 1 54 54 0 +R 246 25 LEU A 25 124 ILE A 124 7.3355 1 1 1 1 57 57 0 +R 247 25 LEU A 25 129 LEU A 129 10.5318 1 1 1 1 126 126 0 +R 248 26 GLY A 26 24 SER A 24 5.5205 1 1 1 1 12 16 0 +R 249 26 GLY A 26 25 LEU A 25 3.8034 1 1 0 0 -35 364 0 +R 250 26 GLY A 26 27 ASN A 27 3.8470 1 1 1 1 17 323 0 +R 251 26 GLY A 26 28 TRP A 28 5.5151 1 0 0 0 0 0 0 +R 252 26 GLY A 26 29 VAL A 29 5.1152 1 0 0 0 0 0 0 +R 253 26 GLY A 26 30 CYS A 30 5.9025 1 1 1 1 93 175 0 +R 254 26 GLY A 26 120 VAL A 120 4.8514 1 1 0 0 -1 120 0 +R 255 26 GLY A 26 123 TRP A 123 5.1305 1 0 0 0 0 0 0 +R 256 26 GLY A 26 124 ILE A 124 5.7057 1 1 0 0 -9 65 0 +R 257 27 ASN A 27 22 GLY A 22 10.0766 0 1 1 1 5 5 0 +R 258 27 ASN A 27 23 TYR A 23 6.2528 1 1 0 0 -6 33 0 +R 259 27 ASN A 27 24 SER A 24 5.6877 1 1 1 1 101 219 0 +R 260 27 ASN A 27 25 LEU A 25 5.4198 1 0 0 0 0 0 0 +R 261 27 ASN A 27 26 GLY A 26 3.8470 1 1 0 0 -20 351 0 +R 262 27 ASN A 27 28 TRP A 28 3.7858 1 1 1 1 4 333 0 +R 263 27 ASN A 27 29 VAL A 29 5.5161 1 0 0 0 0 0 0 +R 264 27 ASN A 27 30 CYS A 30 5.1016 1 0 0 0 0 0 0 +R 265 27 ASN A 27 31 ALA A 31 6.0825 1 1 1 1 119 171 0 +R 266 27 ASN A 27 105 MET A 105 8.5492 1 1 0 0 0 46 0 +R 267 27 ASN A 27 111 TRP A 111 7.6026 1 1 1 1 40 192 0 +R 268 27 ASN A 27 116 LYS A 116 7.7579 0 1 0 0 0 1 0 +R 269 27 ASN A 27 120 VAL A 120 5.7252 1 1 0 0 -82 87 0 +R 270 28 TRP A 28 12 MET A 12 7.8689 1 1 0 0 -32 95 0 +R 271 28 TRP A 28 17 LEU A 17 7.4830 1 1 1 1 81 218 0 +R 272 28 TRP A 28 20 TYR A 20 9.5686 0 1 0 0 -7 7 0 +R 273 28 TRP A 28 23 TYR A 23 7.5595 1 1 1 1 44 60 0 +R 274 28 TRP A 28 24 SER A 24 7.2581 1 1 0 0 -47 49 0 +R 275 28 TRP A 28 25 LEU A 25 5.3994 1 1 0 0 -18 19 0 +R 276 28 TRP A 28 26 GLY A 26 5.5151 1 0 0 0 0 0 0 +R 277 28 TRP A 28 27 ASN A 27 3.7858 1 1 0 0 -7 345 0 +R 278 28 TRP A 28 29 VAL A 29 3.8333 1 1 1 1 2 334 0 +R 279 28 TRP A 28 30 CYS A 30 5.4753 1 0 0 0 0 0 0 +R 280 28 TRP A 28 31 ALA A 31 5.1386 1 1 0 0 -1 1 0 +R 281 28 TRP A 28 32 ALA A 32 6.2956 1 1 1 1 132 132 0 +R 282 28 TRP A 28 56 LEU A 56 8.7724 0 1 1 1 25 25 0 +R 283 28 TRP A 28 95 ALA A 95 9.8227 1 1 1 1 35 35 0 +R 284 28 TRP A 28 99 VAL A 99 10.7709 1 1 1 1 240 240 0 +R 285 28 TRP A 28 105 MET A 105 8.7636 1 1 1 1 15 21 0 +R 286 28 TRP A 28 108 TRP A 108 10.2074 1 1 1 1 113 113 0 +R 287 29 VAL A 29 5 ARG A 5 7.3410 1 1 1 1 10 12 0 +R 288 29 VAL A 29 9 ALA A 9 6.2031 1 1 1 1 17 175 0 +R 289 29 VAL A 29 12 MET A 12 8.1611 1 1 0 0 0 34 0 +R 290 29 VAL A 29 25 LEU A 25 6.4093 1 1 0 0 -65 65 0 +R 291 29 VAL A 29 26 GLY A 26 5.1152 1 1 0 0 -10 10 0 +R 292 29 VAL A 29 27 ASN A 27 5.5161 1 0 0 0 0 0 0 +R 293 29 VAL A 29 28 TRP A 28 3.8333 1 1 0 0 -22 358 0 +R 294 29 VAL A 29 30 CYS A 30 3.7941 1 1 1 1 9 357 0 +R 295 29 VAL A 29 31 ALA A 31 5.3991 1 0 0 0 0 0 0 +R 296 29 VAL A 29 32 ALA A 32 5.1300 1 1 0 0 0 3 0 +R 297 29 VAL A 29 33 LYS A 33 6.2055 1 1 1 1 115 115 0 +R 298 29 VAL A 29 38 PHE A 38 8.4877 1 1 1 1 96 98 0 +R 299 29 VAL A 29 123 TRP A 123 6.3580 1 1 1 1 61 107 0 +R 300 29 VAL A 29 124 ILE A 124 7.6402 1 1 1 1 1 1 0 +R 301 30 CYS A 30 26 GLY A 26 5.9025 1 1 1 0 -65 79 0 +R 302 30 CYS A 30 27 ASN A 27 5.1016 1 1 0 0 -6 6 0 +R 303 30 CYS A 30 28 TRP A 28 5.4753 1 0 0 0 0 0 0 +R 304 30 CYS A 30 29 VAL A 29 3.7941 1 1 0 0 -11 343 0 +R 305 30 CYS A 30 31 ALA A 31 3.7849 1 1 1 1 12 355 0 +R 306 30 CYS A 30 32 ALA A 32 5.5042 1 0 0 0 0 0 0 +R 307 30 CYS A 30 33 LYS A 33 5.1917 1 0 0 0 0 0 0 +R 308 30 CYS A 30 34 PHE A 34 6.3992 1 1 1 1 96 170 0 +R 309 30 CYS A 30 115 CYS A 115 6.0621 1 1 1 1 10 238 0 +R 310 30 CYS A 30 120 VAL A 120 6.6406 1 0 0 0 0 0 0 +R 311 30 CYS A 30 123 TRP A 123 6.2969 1 1 1 1 34 144 0 +R 312 31 ALA A 31 27 ASN A 27 6.0825 1 1 1 0 -56 76 0 +R 313 31 ALA A 31 28 TRP A 28 5.1386 1 1 0 0 -10 10 0 +R 314 31 ALA A 31 29 VAL A 29 5.3991 1 0 0 0 0 0 0 +R 315 31 ALA A 31 30 CYS A 30 3.7849 1 1 0 0 -23 359 0 +R 316 31 ALA A 31 32 ALA A 32 3.8582 1 1 1 1 13 328 0 +R 317 31 ALA A 31 33 LYS A 33 5.4805 1 0 0 0 0 0 0 +R 318 31 ALA A 31 34 PHE A 34 5.3387 1 0 0 0 0 0 0 +R 319 31 ALA A 31 35 GLU A 35 5.8673 1 1 1 1 124 185 0 +R 320 31 ALA A 31 56 LEU A 56 7.1209 1 1 1 1 34 34 0 +R 321 31 ALA A 31 105 MET A 105 8.7729 1 1 1 1 112 112 0 +R 322 31 ALA A 31 111 TRP A 111 4.9166 1 1 1 1 50 56 0 +R 323 31 ALA A 31 115 CYS A 115 6.6938 1 1 0 0 0 26 0 +R 324 32 ALA A 32 8 LEU A 8 8.9719 1 1 1 1 134 134 0 +R 325 32 ALA A 32 12 MET A 12 10.4631 1 1 1 1 13 13 0 +R 326 32 ALA A 32 28 TRP A 28 6.2956 1 1 1 0 -46 72 0 +R 327 32 ALA A 32 29 VAL A 29 5.1300 1 0 0 0 0 0 0 +R 328 32 ALA A 32 30 CYS A 30 5.5042 1 0 0 0 0 0 0 +R 329 32 ALA A 32 31 ALA A 31 3.8582 1 1 0 0 -16 344 0 +R 330 32 ALA A 32 33 LYS A 33 3.7869 1 1 1 1 4 369 0 +R 331 32 ALA A 32 34 PHE A 34 5.4712 1 0 0 0 0 0 0 +R 332 32 ALA A 32 35 GLU A 35 5.0728 1 0 0 0 0 0 0 +R 333 32 ALA A 32 36 SER A 36 5.7631 1 1 1 1 146 146 0 +R 334 32 ALA A 32 37 ASN A 37 6.3799 1 0 0 0 0 0 0 +R 335 32 ALA A 32 38 PHE A 38 5.5773 1 0 0 0 0 0 0 +R 336 32 ALA A 32 55 ILE A 55 5.5963 1 1 1 0 -45 95 0 +R 337 32 ALA A 32 56 LEU A 56 5.4440 1 1 0 0 0 1 0 +R 338 33 LYS A 33 29 VAL A 29 6.2055 1 1 1 0 -25 53 0 +R 339 33 LYS A 33 30 CYS A 30 5.1917 1 1 0 0 -38 38 0 +R 340 33 LYS A 33 31 ALA A 31 5.4805 1 0 0 0 0 0 0 +R 341 33 LYS A 33 32 ALA A 32 3.7869 1 1 0 0 -19 351 0 +R 342 33 LYS A 33 34 PHE A 34 3.7560 1 1 1 1 23 393 0 +R 343 33 LYS A 33 35 GLU A 35 5.7170 1 0 0 0 0 0 0 +R 344 33 LYS A 33 37 ASN A 37 4.3141 1 1 1 1 179 307 0 +R 345 33 LYS A 33 38 PHE A 38 5.2101 1 1 1 1 29 126 0 +R 346 33 LYS A 33 123 TRP A 123 9.2780 1 1 1 1 84 121 0 +R 347 34 PHE A 34 30 CYS A 30 6.3992 1 1 1 0 -61 103 0 +R 348 34 PHE A 34 31 ALA A 31 5.3387 1 0 0 0 0 0 0 +R 349 34 PHE A 34 32 ALA A 32 5.4712 1 0 0 0 0 0 0 +R 350 34 PHE A 34 33 LYS A 33 3.7560 1 1 1 1 17 445 0 +R 351 34 PHE A 34 35 GLU A 35 3.8162 1 1 1 0 -2 355 0 +R 352 34 PHE A 34 36 SER A 36 5.8515 1 0 0 0 0 0 0 +R 353 34 PHE A 34 37 ASN A 37 5.6664 0 1 1 1 3 4 0 +R 354 34 PHE A 34 110 ALA A 110 5.8542 1 1 1 1 62 120 0 +R 355 34 PHE A 34 114 ARG A 114 7.4511 1 1 1 0 -10 291 0 +R 356 34 PHE A 34 115 CYS A 115 8.4896 1 0 0 0 0 0 0 +R 357 34 PHE A 34 123 TRP A 123 11.6342 1 1 1 1 156 156 0 +R 358 35 GLU A 35 31 ALA A 31 5.8673 1 1 1 0 -85 95 0 +R 359 35 GLU A 35 32 ALA A 32 5.0728 1 0 0 0 0 0 0 +R 360 35 GLU A 35 33 LYS A 33 5.7170 1 0 0 0 0 0 0 +R 361 35 GLU A 35 34 PHE A 34 3.8162 1 1 0 0 -42 384 0 +R 362 35 GLU A 35 36 SER A 36 3.7973 1 1 1 0 -1 326 0 +R 363 35 GLU A 35 37 ASN A 37 6.1632 1 0 0 0 0 0 0 +R 364 35 GLU A 35 44 ASN A 44 9.8723 0 1 1 1 31 31 0 +R 365 35 GLU A 35 55 ILE A 55 6.7296 1 1 0 0 -54 54 0 +R 366 35 GLU A 35 56 LEU A 56 5.8960 1 0 0 0 0 0 0 +R 367 35 GLU A 35 57 GLN A 57 6.0016 1 1 1 0 -184 219 0 +R 368 35 GLU A 35 108 TRP A 108 8.1006 1 1 1 0 -6 162 0 +R 369 35 GLU A 35 109 VAL A 109 8.4267 0 1 1 0 -31 49 0 +R 370 35 GLU A 35 110 ALA A 110 6.0785 1 1 1 1 137 176 0 +R 371 36 SER A 36 32 ALA A 32 5.7631 1 1 1 1 38 38 0 +R 372 36 SER A 36 34 PHE A 34 5.8515 1 0 0 0 0 0 0 +R 373 36 SER A 36 35 GLU A 35 3.7973 1 1 0 0 -2 362 0 +R 374 36 SER A 36 37 ASN A 37 3.8326 1 1 1 0 -26 382 0 +R 375 36 SER A 36 38 PHE A 38 5.1834 1 1 1 1 48 48 0 +R 376 36 SER A 36 39 ASN A 39 5.4539 1 1 1 1 3 162 0 +R 377 36 SER A 36 42 ALA A 42 5.5964 1 1 0 0 -9 33 0 +R 378 36 SER A 36 44 ASN A 44 9.2935 0 1 0 0 0 1 0 +R 379 36 SER A 36 54 GLY A 54 6.7929 1 1 0 0 0 40 0 +R 380 36 SER A 36 55 ILE A 55 5.1236 1 1 1 1 79 149 0 +R 381 36 SER A 36 57 GLN A 57 6.6652 1 0 0 0 0 0 0 +R 382 37 ASN A 37 2 VAL A 2 7.9443 0 1 0 0 -59 59 0 +R 383 37 ASN A 37 32 ALA A 32 6.3799 1 0 0 0 0 0 0 +R 384 37 ASN A 37 33 LYS A 33 4.3141 1 1 1 1 185 288 0 +R 385 37 ASN A 37 34 PHE A 34 5.6664 0 1 0 0 0 1 0 +R 386 37 ASN A 37 35 GLU A 35 6.1632 1 1 0 0 0 1 0 +R 387 37 ASN A 37 36 SER A 36 3.8326 1 1 0 0 -43 379 0 +R 388 37 ASN A 37 38 PHE A 38 3.8358 1 1 1 0 -29 388 0 +R 389 37 ASN A 37 39 ASN A 39 5.4975 1 1 1 1 8 18 0 +R 390 38 PHE A 38 1 LYS A 1 8.1596 1 1 0 0 -12 12 0 +R 391 38 PHE A 38 2 VAL A 2 5.5799 1 1 1 1 1 1 0 +R 392 38 PHE A 38 3 PHE A 3 5.3547 1 1 1 0 -5 210 0 +R 393 38 PHE A 38 5 ARG A 5 7.6636 1 1 1 1 21 94 0 +R 394 38 PHE A 38 8 LEU A 8 7.9077 1 1 1 1 78 78 0 +R 395 38 PHE A 38 29 VAL A 29 8.4877 1 1 1 1 43 117 0 +R 396 38 PHE A 38 32 ALA A 32 5.5773 1 0 0 0 0 0 0 +R 397 38 PHE A 38 33 LYS A 33 5.2101 1 1 1 1 22 242 0 +R 398 38 PHE A 38 36 SER A 36 5.1834 1 1 1 1 10 38 0 +R 399 38 PHE A 38 37 ASN A 37 3.8358 1 1 0 0 -67 379 0 +R 400 38 PHE A 38 39 ASN A 39 3.8122 1 1 1 1 24 317 0 +R 401 38 PHE A 38 40 THR A 40 6.4024 1 0 0 0 0 0 0 +R 402 38 PHE A 38 55 ILE A 55 5.7406 1 1 0 0 -18 31 0 +R 403 39 ASN A 39 1 LYS A 1 5.7421 1 1 0 0 -31 40 0 +R 404 39 ASN A 39 2 VAL A 2 4.2809 1 1 1 0 -29 96 0 +R 405 39 ASN A 39 36 SER A 36 5.4539 1 1 1 0 -49 115 0 +R 406 39 ASN A 39 37 ASN A 37 5.4975 1 1 1 0 -4 11 0 +R 407 39 ASN A 39 38 PHE A 38 3.8122 1 1 0 0 -14 363 0 +R 408 39 ASN A 39 40 THR A 40 3.8635 1 1 1 1 36 366 0 +R 409 39 ASN A 39 41 GLN A 41 5.4299 1 1 1 1 18 147 0 +R 410 39 ASN A 39 42 ALA A 42 5.7128 1 1 1 0 -23 110 0 +R 411 39 ASN A 39 55 ILE A 55 5.6995 1 0 0 0 0 0 0 +R 412 40 THR A 40 1 LYS A 1 5.4657 1 1 1 1 155 157 0 +R 413 40 THR A 40 3 PHE A 3 7.9444 1 1 1 1 154 154 0 +R 414 40 THR A 40 38 PHE A 38 6.4024 1 0 0 0 0 0 0 +R 415 40 THR A 40 39 ASN A 39 3.8635 1 1 0 0 0 339 0 +R 416 40 THR A 40 41 GLN A 41 3.8464 1 1 1 1 19 306 0 +R 417 40 THR A 40 42 ALA A 42 5.7069 1 0 0 0 0 0 0 +R 418 40 THR A 40 54 GLY A 54 4.5843 1 1 0 0 0 16 0 +R 419 40 THR A 40 55 ILE A 55 4.5521 1 1 1 1 34 54 0 +R 420 40 THR A 40 84 LEU A 84 5.0346 1 1 1 1 14 184 0 +R 421 40 THR A 40 85 SER A 85 6.2303 1 1 1 0 -71 109 0 +R 422 40 THR A 40 86 SER A 86 6.2290 1 1 0 0 0 2 0 +R 423 40 THR A 40 88 ILE A 88 7.7607 1 1 1 1 13 13 0 +R 424 41 GLN A 41 1 LYS A 1 6.8324 1 1 0 0 -73 76 0 +R 425 41 GLN A 41 39 ASN A 39 5.4299 1 1 1 0 -31 58 0 +R 426 41 GLN A 41 40 THR A 40 3.8464 1 1 0 0 -62 409 0 +R 427 41 GLN A 41 42 ALA A 42 3.8155 1 1 1 1 13 356 0 +R 428 41 GLN A 41 43 THR A 43 6.5152 1 1 1 0 -18 80 0 +R 429 41 GLN A 41 84 LEU A 84 4.8606 1 1 1 0 -79 95 0 +R 430 42 ALA A 42 36 SER A 36 5.5964 1 1 0 0 -19 94 0 +R 431 42 ALA A 42 39 ASN A 39 5.7128 1 1 1 0 -69 103 0 +R 432 42 ALA A 42 40 THR A 40 5.7069 1 0 0 0 0 0 0 +R 433 42 ALA A 42 41 GLN A 41 3.8155 1 1 0 0 -24 359 0 +R 434 42 ALA A 42 43 THR A 43 3.8859 1 1 1 1 5 326 0 +R 435 42 ALA A 42 44 ASN A 44 6.8831 0 1 0 0 -17 17 0 +R 436 42 ALA A 42 53 TYR A 53 6.0588 1 0 0 0 0 0 0 +R 437 42 ALA A 42 54 GLY A 54 5.0278 1 1 1 1 192 192 0 +R 438 42 ALA A 42 57 GLN A 57 7.3752 1 1 1 0 -61 69 0 +R 439 42 ALA A 42 84 LEU A 84 7.3563 1 0 0 0 0 0 0 +R 440 43 THR A 43 41 GLN A 41 6.5152 1 1 1 0 -27 55 0 +R 441 43 THR A 43 42 ALA A 42 3.8859 1 1 0 0 -37 391 0 +R 442 43 THR A 43 44 ASN A 44 3.7688 1 1 1 1 13 431 0 +R 443 43 THR A 43 51 THR A 51 6.7249 1 1 0 0 -1 34 0 +R 444 43 THR A 43 52 ASP A 52 5.4799 1 1 0 0 0 18 0 +R 445 43 THR A 43 53 TYR A 53 4.7167 1 1 1 1 138 138 0 +R 446 43 THR A 43 57 GLN A 57 7.1223 1 0 0 0 0 0 0 +R 447 43 THR A 43 84 LEU A 84 8.5599 1 1 1 1 36 36 0 +R 448 44 ASN A 44 35 GLU A 35 9.8723 0 1 1 1 45 45 0 +R 449 44 ASN A 44 42 ALA A 42 6.8831 0 1 0 0 -12 12 0 +R 450 44 ASN A 44 43 THR A 43 3.7688 1 1 1 0 -15 451 0 +R 451 44 ASN A 44 45 ARG A 45 3.7166 1 1 1 0 0 387 0 +R 452 44 ASN A 44 46 ASN A 46 6.5794 0 1 0 0 -6 6 0 +R 453 44 ASN A 44 51 THR A 51 5.5411 1 0 0 0 0 0 0 +R 454 44 ASN A 44 52 ASP A 52 5.2528 1 1 1 1 122 156 0 +R 455 44 ASN A 44 57 GLN A 57 7.9104 1 1 1 1 80 172 0 +R 456 45 ARG A 45 44 ASN A 44 3.7166 1 1 1 0 -12 381 0 +R 457 45 ARG A 45 46 ASN A 46 3.7641 1 1 1 0 -19 425 0 +R 458 45 ARG A 45 47 THR A 47 6.9141 0 1 1 1 3 4 0 +R 459 45 ARG A 45 49 GLY A 49 6.6305 1 1 1 1 15 60 0 +R 460 45 ARG A 45 50 SER A 50 6.1524 1 1 0 0 0 71 0 +R 461 45 ARG A 45 51 THR A 51 4.1733 1 1 0 0 0 23 0 +R 462 45 ARG A 45 68 ARG A 68 11.3353 1 1 0 0 -168 229 0 +R 463 46 ASN A 46 44 ASN A 44 6.5794 0 1 1 0 -9 12 0 +R 464 46 ASN A 46 45 ARG A 45 3.7641 1 1 1 0 -43 445 0 +R 465 46 ASN A 46 47 THR A 47 3.7875 1 1 1 0 -14 376 0 +R 466 46 ASN A 46 48 ASP A 48 5.4237 1 1 0 0 -52 57 0 +R 467 46 ASN A 46 49 GLY A 49 5.3347 1 1 1 1 86 87 0 +R 468 46 ASN A 46 50 SER A 50 5.3628 1 1 1 1 25 51 0 +R 469 46 ASN A 46 51 THR A 51 5.5953 1 0 0 0 0 0 0 +R 470 46 ASN A 46 52 ASP A 52 7.6137 1 1 1 1 75 130 0 +R 471 46 ASN A 46 59 ASN A 59 9.1269 1 1 1 1 182 188 0 +R 472 47 THR A 47 46 ASN A 46 3.7875 1 1 1 0 -15 361 0 +R 473 47 THR A 47 48 ASP A 48 3.7632 1 1 1 1 28 353 0 +R 474 47 THR A 47 49 GLY A 49 5.2181 1 1 1 1 35 47 0 +R 475 48 ASP A 48 46 ASN A 46 5.4237 1 1 0 0 -19 25 0 +R 476 48 ASP A 48 47 THR A 47 3.7632 1 1 0 0 -29 389 0 +R 477 48 ASP A 48 49 GLY A 49 3.7979 1 1 1 1 21 317 0 +R 478 48 ASP A 48 50 SER A 50 5.5073 1 1 1 1 235 235 0 +R 479 48 ASP A 48 59 ASN A 59 10.9299 0 1 1 0 -2 6 0 +R 480 48 ASP A 48 61 ARG A 61 8.7820 1 1 1 1 155 237 0 +R 481 48 ASP A 48 69 THR A 69 8.8838 0 1 0 0 -1 1 0 +R 482 49 GLY A 49 45 ARG A 45 6.6305 1 1 0 0 0 89 0 +R 483 49 GLY A 49 46 ASN A 46 5.3347 1 1 1 1 19 57 0 +R 484 49 GLY A 49 47 THR A 47 5.2181 1 1 0 0 0 17 0 +R 485 49 GLY A 49 48 ASP A 48 3.7979 1 1 0 0 -29 387 0 +R 486 49 GLY A 49 50 SER A 50 3.7017 1 1 1 1 14 349 0 +R 487 49 GLY A 49 51 THR A 51 6.5946 0 1 1 1 2 2 0 +R 488 49 GLY A 49 68 ARG A 68 8.1773 0 1 0 0 -40 53 0 +R 489 49 GLY A 49 69 THR A 69 6.4717 0 1 1 1 69 70 0 +R 490 49 GLY A 49 70 PRO A 70 8.6350 0 1 0 0 0 6 0 +R 491 50 SER A 50 45 ARG A 45 6.1524 1 0 0 0 0 0 0 +R 492 50 SER A 50 46 ASN A 46 5.3628 1 1 1 1 179 179 0 +R 493 50 SER A 50 48 ASP A 48 5.5073 1 1 1 1 91 116 0 +R 494 50 SER A 50 49 GLY A 49 3.7017 1 1 0 0 -24 393 0 +R 495 50 SER A 50 51 THR A 51 3.9416 1 1 1 1 36 307 0 +R 496 50 SER A 50 59 ASN A 59 6.7524 1 1 1 1 104 162 0 +R 497 50 SER A 50 60 SER A 60 5.4691 1 1 0 0 0 67 0 +R 498 50 SER A 50 61 ARG A 61 5.5177 1 1 0 0 0 6 0 +R 499 50 SER A 50 69 THR A 69 5.5332 1 1 0 0 0 50 0 +R 500 51 THR A 51 43 THR A 43 6.7249 1 1 0 0 0 19 0 +R 501 51 THR A 51 44 ASN A 44 5.5411 1 1 0 0 -64 88 0 +R 502 51 THR A 51 45 ARG A 45 4.1733 1 1 0 0 0 2 0 +R 503 51 THR A 51 46 ASN A 46 5.5953 1 0 0 0 0 0 0 +R 504 51 THR A 51 50 SER A 50 3.9416 1 1 1 1 10 379 0 +R 505 51 THR A 51 52 ASP A 52 3.8949 1 1 1 0 -40 355 0 +R 506 51 THR A 51 53 TYR A 53 6.5005 1 1 1 1 70 146 0 +R 507 51 THR A 51 59 ASN A 59 5.7402 1 0 0 0 0 0 0 +R 508 51 THR A 51 60 SER A 60 5.4996 1 1 1 1 168 168 0 +R 509 51 THR A 51 66 ASP A 66 8.3256 1 0 0 0 0 0 0 +R 510 51 THR A 51 68 ARG A 68 9.1481 1 1 1 1 115 157 0 +R 511 52 ASP A 52 43 THR A 43 5.4799 1 1 0 0 0 12 0 +R 512 52 ASP A 52 44 ASN A 44 5.2528 1 1 1 1 110 126 0 +R 513 52 ASP A 52 46 ASN A 46 7.6137 1 1 1 1 134 134 0 +R 514 52 ASP A 52 51 THR A 51 3.8949 1 1 0 0 -5 337 0 +R 515 52 ASP A 52 53 TYR A 53 3.7885 1 1 1 1 18 345 0 +R 516 52 ASP A 52 57 GLN A 57 4.5222 1 1 0 0 -155 164 0 +R 517 52 ASP A 52 58 ILE A 58 4.9171 1 1 0 0 0 5 0 +R 518 52 ASP A 52 59 ASN A 59 4.3832 1 1 1 1 120 202 0 +R 519 53 TYR A 53 42 ALA A 42 6.0588 1 1 0 0 0 1 0 +R 520 53 TYR A 53 43 THR A 43 4.7167 1 1 1 1 111 111 0 +R 521 53 TYR A 53 51 THR A 51 6.5005 1 1 1 0 -111 172 0 +R 522 53 TYR A 53 52 ASP A 52 3.7885 1 1 0 0 -1 354 0 +R 523 53 TYR A 53 54 GLY A 54 3.8089 1 1 1 1 16 350 0 +R 524 53 TYR A 53 57 GLN A 57 4.4524 1 1 1 1 4 4 0 +R 525 53 TYR A 53 58 ILE A 58 5.1266 1 1 1 1 72 153 0 +R 526 53 TYR A 53 60 SER A 60 7.7842 1 0 0 0 0 0 0 +R 527 53 TYR A 53 64 CYS A 64 9.1195 1 0 0 0 0 0 0 +R 528 53 TYR A 53 66 ASP A 66 9.7084 1 1 1 1 80 176 0 +R 529 53 TYR A 53 68 ARG A 68 13.3743 0 1 1 1 27 30 0 +R 530 53 TYR A 53 80 CYS A 80 6.5643 1 1 1 1 41 211 0 +R 531 53 TYR A 53 81 SER A 81 7.5160 0 1 0 0 -4 10 0 +R 532 53 TYR A 53 83 LEU A 83 6.1854 1 1 1 0 -3 11 0 +R 533 53 TYR A 53 84 LEU A 84 6.6054 1 1 1 1 22 22 0 +R 534 54 GLY A 54 36 SER A 36 6.7929 1 1 0 0 0 9 0 +R 535 54 GLY A 54 39 ASN A 39 7.0228 0 1 0 0 0 5 0 +R 536 54 GLY A 54 40 THR A 40 4.5843 1 1 0 0 0 102 0 +R 537 54 GLY A 54 42 ALA A 42 5.0278 1 1 1 1 49 51 0 +R 538 54 GLY A 54 53 TYR A 53 3.8089 1 1 0 0 -7 353 0 +R 539 54 GLY A 54 55 ILE A 55 3.7039 1 1 1 1 29 356 0 +R 540 54 GLY A 54 56 LEU A 56 5.3851 1 1 0 0 0 1 0 +R 541 54 GLY A 54 57 GLN A 57 4.9429 1 1 1 1 146 146 0 +R 542 54 GLY A 54 83 LEU A 83 5.3232 1 1 0 0 0 41 0 +R 543 54 GLY A 54 84 LEU A 84 4.8428 1 1 0 0 -4 4 0 +R 544 55 ILE A 55 3 PHE A 3 9.3473 1 1 1 1 98 98 0 +R 545 55 ILE A 55 8 LEU A 8 10.0426 1 1 1 1 62 62 0 +R 546 55 ILE A 55 12 MET A 12 11.3010 0 1 1 1 2 2 0 +R 547 55 ILE A 55 32 ALA A 32 5.5963 1 1 1 1 39 91 0 +R 548 55 ILE A 55 35 GLU A 35 6.7296 1 1 0 0 -1 1 0 +R 549 55 ILE A 55 36 SER A 36 5.1236 1 1 1 1 50 166 0 +R 550 55 ILE A 55 38 PHE A 38 5.7406 1 1 0 0 -109 112 0 +R 551 55 ILE A 55 39 ASN A 39 5.6995 1 1 1 1 2 2 0 +R 552 55 ILE A 55 40 THR A 40 4.5521 1 1 1 1 15 24 0 +R 553 55 ILE A 55 54 GLY A 54 3.7039 1 1 0 0 0 341 0 +R 554 55 ILE A 55 56 LEU A 56 3.7519 1 1 1 1 25 367 0 +R 555 55 ILE A 55 57 GLN A 57 5.6235 1 0 0 0 0 0 0 +R 556 55 ILE A 55 88 ILE A 88 8.0660 1 1 1 1 37 37 0 +R 557 55 ILE A 55 91 SER A 91 7.4339 1 1 0 0 -81 118 0 +R 558 56 LEU A 56 12 MET A 12 11.5983 1 1 1 1 79 79 0 +R 559 56 LEU A 56 28 TRP A 28 8.7724 0 1 1 0 -1 19 0 +R 560 56 LEU A 56 31 ALA A 31 7.1209 1 1 1 1 70 70 0 +R 561 56 LEU A 56 32 ALA A 32 5.4440 1 1 1 0 -98 114 0 +R 562 56 LEU A 56 35 GLU A 35 5.8960 1 1 0 0 0 1 0 +R 563 56 LEU A 56 54 GLY A 54 5.3851 1 1 0 0 0 3 0 +R 564 56 LEU A 56 55 ILE A 55 3.7519 1 1 1 0 -20 429 0 +R 565 56 LEU A 56 57 GLN A 57 3.7252 1 1 1 1 12 337 0 +R 566 56 LEU A 56 58 ILE A 58 5.6664 1 1 1 1 37 37 0 +R 567 56 LEU A 56 91 SER A 91 6.9590 0 1 0 0 -29 32 0 +R 568 56 LEU A 56 92 VAL A 92 8.3697 0 1 0 0 0 1 0 +R 569 56 LEU A 56 95 ALA A 95 7.7189 1 1 1 1 140 140 0 +R 570 56 LEU A 56 108 TRP A 108 8.2153 1 1 1 1 131 203 0 +R 571 57 GLN A 57 35 GLU A 35 6.0016 1 1 0 0 -170 175 0 +R 572 57 GLN A 57 36 SER A 36 6.6652 1 0 0 0 0 0 0 +R 573 57 GLN A 57 42 ALA A 42 7.3752 1 1 1 1 118 142 0 +R 574 57 GLN A 57 43 THR A 43 7.1223 1 0 0 0 0 0 0 +R 575 57 GLN A 57 44 ASN A 44 7.9104 1 1 1 1 150 163 0 +R 576 57 GLN A 57 52 ASP A 52 4.5222 1 1 1 0 -86 120 0 +R 577 57 GLN A 57 53 TYR A 53 4.4524 1 1 0 0 0 5 0 +R 578 57 GLN A 57 54 GLY A 54 4.9429 1 1 1 1 108 124 0 +R 579 57 GLN A 57 55 ILE A 55 5.6235 1 0 0 0 0 0 0 +R 580 57 GLN A 57 56 LEU A 56 3.7252 1 1 0 0 -62 391 0 +R 581 57 GLN A 57 58 ILE A 58 3.8369 1 1 1 1 20 351 0 +R 582 57 GLN A 57 59 ASN A 59 6.4000 1 1 1 1 9 19 0 +R 583 57 GLN A 57 108 TRP A 108 8.2910 0 1 1 1 13 33 0 +R 584 58 ILE A 58 52 ASP A 52 4.9171 1 1 0 0 0 1 0 +R 585 58 ILE A 58 53 TYR A 53 5.1266 1 1 1 1 85 125 0 +R 586 58 ILE A 58 56 LEU A 56 5.6664 1 1 1 0 -21 50 0 +R 587 58 ILE A 58 57 GLN A 57 3.8369 1 1 0 0 -1 340 0 +R 588 58 ILE A 58 59 ASN A 59 3.7920 1 1 1 1 8 375 0 +R 589 58 ILE A 58 63 TRP A 63 6.7289 1 1 1 1 142 142 0 +R 590 58 ILE A 58 83 LEU A 83 7.8716 1 1 1 1 62 62 0 +R 591 58 ILE A 58 91 SER A 91 7.7587 1 1 0 0 -148 183 0 +R 592 58 ILE A 58 94 CYS A 94 8.1513 1 1 1 1 27 28 0 +R 593 58 ILE A 58 95 ALA A 95 7.7436 1 1 0 0 -3 9 0 +R 594 58 ILE A 58 98 ILE A 98 8.9872 1 1 1 1 91 96 0 +R 595 59 ASN A 59 46 ASN A 46 9.1269 1 1 1 1 18 18 0 +R 596 59 ASN A 59 48 ASP A 48 10.9299 0 1 1 1 4 7 0 +R 597 59 ASN A 59 50 SER A 50 6.7524 1 1 1 1 128 134 0 +R 598 59 ASN A 59 51 THR A 51 5.7402 1 0 0 0 0 0 0 +R 599 59 ASN A 59 52 ASP A 52 4.3832 1 1 1 1 78 125 0 +R 600 59 ASN A 59 57 GLN A 57 6.4000 1 1 0 0 -7 7 0 +R 601 59 ASN A 59 58 ILE A 58 3.7920 1 1 0 0 -9 353 0 +R 602 59 ASN A 59 60 SER A 60 3.8442 1 1 1 1 25 327 0 +R 603 59 ASN A 59 61 ARG A 61 5.5522 1 1 1 1 50 218 0 +R 604 59 ASN A 59 62 TRP A 62 6.1912 1 1 1 1 1 30 0 +R 605 59 ASN A 59 63 TRP A 63 5.8889 1 1 1 1 162 200 0 +R 606 60 SER A 60 50 SER A 50 5.4691 1 0 0 0 0 0 0 +R 607 60 SER A 60 51 THR A 51 5.4996 1 1 1 1 101 120 0 +R 608 60 SER A 60 53 TYR A 53 7.7842 1 0 0 0 0 0 0 +R 609 60 SER A 60 59 ASN A 59 3.8442 1 1 0 0 0 339 0 +R 610 60 SER A 60 61 ARG A 61 3.8908 1 1 1 1 17 283 0 +R 611 60 SER A 60 62 TRP A 62 5.5049 1 0 0 0 0 0 0 +R 612 60 SER A 60 64 CYS A 64 5.0013 1 1 0 0 -1 31 0 +R 613 60 SER A 60 66 ASP A 66 6.3315 1 1 0 0 0 125 0 +R 614 60 SER A 60 69 THR A 69 6.5717 1 1 1 1 101 105 0 +R 615 60 SER A 60 72 SER A 72 6.4249 1 1 1 1 199 206 0 +R 616 60 SER A 60 80 CYS A 80 6.8143 1 1 0 0 0 32 0 +R 617 61 ARG A 61 48 ASP A 48 8.7820 1 1 1 1 204 281 0 +R 618 61 ARG A 61 50 SER A 50 5.5177 1 1 0 0 0 4 0 +R 619 61 ARG A 61 59 ASN A 59 5.5522 1 1 1 0 -68 70 0 +R 620 61 ARG A 61 60 SER A 60 3.8908 1 1 1 0 -12 362 0 +R 621 61 ARG A 61 62 TRP A 62 3.8101 1 1 1 1 110 481 0 +R 622 61 ARG A 61 69 THR A 69 6.2823 1 1 0 0 -70 92 0 +R 623 61 ARG A 61 70 PRO A 70 8.0292 1 1 1 1 167 167 0 +R 624 61 ARG A 61 71 GLY A 71 7.0231 0 1 0 0 -2 17 0 +R 625 61 ARG A 61 72 SER A 72 4.5693 1 1 0 0 0 14 0 +R 626 61 ARG A 61 73 ARG A 73 6.4875 1 1 1 1 130 130 0 +R 627 62 TRP A 62 59 ASN A 59 6.1912 1 1 1 0 -15 51 0 +R 628 62 TRP A 62 60 SER A 60 5.5049 1 0 0 0 0 0 0 +R 629 62 TRP A 62 61 ARG A 61 3.8101 1 1 1 1 9 531 0 +R 630 62 TRP A 62 63 TRP A 63 3.7646 1 1 1 0 -14 426 0 +R 631 62 TRP A 62 64 CYS A 64 6.3048 1 1 0 0 0 3 0 +R 632 62 TRP A 62 73 ARG A 73 4.7823 1 1 1 0 -49 187 0 +R 633 62 TRP A 62 74 ASN A 74 5.5079 1 1 1 1 11 11 0 +R 634 62 TRP A 62 75 LEU A 75 5.9402 1 1 1 1 178 204 0 +R 635 63 TRP A 63 58 ILE A 58 6.7289 1 1 1 1 89 89 0 +R 636 63 TRP A 63 59 ASN A 59 5.8889 1 1 0 0 -69 69 0 +R 637 63 TRP A 63 62 TRP A 62 3.7646 1 1 1 0 -6 481 0 +R 638 63 TRP A 63 64 CYS A 64 3.7610 1 1 1 0 -5 343 0 +R 639 63 TRP A 63 74 ASN A 74 4.6495 1 0 0 0 0 0 0 +R 640 63 TRP A 63 75 LEU A 75 4.5592 1 1 1 1 117 117 0 +R 641 63 TRP A 63 76 CYS A 76 5.1313 1 1 1 1 103 169 0 +R 642 63 TRP A 63 78 ILE A 78 7.9100 1 0 0 0 0 0 0 +R 643 63 TRP A 63 94 CYS A 94 7.4243 1 1 0 0 0 1 0 +R 644 63 TRP A 63 97 LYS A 97 9.0609 1 1 1 1 22 24 0 +R 645 63 TRP A 63 98 ILE A 98 8.1327 1 1 1 1 99 261 0 +R 646 63 TRP A 63 101 ASP A 101 11.5849 1 1 0 0 -76 144 0 +R 647 63 TRP A 63 107 ALA A 107 11.8922 0 1 1 1 4 4 0 +R 648 64 CYS A 64 53 TYR A 53 9.1195 1 1 0 0 0 10 0 +R 649 64 CYS A 64 59 ASN A 59 6.9688 0 1 0 0 0 4 0 +R 650 64 CYS A 64 60 SER A 60 5.0013 1 1 0 0 -120 167 0 +R 651 64 CYS A 64 62 TRP A 62 6.3048 1 1 0 0 0 3 0 +R 652 64 CYS A 64 63 TRP A 63 3.7610 1 1 0 0 -18 385 0 +R 653 64 CYS A 64 65 ASN A 65 3.7533 1 1 1 1 19 339 0 +R 654 64 CYS A 64 72 SER A 72 7.6034 1 1 1 1 5 5 0 +R 655 64 CYS A 64 74 ASN A 74 4.3585 1 1 0 0 0 24 0 +R 656 64 CYS A 64 78 ILE A 78 5.2721 1 1 1 0 -50 52 0 +R 657 64 CYS A 64 79 PRO A 79 5.5062 1 0 0 0 0 0 0 +R 658 64 CYS A 64 80 CYS A 80 4.9610 1 1 0 0 0 244 0 +R 659 64 CYS A 64 83 LEU A 83 8.6424 1 1 1 1 39 94 0 +R 660 65 ASN A 65 64 CYS A 64 3.7533 1 1 0 0 0 356 0 +R 661 65 ASN A 65 66 ASP A 66 3.8054 1 1 1 1 25 333 0 +R 662 65 ASN A 65 67 GLY A 67 5.7673 1 1 1 1 35 159 0 +R 663 65 ASN A 65 72 SER A 72 6.7196 0 1 1 1 39 61 0 +R 664 65 ASN A 65 74 ASN A 74 5.3596 1 1 1 0 -106 121 0 +R 665 65 ASN A 65 78 ILE A 78 6.2178 1 1 1 1 4 14 0 +R 666 65 ASN A 65 79 PRO A 79 4.7112 1 1 1 0 -55 57 0 +R 667 65 ASN A 65 80 CYS A 80 5.3811 1 1 1 1 88 88 0 +R 668 66 ASP A 66 51 THR A 51 8.3256 1 1 0 0 0 7 0 +R 669 66 ASP A 66 53 TYR A 53 9.7084 1 1 1 1 36 176 0 +R 670 66 ASP A 66 60 SER A 60 6.3315 1 1 1 1 32 36 0 +R 671 66 ASP A 66 65 ASN A 65 3.8054 1 1 0 0 0 362 0 +R 672 66 ASP A 66 67 GLY A 67 3.8249 1 1 1 1 10 319 0 +R 673 66 ASP A 66 68 ARG A 68 5.5275 1 1 1 0 -7 127 0 +R 674 66 ASP A 66 69 THR A 69 6.6481 1 1 1 1 191 194 0 +R 675 66 ASP A 66 79 PRO A 79 5.9021 0 1 0 0 0 3 0 +R 676 66 ASP A 66 80 CYS A 80 5.2749 1 1 1 1 7 42 0 +R 677 66 ASP A 66 81 SER A 81 7.3090 0 1 0 0 -1 5 0 +R 678 67 GLY A 67 65 ASN A 65 5.7673 1 1 1 1 14 97 0 +R 679 67 GLY A 67 66 ASP A 66 3.8249 1 1 1 0 -35 376 0 +R 680 67 GLY A 67 68 ARG A 68 3.7098 1 1 1 1 4 349 0 +R 681 67 GLY A 67 69 THR A 69 6.0387 1 1 0 0 0 3 0 +R 682 68 ARG A 68 45 ARG A 45 11.3353 1 1 0 0 -233 270 0 +R 683 68 ARG A 68 49 GLY A 49 8.1773 0 1 0 0 -21 24 0 +R 684 68 ARG A 68 51 THR A 51 9.1481 1 1 1 1 73 136 0 +R 685 68 ARG A 68 53 TYR A 53 13.3743 0 1 1 1 8 18 0 +R 686 68 ARG A 68 66 ASP A 66 5.5275 1 1 1 0 -50 78 0 +R 687 68 ARG A 68 67 GLY A 67 3.7098 1 1 0 0 -29 397 0 +R 688 68 ARG A 68 69 THR A 69 3.8098 1 1 1 1 2 345 0 +R 689 68 ARG A 68 70 PRO A 70 6.1627 1 1 0 0 -60 79 0 +R 690 69 THR A 69 49 GLY A 49 6.4717 0 1 1 1 9 9 0 +R 691 69 THR A 69 50 SER A 50 5.5332 1 1 0 0 0 60 0 +R 692 69 THR A 69 60 SER A 60 6.5717 1 1 1 0 -24 149 0 +R 693 69 THR A 69 61 ARG A 61 6.2823 1 1 0 0 -127 127 0 +R 694 69 THR A 69 66 ASP A 66 6.6481 1 1 1 1 128 149 0 +R 695 69 THR A 69 67 GLY A 67 6.0387 1 0 0 0 0 0 0 +R 696 69 THR A 69 68 ARG A 68 3.8098 1 1 1 0 -11 357 0 +R 697 69 THR A 69 70 PRO A 70 3.8378 1 1 0 0 -10 323 0 +R 698 69 THR A 69 71 GLY A 71 6.1353 1 1 1 1 1 1 0 +R 699 69 THR A 69 72 SER A 72 5.4835 1 1 1 1 166 196 0 +R 700 70 PRO A 70 49 GLY A 49 8.6350 0 1 0 0 -12 17 0 +R 701 70 PRO A 70 61 ARG A 61 8.0292 1 1 1 1 74 96 0 +R 702 70 PRO A 70 68 ARG A 68 6.1627 1 1 0 0 -40 50 0 +R 703 70 PRO A 70 69 THR A 69 3.8378 1 1 1 0 -8 416 0 +R 704 70 PRO A 70 71 GLY A 71 3.7037 1 1 1 0 -7 364 0 +R 705 70 PRO A 70 72 SER A 72 5.5397 1 0 0 0 0 0 0 +R 706 71 GLY A 71 61 ARG A 61 7.0231 0 1 1 0 -8 65 0 +R 707 71 GLY A 71 69 THR A 69 6.1353 1 1 1 1 1 1 0 +R 708 71 GLY A 71 70 PRO A 70 3.7037 1 1 0 0 -62 367 0 +R 709 71 GLY A 71 72 SER A 72 3.7913 1 1 1 1 16 371 0 +R 710 71 GLY A 71 73 ARG A 73 6.3954 1 1 1 0 -31 70 0 +R 711 72 SER A 72 60 SER A 60 6.4249 1 1 1 1 96 125 0 +R 712 72 SER A 72 61 ARG A 61 4.5693 1 1 0 0 0 31 0 +R 713 72 SER A 72 64 CYS A 64 7.6034 1 1 1 1 90 93 0 +R 714 72 SER A 72 65 ASN A 65 6.7196 0 1 0 0 0 44 0 +R 715 72 SER A 72 69 THR A 69 5.4835 1 1 1 1 6 95 0 +R 716 72 SER A 72 70 PRO A 70 5.5397 1 0 0 0 0 0 0 +R 717 72 SER A 72 71 GLY A 71 3.7913 1 1 1 0 -18 376 0 +R 718 72 SER A 72 73 ARG A 73 3.8449 1 1 1 1 35 355 0 +R 719 72 SER A 72 74 ASN A 74 5.9277 1 1 1 1 7 24 0 +R 720 73 ARG A 73 61 ARG A 61 6.4875 1 1 1 1 13 13 0 +R 721 73 ARG A 73 62 TRP A 62 4.7823 1 1 1 0 -114 187 0 +R 722 73 ARG A 73 71 GLY A 71 6.3954 1 1 0 0 -41 43 0 +R 723 73 ARG A 73 72 SER A 72 3.8449 1 1 0 0 -4 357 0 +R 724 73 ARG A 73 74 ASN A 74 3.8190 1 1 1 0 -20 388 0 +R 725 73 ARG A 73 75 LEU A 75 5.6080 1 1 1 0 -44 102 0 +R 726 74 ASN A 74 62 TRP A 62 5.5079 1 1 1 1 13 21 0 +R 727 74 ASN A 74 63 TRP A 63 4.6495 1 1 0 0 0 12 0 +R 728 74 ASN A 74 64 CYS A 64 4.3585 1 1 0 0 0 15 0 +R 729 74 ASN A 74 65 ASN A 65 5.3596 1 1 1 0 -112 159 0 +R 730 74 ASN A 74 72 SER A 72 5.9277 1 1 1 0 -2 24 0 +R 731 74 ASN A 74 73 ARG A 73 3.8190 1 1 0 0 -48 374 0 +R 732 74 ASN A 74 75 LEU A 75 3.7831 1 1 1 1 15 371 0 +R 733 74 ASN A 74 76 CYS A 76 5.6175 1 0 0 0 0 0 0 +R 734 74 ASN A 74 77 ASN A 77 5.1976 1 1 1 1 25 156 0 +R 735 74 ASN A 74 78 ILE A 78 6.8599 1 1 1 1 14 235 0 +R 736 74 ASN A 74 79 PRO A 79 8.2352 0 1 0 0 -2 3 0 +R 737 75 LEU A 75 62 TRP A 62 5.9402 1 1 1 0 0 128 0 +R 738 75 LEU A 75 63 TRP A 63 4.5592 1 1 1 1 134 134 0 +R 739 75 LEU A 75 73 ARG A 73 5.6080 1 1 1 0 -23 144 0 +R 740 75 LEU A 75 74 ASN A 74 3.7831 1 1 0 0 -13 349 0 +R 741 75 LEU A 75 76 CYS A 76 3.8164 1 1 1 1 18 338 0 +R 742 75 LEU A 75 77 ASN A 77 5.4213 1 1 1 0 -15 21 0 +R 743 75 LEU A 75 97 LYS A 97 8.3701 0 1 1 0 -39 65 0 +R 744 75 LEU A 75 101 ASP A 101 10.9431 0 1 0 0 -36 36 0 +R 745 76 CYS A 76 63 TRP A 63 5.1313 1 1 1 0 -12 99 0 +R 746 76 CYS A 76 74 ASN A 74 5.6175 1 0 0 0 0 0 0 +R 747 76 CYS A 76 75 LEU A 75 3.8164 1 1 0 0 -15 369 0 +R 748 76 CYS A 76 77 ASN A 77 3.7920 1 1 1 0 -31 391 0 +R 749 76 CYS A 76 78 ILE A 78 5.6591 1 1 1 0 -13 45 0 +R 750 76 CYS A 76 94 CYS A 94 5.4641 1 1 1 1 31 297 0 +R 751 76 CYS A 76 97 LYS A 97 7.3462 1 1 1 1 1 27 0 +R 752 77 ASN A 77 74 ASN A 74 5.1976 1 1 1 0 -37 102 0 +R 753 77 ASN A 77 75 LEU A 75 5.4213 1 1 0 0 -13 13 0 +R 754 77 ASN A 77 76 CYS A 76 3.7920 1 1 0 0 -63 407 0 +R 755 77 ASN A 77 78 ILE A 78 3.7096 1 1 1 0 -12 368 0 +R 756 77 ASN A 77 79 PRO A 79 7.0593 0 1 0 0 -8 8 0 +R 757 78 ILE A 78 63 TRP A 63 7.9100 1 0 0 0 0 0 0 +R 758 78 ILE A 78 64 CYS A 64 5.2721 1 1 1 1 22 22 0 +R 759 78 ILE A 78 65 ASN A 65 6.2178 1 1 1 1 125 126 0 +R 760 78 ILE A 78 74 ASN A 74 6.8599 1 1 1 0 0 12 0 +R 761 78 ILE A 78 76 CYS A 76 5.6591 1 1 1 1 40 132 0 +R 762 78 ILE A 78 77 ASN A 77 3.7096 1 1 0 0 -33 394 0 +R 763 78 ILE A 78 79 PRO A 79 3.7780 1 1 1 0 -15 412 0 +R 764 78 ILE A 78 80 CYS A 80 6.2029 1 0 0 0 0 0 0 +R 765 78 ILE A 78 82 ALA A 82 6.8387 1 1 1 1 55 55 0 +R 766 78 ILE A 78 83 LEU A 83 8.3786 1 1 1 1 191 191 0 +R 767 78 ILE A 78 90 ALA A 90 8.2888 0 1 1 1 46 47 0 +R 768 78 ILE A 78 94 CYS A 94 8.8596 1 1 1 1 5 5 0 +R 769 79 PRO A 79 64 CYS A 64 5.5062 1 0 0 0 0 0 0 +R 770 79 PRO A 79 65 ASN A 65 4.7112 1 1 1 0 -57 79 0 +R 771 79 PRO A 79 66 ASP A 66 5.9021 0 1 0 0 0 2 0 +R 772 79 PRO A 79 74 ASN A 74 8.2352 0 1 0 0 -5 5 0 +R 773 79 PRO A 79 77 ASN A 77 7.0593 0 1 0 0 -8 8 0 +R 774 79 PRO A 79 78 ILE A 78 3.7780 1 1 1 1 24 426 0 +R 775 79 PRO A 79 80 CYS A 80 3.8413 1 1 1 0 -13 376 0 +R 776 79 PRO A 79 81 SER A 81 5.4310 1 1 0 0 -74 74 0 +R 777 79 PRO A 79 82 ALA A 82 5.6534 1 1 1 1 81 143 0 +R 778 80 CYS A 80 53 TYR A 53 6.5643 1 1 1 1 74 104 0 +R 779 80 CYS A 80 60 SER A 60 6.8143 1 1 0 0 0 16 0 +R 780 80 CYS A 80 64 CYS A 64 4.9610 1 1 0 0 0 284 0 +R 781 80 CYS A 80 65 ASN A 65 5.3811 1 1 1 1 23 52 0 +R 782 80 CYS A 80 66 ASP A 66 5.2749 1 1 1 1 11 49 0 +R 783 80 CYS A 80 78 ILE A 78 6.2029 1 0 0 0 0 0 0 +R 784 80 CYS A 80 79 PRO A 79 3.8413 1 1 0 0 -57 340 0 +R 785 80 CYS A 80 81 SER A 81 3.8305 1 1 1 1 7 326 0 +R 786 80 CYS A 80 82 ALA A 82 5.3155 1 0 0 0 0 0 0 +R 787 80 CYS A 80 83 LEU A 83 5.4505 1 1 1 1 57 153 0 +R 788 81 SER A 81 53 TYR A 53 7.5160 0 1 0 0 0 9 0 +R 789 81 SER A 81 79 PRO A 79 5.4310 1 1 0 0 -86 87 0 +R 790 81 SER A 81 80 CYS A 80 3.8305 1 1 0 0 -25 371 0 +R 791 81 SER A 81 82 ALA A 82 3.8111 1 1 1 1 44 373 0 +R 792 81 SER A 81 83 LEU A 83 5.1899 1 0 0 0 0 0 0 +R 793 81 SER A 81 84 LEU A 84 5.4183 1 1 1 1 42 165 0 +R 794 81 SER A 81 85 SER A 85 7.5229 0 1 1 1 10 14 0 +R 795 82 ALA A 82 78 ILE A 78 6.8387 1 1 1 1 107 107 0 +R 796 82 ALA A 82 79 PRO A 79 5.6534 1 1 1 0 -24 101 0 +R 797 82 ALA A 82 80 CYS A 80 5.3155 1 0 0 0 0 0 0 +R 798 82 ALA A 82 81 SER A 81 3.8111 1 1 1 0 -1 378 0 +R 799 82 ALA A 82 83 LEU A 83 3.7944 1 1 1 1 8 341 0 +R 800 82 ALA A 82 84 LEU A 84 5.4609 1 1 1 1 13 13 0 +R 801 82 ALA A 82 85 SER A 85 5.9325 1 1 0 0 0 115 0 +R 802 82 ALA A 82 90 ALA A 90 6.7558 1 1 1 0 -10 50 0 +R 803 83 LEU A 83 40 THR A 40 7.4963 0 1 0 0 -2 3 0 +R 804 83 LEU A 83 53 TYR A 53 6.1854 1 1 1 1 30 30 0 +R 805 83 LEU A 83 54 GLY A 54 5.3232 1 1 0 0 0 93 0 +R 806 83 LEU A 83 55 ILE A 55 7.8149 0 1 1 1 1 1 0 +R 807 83 LEU A 83 58 ILE A 58 7.8716 1 1 1 1 103 103 0 +R 808 83 LEU A 83 64 CYS A 64 8.6424 1 1 1 1 7 170 0 +R 809 83 LEU A 83 78 ILE A 78 8.3786 1 1 1 1 102 102 0 +R 810 83 LEU A 83 80 CYS A 80 5.4505 1 1 0 0 -36 36 0 +R 811 83 LEU A 83 81 SER A 81 5.1899 1 0 0 0 0 0 0 +R 812 83 LEU A 83 82 ALA A 82 3.7944 1 1 0 0 -15 371 0 +R 813 83 LEU A 83 84 LEU A 84 3.8682 1 1 1 1 25 309 0 +R 814 83 LEU A 83 85 SER A 85 5.7541 1 1 1 1 2 4 0 +R 815 83 LEU A 83 90 ALA A 90 6.0317 1 1 0 0 -1 2 0 +R 816 83 LEU A 83 91 SER A 91 5.2891 1 1 1 0 -36 193 0 +R 817 83 LEU A 83 94 CYS A 94 8.8633 1 1 1 1 3 3 0 +R 818 84 LEU A 84 40 THR A 40 5.0346 1 1 1 1 15 152 0 +R 819 84 LEU A 84 41 GLN A 41 4.8606 1 1 1 0 -53 101 0 +R 820 84 LEU A 84 42 ALA A 42 7.3563 1 1 0 0 -30 30 0 +R 821 84 LEU A 84 43 THR A 43 8.5599 1 1 1 1 95 95 0 +R 822 84 LEU A 84 53 TYR A 53 6.6054 1 1 1 1 40 40 0 +R 823 84 LEU A 84 54 GLY A 54 4.8428 1 1 0 0 -115 115 0 +R 824 84 LEU A 84 80 CYS A 80 7.5698 0 1 0 0 -15 15 0 +R 825 84 LEU A 84 81 SER A 81 5.4183 1 1 0 0 -39 91 0 +R 826 84 LEU A 84 82 ALA A 82 5.4609 1 0 0 0 0 0 0 +R 827 84 LEU A 84 83 LEU A 83 3.8682 1 1 0 0 -13 366 0 +R 828 84 LEU A 84 85 SER A 85 3.7737 1 1 1 1 10 356 0 +R 829 84 LEU A 84 86 SER A 86 6.7769 0 1 1 1 3 3 0 +R 830 85 SER A 85 40 THR A 40 6.2303 1 1 0 0 -14 75 0 +R 831 85 SER A 85 81 SER A 81 7.5229 0 1 1 1 2 13 0 +R 832 85 SER A 85 82 ALA A 82 5.9325 1 1 0 0 0 73 0 +R 833 85 SER A 85 83 LEU A 83 5.7541 1 1 0 0 -1 1 0 +R 834 85 SER A 85 84 LEU A 84 3.7737 1 1 0 0 -16 376 0 +R 835 85 SER A 85 86 SER A 86 3.8390 1 1 1 1 59 381 0 +R 836 85 SER A 85 87 ASP A 87 5.2323 1 1 1 1 8 169 0 +R 837 86 SER A 86 1 LYS A 1 5.1894 1 1 1 0 -65 208 0 +R 838 86 SER A 86 3 PHE A 3 8.8941 1 1 0 0 -115 115 0 +R 839 86 SER A 86 40 THR A 40 6.2290 1 0 0 0 0 0 0 +R 840 86 SER A 86 84 LEU A 84 6.7769 0 1 1 1 2 2 0 +R 841 86 SER A 86 85 SER A 85 3.8390 1 1 1 1 5 348 0 +R 842 86 SER A 86 87 ASP A 87 3.8507 1 1 1 1 20 342 0 +R 843 86 SER A 86 88 ILE A 88 6.0595 1 1 1 1 25 25 0 +R 844 87 ASP A 87 3 PHE A 3 10.7648 0 1 0 0 0 1 0 +R 845 87 ASP A 87 15 HIS A 15 10.7991 0 1 1 1 6 22 0 +R 846 87 ASP A 87 85 SER A 85 5.2323 1 1 0 0 -45 134 0 +R 847 87 ASP A 87 86 SER A 86 3.8507 1 1 0 0 -16 361 0 +R 848 87 ASP A 87 88 ILE A 88 3.8129 1 1 1 1 35 371 0 +R 849 87 ASP A 87 89 THR A 89 5.6671 1 1 1 1 207 234 0 +R 850 87 ASP A 87 90 ALA A 90 7.7602 0 1 1 1 9 9 0 +R 851 88 ILE A 88 3 PHE A 3 10.4372 1 1 1 1 143 143 0 +R 852 88 ILE A 88 8 LEU A 8 9.1166 1 0 0 0 0 0 0 +R 853 88 ILE A 88 11 ALA A 11 7.9512 1 1 1 1 135 162 0 +R 854 88 ILE A 88 12 MET A 12 8.1191 1 1 1 1 11 35 0 +R 855 88 ILE A 88 15 HIS A 15 8.6713 1 1 1 0 -29 35 0 +R 856 88 ILE A 88 40 THR A 40 7.7607 1 1 1 1 47 47 0 +R 857 88 ILE A 88 55 ILE A 55 8.0660 1 1 1 1 35 35 0 +R 858 88 ILE A 88 86 SER A 86 6.0595 1 1 0 0 -4 4 0 +R 859 88 ILE A 88 87 ASP A 87 3.8129 1 1 1 1 1 353 0 +R 860 88 ILE A 88 89 THR A 89 3.7790 1 1 1 1 2 372 0 +R 861 88 ILE A 88 90 ALA A 90 5.7738 1 1 0 0 0 1 0 +R 862 88 ILE A 88 91 SER A 91 5.4216 1 1 1 1 4 23 0 +R 863 88 ILE A 88 92 VAL A 92 6.1853 1 1 1 1 212 212 0 +R 864 89 THR A 89 14 ARG A 14 10.0339 0 1 1 1 3 3 0 +R 865 89 THR A 89 15 HIS A 15 7.1554 1 1 1 1 55 149 0 +R 866 89 THR A 89 87 ASP A 87 5.6671 1 1 1 1 106 158 0 +R 867 89 THR A 89 88 ILE A 88 3.7790 1 1 0 0 -8 335 0 +R 868 89 THR A 89 90 ALA A 90 3.8512 1 1 1 1 13 372 0 +R 869 89 THR A 89 91 SER A 91 5.5409 1 0 0 0 0 0 0 +R 870 89 THR A 89 92 VAL A 92 5.2314 1 0 0 0 0 0 0 +R 871 89 THR A 89 93 ASN A 93 6.2336 1 1 1 1 47 199 0 +R 872 90 ALA A 90 78 ILE A 78 8.2888 0 1 1 1 45 45 0 +R 873 90 ALA A 90 82 ALA A 82 6.7558 1 1 1 0 -58 158 0 +R 874 90 ALA A 90 83 LEU A 83 6.0317 1 1 1 1 27 27 0 +R 875 90 ALA A 90 87 ASP A 87 7.7602 0 1 1 0 -2 4 0 +R 876 90 ALA A 90 88 ILE A 88 5.7738 1 0 0 0 0 0 0 +R 877 90 ALA A 90 89 THR A 89 3.8512 1 1 1 0 -8 373 0 +R 878 90 ALA A 90 91 SER A 91 3.8404 1 1 1 1 8 356 0 +R 879 90 ALA A 90 92 VAL A 92 5.4287 1 0 0 0 0 0 0 +R 880 90 ALA A 90 93 ASN A 93 5.1567 1 1 0 0 -1 28 0 +R 881 90 ALA A 90 94 CYS A 94 6.0715 1 1 1 1 85 133 0 +R 882 91 SER A 91 55 ILE A 55 7.4339 1 1 1 0 -16 119 0 +R 883 91 SER A 91 58 ILE A 58 7.7587 1 1 0 0 -3 14 0 +R 884 91 SER A 91 83 LEU A 83 5.2891 1 1 1 1 145 220 0 +R 885 91 SER A 91 88 ILE A 88 5.4216 1 1 0 0 0 37 0 +R 886 91 SER A 91 89 THR A 89 5.5409 1 0 0 0 0 0 0 +R 887 91 SER A 91 90 ALA A 90 3.8404 1 1 0 0 -14 349 0 +R 888 91 SER A 91 92 VAL A 92 3.7489 1 1 1 1 20 342 0 +R 889 91 SER A 91 93 ASN A 93 5.6148 1 0 0 0 0 0 0 +R 890 91 SER A 91 94 CYS A 94 5.2309 1 0 0 0 0 0 0 +R 891 91 SER A 91 95 ALA A 95 5.9715 1 1 1 1 115 161 0 +R 892 92 VAL A 92 12 MET A 12 7.4759 0 1 1 1 3 3 0 +R 893 92 VAL A 92 15 HIS A 15 7.1674 1 1 1 1 73 167 0 +R 894 92 VAL A 92 17 LEU A 17 7.6268 1 1 1 1 98 98 0 +R 895 92 VAL A 92 56 LEU A 56 8.3697 0 1 1 1 3 3 0 +R 896 92 VAL A 92 88 ILE A 88 6.1853 1 1 1 1 57 201 0 +R 897 92 VAL A 92 89 THR A 89 5.2314 1 1 0 0 -8 9 0 +R 898 92 VAL A 92 90 ALA A 90 5.4287 1 0 0 0 0 0 0 +R 899 92 VAL A 92 91 SER A 91 3.7489 1 1 0 0 -15 368 0 +R 900 92 VAL A 92 93 ASN A 93 3.8908 1 1 1 0 0 322 0 +R 901 92 VAL A 92 94 CYS A 94 5.4376 1 0 0 0 0 0 0 +R 902 92 VAL A 92 95 ALA A 95 4.9484 1 1 0 0 0 11 0 +R 903 92 VAL A 92 96 LYS A 96 6.2030 1 1 1 1 105 187 0 +R 904 93 ASN A 93 15 HIS A 15 8.5240 0 1 1 0 -2 4 0 +R 905 93 ASN A 93 89 THR A 89 6.2336 1 1 1 0 -125 178 0 +R 906 93 ASN A 93 90 ALA A 90 5.1567 1 1 1 0 -12 29 0 +R 907 93 ASN A 93 91 SER A 91 5.6148 1 0 0 0 0 0 0 +R 908 93 ASN A 93 92 VAL A 92 3.8908 1 1 0 0 -18 349 0 +R 909 93 ASN A 93 94 CYS A 94 3.7884 1 1 1 0 -4 357 0 +R 910 93 ASN A 93 95 ALA A 95 5.4444 1 0 0 0 0 0 0 +R 911 93 ASN A 93 96 LYS A 96 5.2091 1 1 1 0 -70 183 0 +R 912 93 ASN A 93 97 LYS A 97 6.7656 1 1 1 1 21 82 0 +R 913 94 CYS A 94 58 ILE A 58 8.1513 1 1 1 1 12 144 0 +R 914 94 CYS A 94 63 TRP A 63 7.4243 1 1 0 0 0 1 0 +R 915 94 CYS A 94 76 CYS A 76 5.4641 1 1 1 1 17 234 0 +R 916 94 CYS A 94 78 ILE A 78 8.8596 1 1 1 1 8 9 0 +R 917 94 CYS A 94 83 LEU A 83 8.8633 1 0 0 0 0 0 0 +R 918 94 CYS A 94 90 ALA A 90 6.0715 1 1 1 0 -62 76 0 +R 919 94 CYS A 94 91 SER A 91 5.2309 1 1 0 0 -11 11 0 +R 920 94 CYS A 94 92 VAL A 92 5.4376 1 0 0 0 0 0 0 +R 921 94 CYS A 94 93 ASN A 93 3.7884 1 1 0 0 -18 346 0 +R 922 94 CYS A 94 95 ALA A 95 3.8019 1 1 1 1 14 349 0 +R 923 94 CYS A 94 96 LYS A 96 5.3813 1 0 0 0 0 0 0 +R 924 94 CYS A 94 97 LYS A 97 5.2610 1 1 1 1 58 70 0 +R 925 94 CYS A 94 98 ILE A 98 6.4204 1 1 1 1 41 63 0 +R 926 95 ALA A 95 28 TRP A 28 9.8227 1 1 1 1 23 23 0 +R 927 95 ALA A 95 56 LEU A 56 7.7189 1 1 1 1 73 73 0 +R 928 95 ALA A 95 58 ILE A 58 7.7436 1 0 0 0 0 0 0 +R 929 95 ALA A 95 91 SER A 91 5.9715 1 1 1 0 -55 81 0 +R 930 95 ALA A 95 92 VAL A 92 4.9484 1 1 0 0 -18 18 0 +R 931 95 ALA A 95 93 ASN A 93 5.4444 1 0 0 0 0 0 0 +R 932 95 ALA A 95 94 CYS A 94 3.8019 1 1 0 0 -25 362 0 +R 933 95 ALA A 95 96 LYS A 96 3.7722 1 1 1 1 15 324 0 +R 934 95 ALA A 95 97 LYS A 97 5.3622 1 0 0 0 0 0 0 +R 935 95 ALA A 95 98 ILE A 98 4.9201 1 1 0 0 0 11 0 +R 936 95 ALA A 95 99 VAL A 99 6.0948 1 1 1 1 142 164 0 +R 937 95 ALA A 95 108 TRP A 108 10.0572 1 1 1 1 87 115 0 +R 938 96 LYS A 96 15 HIS A 15 10.3010 1 1 1 1 121 172 0 +R 939 96 LYS A 96 16 GLY A 16 9.2491 1 1 0 0 0 33 0 +R 940 96 LYS A 96 17 LEU A 17 7.9140 1 1 1 1 21 25 0 +R 941 96 LYS A 96 20 TYR A 20 7.7283 1 1 1 1 24 198 0 +R 942 96 LYS A 96 92 VAL A 92 6.2030 1 1 1 0 -37 54 0 +R 943 96 LYS A 96 93 ASN A 93 5.2091 1 1 0 0 -108 108 0 +R 944 96 LYS A 96 94 CYS A 94 5.3813 1 0 0 0 0 0 0 +R 945 96 LYS A 96 95 ALA A 95 3.7722 1 1 0 0 -8 346 0 +R 946 96 LYS A 96 97 LYS A 97 3.8989 1 1 1 1 13 346 0 +R 947 96 LYS A 96 98 ILE A 98 5.4629 1 0 0 0 0 0 0 +R 948 96 LYS A 96 99 VAL A 99 5.3592 1 1 0 0 0 2 0 +R 949 96 LYS A 96 100 SER A 100 6.2176 1 1 1 1 160 160 0 +R 950 97 LYS A 97 63 TRP A 63 9.0609 1 1 1 1 19 21 0 +R 951 97 LYS A 97 75 LEU A 75 8.3701 0 1 0 0 -14 51 0 +R 952 97 LYS A 97 76 CYS A 76 7.3462 1 1 1 1 4 83 0 +R 953 97 LYS A 97 93 ASN A 93 6.7656 1 1 0 0 -41 44 0 +R 954 97 LYS A 97 94 CYS A 94 5.2610 1 1 0 0 -30 31 0 +R 955 97 LYS A 97 95 ALA A 95 5.3622 1 0 0 0 0 0 0 +R 956 97 LYS A 97 96 LYS A 96 3.8989 1 1 0 0 -9 339 0 +R 957 97 LYS A 97 98 ILE A 98 3.7983 1 1 1 0 -7 374 0 +R 958 97 LYS A 97 99 VAL A 99 5.7111 1 0 0 0 0 0 0 +R 959 97 LYS A 97 100 SER A 100 5.2541 1 1 1 1 55 84 0 +R 960 97 LYS A 97 101 ASP A 101 6.4431 1 1 1 1 20 69 0 +R 961 98 ILE A 98 58 ILE A 58 8.9872 1 1 1 1 183 184 0 +R 962 98 ILE A 98 63 TRP A 63 8.1327 1 1 1 1 140 169 0 +R 963 98 ILE A 98 94 CYS A 94 6.4204 1 1 0 0 -44 44 0 +R 964 98 ILE A 98 95 ALA A 95 4.9201 1 1 0 0 -12 12 0 +R 965 98 ILE A 98 96 LYS A 96 5.4629 1 0 0 0 0 0 0 +R 966 98 ILE A 98 97 LYS A 97 3.7983 1 1 0 0 -16 354 0 +R 967 98 ILE A 98 99 VAL A 99 3.8242 1 1 1 1 2 332 0 +R 968 98 ILE A 98 100 SER A 100 5.4112 1 0 0 0 0 0 0 +R 969 98 ILE A 98 101 ASP A 101 5.2299 1 1 0 0 -140 143 0 +R 970 98 ILE A 98 104 GLY A 104 7.3510 0 1 0 0 -10 10 0 +R 971 98 ILE A 98 107 ALA A 107 7.4522 1 1 1 1 145 145 0 +R 972 98 ILE A 98 108 TRP A 108 9.5294 1 1 1 1 25 25 0 +R 973 99 VAL A 99 20 TYR A 20 8.7657 1 1 1 1 115 115 0 +R 974 99 VAL A 99 21 ARG A 21 7.5366 1 1 1 0 -13 25 0 +R 975 99 VAL A 99 23 TYR A 23 9.4052 1 1 1 1 105 105 0 +R 976 99 VAL A 99 28 TRP A 28 10.7709 1 1 1 1 28 28 0 +R 977 99 VAL A 99 95 ALA A 95 6.0948 1 1 1 0 -50 86 0 +R 978 99 VAL A 99 96 LYS A 96 5.3592 1 1 0 0 -29 29 0 +R 979 99 VAL A 99 97 LYS A 97 5.7111 1 0 0 0 0 0 0 +R 980 99 VAL A 99 98 ILE A 98 3.8242 1 1 0 0 -4 345 0 +R 981 99 VAL A 99 100 SER A 100 3.8421 1 1 1 0 -7 356 0 +R 982 99 VAL A 99 101 ASP A 101 5.3917 1 0 0 0 0 0 0 +R 983 99 VAL A 99 102 GLY A 102 7.0039 0 1 1 1 1 1 0 +R 984 99 VAL A 99 104 GLY A 104 4.3408 1 1 0 0 0 177 0 +R 985 99 VAL A 99 105 MET A 105 5.6156 1 1 1 1 46 46 0 +R 986 99 VAL A 99 108 TRP A 108 9.1731 1 1 1 1 5 5 0 +R 987 100 SER A 100 20 TYR A 20 9.2326 1 1 1 1 32 33 0 +R 988 100 SER A 100 21 ARG A 21 7.2028 1 1 1 1 183 249 0 +R 989 100 SER A 100 96 LYS A 96 6.2176 1 1 1 1 89 119 0 +R 990 100 SER A 100 97 LYS A 97 5.2541 1 1 0 0 0 48 0 +R 991 100 SER A 100 98 ILE A 98 5.4112 1 0 0 0 0 0 0 +R 992 100 SER A 100 99 VAL A 99 3.8421 1 1 0 0 -13 357 0 +R 993 100 SER A 100 101 ASP A 101 3.8203 1 1 1 1 13 316 0 +R 994 100 SER A 100 102 GLY A 102 5.9600 1 1 1 1 44 50 0 +R 995 101 ASP A 101 63 TRP A 63 11.5849 1 1 0 0 -131 140 0 +R 996 101 ASP A 101 75 LEU A 75 10.9431 0 1 0 0 -44 44 0 +R 997 101 ASP A 101 97 LYS A 97 6.4431 1 1 0 0 -35 37 0 +R 998 101 ASP A 101 98 ILE A 98 5.2299 1 1 0 0 -86 92 0 +R 999 101 ASP A 101 99 VAL A 99 5.3917 1 0 0 0 0 0 0 +R 1000 101 ASP A 101 100 SER A 100 3.8203 1 1 0 0 -8 347 0 +R 1001 101 ASP A 101 102 GLY A 102 3.7587 1 1 1 1 27 326 0 +R 1002 101 ASP A 101 103 ASN A 103 6.3794 1 1 1 1 17 20 0 +R 1003 102 GLY A 102 99 VAL A 99 7.0039 0 1 0 0 0 1 0 +R 1004 102 GLY A 102 100 SER A 100 5.9600 1 1 1 1 29 43 0 +R 1005 102 GLY A 102 101 ASP A 101 3.7587 1 1 0 0 -28 409 0 +R 1006 102 GLY A 102 103 ASN A 103 3.8452 1 1 1 1 49 380 0 +R 1007 102 GLY A 102 104 GLY A 104 5.4960 1 1 1 1 2 18 0 +R 1008 103 ASN A 103 23 TYR A 23 12.4992 0 1 0 0 0 1 0 +R 1009 103 ASN A 103 101 ASP A 101 6.3794 1 1 1 0 -1 11 0 +R 1010 103 ASN A 103 102 GLY A 102 3.8452 1 1 1 1 10 398 0 +R 1011 103 ASN A 103 104 GLY A 104 3.8263 1 1 1 1 18 340 0 +R 1012 103 ASN A 103 105 MET A 105 6.4440 1 0 0 0 0 0 0 +R 1013 103 ASN A 103 106 ASN A 106 5.4867 1 1 1 1 228 242 0 +R 1014 103 ASN A 103 107 ALA A 107 6.1089 0 1 1 0 -27 32 0 +R 1015 104 GLY A 104 23 TYR A 23 8.8920 1 1 0 0 0 56 0 +R 1016 104 GLY A 104 99 VAL A 99 4.3408 1 1 1 1 6 132 0 +R 1017 104 GLY A 104 102 GLY A 102 5.4960 1 1 1 1 2 26 0 +R 1018 104 GLY A 104 103 ASN A 103 3.8263 1 1 0 0 -32 376 0 +R 1019 104 GLY A 104 105 MET A 105 3.8395 1 1 1 1 27 367 0 +R 1020 104 GLY A 104 106 ASN A 106 5.3817 1 1 1 1 5 5 0 +R 1021 104 GLY A 104 107 ALA A 107 6.2555 1 1 1 0 -10 94 0 +R 1022 105 MET A 105 23 TYR A 23 8.1535 1 1 1 1 72 178 0 +R 1023 105 MET A 105 27 ASN A 27 8.5492 1 1 0 0 -13 66 0 +R 1024 105 MET A 105 28 TRP A 28 8.7636 1 1 1 1 53 65 0 +R 1025 105 MET A 105 31 ALA A 31 8.7729 1 1 1 1 99 99 0 +R 1026 105 MET A 105 99 VAL A 99 5.6156 1 1 1 1 57 57 0 +R 1027 105 MET A 105 103 ASN A 103 6.4440 1 0 0 0 0 0 0 +R 1028 105 MET A 105 104 GLY A 104 3.8395 1 1 0 0 0 343 0 +R 1029 105 MET A 105 106 ASN A 106 3.7700 1 1 1 1 18 321 0 +R 1030 105 MET A 105 107 ALA A 107 5.0282 1 1 0 0 0 4 0 +R 1031 105 MET A 105 108 TRP A 108 5.6343 1 1 1 1 127 148 0 +R 1032 105 MET A 105 111 TRP A 111 6.7413 1 1 1 1 127 195 0 +R 1033 106 ASN A 106 23 TYR A 23 11.3626 0 1 1 1 22 22 0 +R 1034 106 ASN A 106 103 ASN A 103 5.4867 1 1 1 1 84 175 0 +R 1035 106 ASN A 106 104 GLY A 104 5.3817 1 0 0 0 0 0 0 +R 1036 106 ASN A 106 105 MET A 105 3.7700 1 1 0 0 -17 357 0 +R 1037 106 ASN A 106 107 ALA A 107 3.8144 1 1 1 1 11 348 0 +R 1038 106 ASN A 106 108 TRP A 108 5.0992 1 1 1 1 12 12 0 +R 1039 106 ASN A 106 111 TRP A 111 6.6687 1 1 0 0 -47 56 0 +R 1040 106 ASN A 106 112 ARG A 112 5.3634 1 1 1 1 52 179 0 +R 1041 106 ASN A 106 116 LYS A 116 8.4376 1 1 1 1 81 209 0 +R 1042 107 ALA A 107 63 TRP A 63 11.8922 0 1 1 1 15 15 0 +R 1043 107 ALA A 107 98 ILE A 98 7.4522 1 1 1 1 134 144 0 +R 1044 107 ALA A 107 103 ASN A 103 6.1089 0 1 1 1 17 34 0 +R 1045 107 ALA A 107 104 GLY A 104 6.2555 1 1 1 0 -68 78 0 +R 1046 107 ALA A 107 105 MET A 105 5.0282 1 0 0 0 0 0 0 +R 1047 107 ALA A 107 106 ASN A 106 3.8144 1 1 0 0 -31 366 0 +R 1048 107 ALA A 107 108 TRP A 108 3.8323 1 1 1 1 1 344 0 +R 1049 107 ALA A 107 109 VAL A 109 6.1899 1 1 1 1 11 40 0 +R 1050 107 ALA A 107 112 ARG A 112 7.9613 0 1 1 1 4 4 0 +R 1051 108 TRP A 108 28 TRP A 28 10.2074 1 1 1 1 79 79 0 +R 1052 108 TRP A 108 31 ALA A 31 7.3841 0 1 1 1 1 1 0 +R 1053 108 TRP A 108 35 GLU A 35 8.1006 1 1 1 0 -56 82 0 +R 1054 108 TRP A 108 56 LEU A 56 8.2153 1 1 1 1 43 175 0 +R 1055 108 TRP A 108 57 GLN A 57 8.2910 0 1 1 1 8 22 0 +R 1056 108 TRP A 108 58 ILE A 58 8.7782 0 1 0 0 -2 2 0 +R 1057 108 TRP A 108 95 ALA A 95 10.0572 1 1 1 1 155 217 0 +R 1058 108 TRP A 108 98 ILE A 98 9.5294 1 1 1 1 106 112 0 +R 1059 108 TRP A 108 99 VAL A 99 9.1731 1 1 1 1 4 4 0 +R 1060 108 TRP A 108 105 MET A 105 5.6343 1 1 1 0 -53 139 0 +R 1061 108 TRP A 108 106 ASN A 106 5.0992 1 0 0 0 0 0 0 +R 1062 108 TRP A 108 107 ALA A 107 3.8323 1 1 0 0 -33 366 0 +R 1063 108 TRP A 108 109 VAL A 109 3.7513 1 1 1 1 24 373 0 +R 1064 108 TRP A 108 110 ALA A 110 5.5900 1 0 0 0 0 0 0 +R 1065 108 TRP A 108 111 TRP A 111 5.1466 1 1 1 1 47 47 0 +R 1066 108 TRP A 108 112 ARG A 112 6.3103 1 1 1 1 120 126 0 +R 1067 109 VAL A 109 35 GLU A 35 8.4267 0 1 0 0 -59 59 0 +R 1068 109 VAL A 109 107 ALA A 107 6.1899 1 1 1 0 -7 19 0 +R 1069 109 VAL A 109 108 TRP A 108 3.7513 1 1 0 0 -3 339 0 +R 1070 109 VAL A 109 110 ALA A 110 3.8699 1 1 1 0 -4 348 0 +R 1071 109 VAL A 109 111 TRP A 111 5.3384 1 0 0 0 0 0 0 +R 1072 109 VAL A 109 112 ARG A 112 5.1089 1 1 0 0 -73 99 0 +R 1073 109 VAL A 109 113 ASN A 113 6.1028 1 1 1 1 44 250 0 +R 1074 110 ALA A 110 34 PHE A 34 5.8542 1 1 1 1 122 157 0 +R 1075 110 ALA A 110 35 GLU A 35 6.0785 1 1 0 0 -66 82 0 +R 1076 110 ALA A 110 108 TRP A 108 5.5900 1 0 0 0 0 0 0 +R 1077 110 ALA A 110 109 VAL A 109 3.8699 1 1 1 0 -23 376 0 +R 1078 110 ALA A 110 111 TRP A 111 3.7781 1 1 1 1 1 300 0 +R 1079 110 ALA A 110 112 ARG A 112 5.4225 1 0 0 0 0 0 0 +R 1080 110 ALA A 110 113 ASN A 113 5.0166 1 1 0 0 0 2 0 +R 1081 110 ALA A 110 114 ARG A 114 5.4505 1 1 1 1 153 261 0 +R 1082 110 ALA A 110 115 CYS A 115 7.0432 1 0 0 0 0 0 0 +R 1083 111 TRP A 111 23 TYR A 23 11.4919 1 1 1 1 99 99 0 +R 1084 111 TRP A 111 27 ASN A 27 7.6026 1 1 1 1 11 193 0 +R 1085 111 TRP A 111 31 ALA A 31 4.9166 1 1 1 1 14 14 0 +R 1086 111 TRP A 111 105 MET A 105 6.7413 1 1 1 1 2 178 0 +R 1087 111 TRP A 111 106 ASN A 106 6.6687 1 1 0 0 -113 113 0 +R 1088 111 TRP A 111 108 TRP A 108 5.1466 1 1 1 1 38 95 0 +R 1089 111 TRP A 111 109 VAL A 109 5.3384 1 0 0 0 0 0 0 +R 1090 111 TRP A 111 110 ALA A 110 3.7781 1 1 0 0 -34 370 0 +R 1091 111 TRP A 111 112 ARG A 112 3.7781 1 1 1 0 -31 326 0 +R 1092 111 TRP A 111 113 ASN A 113 5.5291 1 0 0 0 0 0 0 +R 1093 111 TRP A 111 114 ARG A 114 5.3790 1 0 0 0 0 0 0 +R 1094 111 TRP A 111 115 CYS A 115 4.7065 1 1 1 1 79 128 0 +R 1095 111 TRP A 111 116 LYS A 116 5.8402 1 1 1 1 317 340 0 +R 1096 111 TRP A 111 117 GLY A 117 9.5925 0 1 0 0 -2 2 0 +R 1097 112 ARG A 112 106 ASN A 106 5.3634 1 1 1 1 43 215 0 +R 1098 112 ARG A 112 107 ALA A 107 7.9613 0 1 1 1 6 6 0 +R 1099 112 ARG A 112 108 TRP A 108 6.3103 1 1 1 0 -6 24 0 +R 1100 112 ARG A 112 109 VAL A 109 5.1089 1 1 0 0 -58 149 0 +R 1101 112 ARG A 112 110 ALA A 110 5.4225 1 0 0 0 0 0 0 +R 1102 112 ARG A 112 111 TRP A 111 3.7781 1 1 0 0 -46 402 0 +R 1103 112 ARG A 112 113 ASN A 113 3.8018 1 1 1 1 50 413 0 +R 1104 112 ARG A 112 114 ARG A 114 5.8854 1 0 0 0 0 0 0 +R 1105 112 ARG A 112 116 LYS A 116 5.0012 1 1 1 0 -56 117 0 +R 1106 113 ASN A 113 109 VAL A 109 6.1028 1 1 0 0 -184 184 0 +R 1107 113 ASN A 113 110 ALA A 110 5.0166 1 1 0 0 0 1 0 +R 1108 113 ASN A 113 111 TRP A 111 5.5291 1 0 0 0 0 0 0 +R 1109 113 ASN A 113 112 ARG A 112 3.8018 1 1 1 1 12 483 0 +R 1110 113 ASN A 113 114 ARG A 114 3.7971 1 1 1 1 50 378 0 +R 1111 113 ASN A 113 115 CYS A 115 6.1707 1 0 0 0 0 0 0 +R 1112 114 ARG A 114 30 CYS A 30 8.0485 0 1 0 0 0 14 0 +R 1113 114 ARG A 114 34 PHE A 34 7.4511 1 1 1 0 -135 302 0 +R 1114 114 ARG A 114 110 ALA A 110 5.4505 1 1 1 0 -36 105 0 +R 1115 114 ARG A 114 111 TRP A 111 5.3790 1 0 0 0 0 0 0 +R 1116 114 ARG A 114 112 ARG A 112 5.8854 1 0 0 0 0 0 0 +R 1117 114 ARG A 114 113 ASN A 113 3.7971 1 1 1 1 11 420 0 +R 1118 114 ARG A 114 115 CYS A 115 3.7433 1 1 1 1 15 327 0 +R 1119 114 ARG A 114 116 LYS A 116 6.0770 1 0 0 0 0 0 0 +R 1120 114 ARG A 114 118 THR A 118 7.6414 1 1 1 0 -71 93 0 +R 1121 115 CYS A 115 30 CYS A 30 6.0621 1 1 1 1 1 281 0 +R 1122 115 CYS A 115 31 ALA A 31 6.6938 1 1 0 0 0 11 0 +R 1123 115 CYS A 115 34 PHE A 34 8.4896 1 1 0 0 0 16 0 +R 1124 115 CYS A 115 110 ALA A 110 7.0432 1 0 0 0 0 0 0 +R 1125 115 CYS A 115 111 TRP A 111 4.7065 1 1 1 1 89 123 0 +R 1126 115 CYS A 115 113 ASN A 113 6.1707 1 0 0 0 0 0 0 +R 1127 115 CYS A 115 114 ARG A 114 3.7433 1 1 0 0 -25 384 0 +R 1128 115 CYS A 115 116 LYS A 116 3.7040 1 1 1 0 -10 351 0 +R 1129 115 CYS A 115 117 GLY A 117 6.2355 1 1 1 1 2 2 0 +R 1130 115 CYS A 115 118 THR A 118 5.5424 1 1 1 1 145 145 0 +R 1131 115 CYS A 115 120 VAL A 120 6.5881 1 1 0 0 -19 19 0 +R 1132 116 LYS A 116 106 ASN A 106 8.4376 1 1 1 1 80 167 0 +R 1133 116 LYS A 116 111 TRP A 111 5.8402 1 1 1 1 35 186 0 +R 1134 116 LYS A 116 112 ARG A 112 5.0012 1 1 1 0 -34 104 0 +R 1135 116 LYS A 116 113 ASN A 113 6.5212 0 1 0 0 0 1 0 +R 1136 116 LYS A 116 114 ARG A 114 6.0770 1 1 1 1 1 1 0 +R 1137 116 LYS A 116 115 CYS A 115 3.7040 1 1 0 0 -6 350 0 +R 1138 116 LYS A 116 117 GLY A 117 3.8305 1 1 1 0 -5 378 0 +R 1139 116 LYS A 116 118 THR A 118 5.6274 1 1 1 0 -36 42 0 +R 1140 117 GLY A 117 111 TRP A 111 9.5925 0 1 0 0 -11 11 0 +R 1141 117 GLY A 117 115 CYS A 115 6.2355 1 1 1 1 2 2 0 +R 1142 117 GLY A 117 116 LYS A 116 3.8305 1 1 0 0 -24 389 0 +R 1143 117 GLY A 117 118 THR A 118 3.8121 1 1 1 1 5 362 0 +R 1144 117 GLY A 117 119 ASP A 119 6.8454 0 1 1 1 3 3 0 +R 1145 117 GLY A 117 120 VAL A 120 7.8645 0 1 0 0 -1 1 0 +R 1146 118 THR A 118 30 CYS A 30 9.7068 0 1 0 0 0 8 0 +R 1147 118 THR A 118 114 ARG A 114 7.6414 1 1 1 0 -66 98 0 +R 1148 118 THR A 118 115 CYS A 115 5.5424 1 1 1 1 38 121 0 +R 1149 118 THR A 118 116 LYS A 116 5.6274 1 1 0 0 -51 51 0 +R 1150 118 THR A 118 117 GLY A 117 3.8121 1 1 0 0 -20 397 0 +R 1151 118 THR A 118 119 ASP A 119 3.8550 1 1 1 1 39 360 0 +R 1152 118 THR A 118 120 VAL A 120 5.5102 1 1 1 0 -26 145 0 +R 1153 118 THR A 118 123 TRP A 123 10.4382 0 1 1 1 4 4 0 +R 1154 119 ASP A 119 117 GLY A 117 6.8454 0 1 1 1 2 2 0 +R 1155 119 ASP A 119 118 THR A 118 3.8550 1 1 1 1 2 342 0 +R 1156 119 ASP A 119 120 VAL A 120 3.7995 1 1 1 1 24 333 0 +R 1157 119 ASP A 119 121 GLN A 121 5.3570 1 1 1 0 -131 165 0 +R 1158 119 ASP A 119 122 ALA A 122 5.9464 1 1 1 0 -52 178 0 +R 1159 119 ASP A 119 123 TRP A 123 8.2961 0 1 1 0 -5 7 0 +R 1160 120 VAL A 120 24 SER A 24 8.3132 1 1 0 0 -27 27 0 +R 1161 120 VAL A 120 26 GLY A 26 4.8514 1 1 0 0 -2 84 0 +R 1162 120 VAL A 120 27 ASN A 27 5.7252 1 1 0 0 -182 182 0 +R 1163 120 VAL A 120 30 CYS A 30 6.6406 1 1 1 1 5 5 0 +R 1164 120 VAL A 120 115 CYS A 115 6.5881 1 1 1 0 -114 184 0 +R 1165 120 VAL A 120 118 THR A 118 5.5102 1 1 1 0 -21 53 0 +R 1166 120 VAL A 120 119 ASP A 119 3.7995 1 1 0 0 0 339 0 +R 1167 120 VAL A 120 121 GLN A 121 3.7722 1 1 1 1 5 364 0 +R 1168 120 VAL A 120 122 ALA A 122 5.1321 1 1 0 0 0 4 0 +R 1169 120 VAL A 120 123 TRP A 123 5.6692 1 1 1 1 75 93 0 +R 1170 121 GLN A 121 24 SER A 24 8.0270 0 1 0 0 -27 39 0 +R 1171 121 GLN A 121 119 ASP A 119 5.3570 1 1 1 0 -40 78 0 +R 1172 121 GLN A 121 120 VAL A 120 3.7722 1 1 1 1 14 385 0 +R 1173 121 GLN A 121 122 ALA A 122 3.7981 1 1 1 1 20 347 0 +R 1174 121 GLN A 121 123 TRP A 123 5.2614 1 0 0 0 0 0 0 +R 1175 121 GLN A 121 124 ILE A 124 5.7666 1 1 1 0 -5 212 0 +R 1176 121 GLN A 121 125 ARG A 125 6.5900 1 1 1 1 15 31 0 +R 1177 122 ALA A 122 5 ARG A 5 10.7979 1 1 1 1 28 33 0 +R 1178 122 ALA A 122 119 ASP A 119 5.9464 1 1 1 0 -111 132 0 +R 1179 122 ALA A 122 120 VAL A 120 5.1321 1 0 0 0 0 0 0 +R 1180 122 ALA A 122 121 GLN A 121 3.7981 1 1 0 0 -25 367 0 +R 1181 122 ALA A 122 123 TRP A 123 3.8012 1 1 1 1 22 381 0 +R 1182 122 ALA A 122 124 ILE A 124 5.5575 1 1 1 1 12 12 0 +R 1183 122 ALA A 122 125 ARG A 125 5.1332 1 1 1 0 -27 197 0 +R 1184 123 TRP A 123 5 ARG A 5 7.4230 1 1 1 1 60 235 0 +R 1185 123 TRP A 123 26 GLY A 26 5.1305 1 1 0 0 -12 12 0 +R 1186 123 TRP A 123 29 VAL A 29 6.3580 1 1 1 1 87 87 0 +R 1187 123 TRP A 123 30 CYS A 30 6.2969 1 1 1 1 63 137 0 +R 1188 123 TRP A 123 33 LYS A 33 9.2780 1 1 1 1 169 181 0 +R 1189 123 TRP A 123 34 PHE A 34 11.6342 1 1 1 1 115 121 0 +R 1190 123 TRP A 123 118 THR A 118 10.4382 0 1 1 1 12 12 0 +R 1191 123 TRP A 123 119 ASP A 119 8.2961 0 1 1 1 14 14 0 +R 1192 123 TRP A 123 120 VAL A 120 5.6692 1 1 0 0 -65 95 0 +R 1193 123 TRP A 123 121 GLN A 121 5.2614 1 0 0 0 0 0 0 +R 1194 123 TRP A 123 122 ALA A 122 3.8012 1 1 0 0 -32 379 0 +R 1195 123 TRP A 123 124 ILE A 124 3.7623 1 1 1 1 15 327 0 +R 1196 123 TRP A 123 125 ARG A 125 5.6814 1 0 0 0 0 0 0 +R 1197 124 ILE A 124 5 ARG A 5 7.5648 1 1 0 0 0 6 0 +R 1198 124 ILE A 124 9 ALA A 9 6.6308 1 1 1 1 111 111 0 +R 1199 124 ILE A 124 25 LEU A 25 7.3355 1 1 1 1 109 113 0 +R 1200 124 ILE A 124 26 GLY A 26 5.7057 1 1 0 0 -36 41 0 +R 1201 124 ILE A 124 29 VAL A 29 7.6402 1 1 1 1 2 2 0 +R 1202 124 ILE A 124 121 GLN A 121 5.7666 1 1 1 0 -135 159 0 +R 1203 124 ILE A 124 122 ALA A 122 5.5575 1 0 0 0 0 0 0 +R 1204 124 ILE A 124 123 TRP A 123 3.7623 1 1 0 0 -12 388 0 +R 1205 124 ILE A 124 125 ARG A 125 3.8072 1 1 1 1 13 344 0 +R 1206 124 ILE A 124 126 GLY A 126 6.3927 1 1 1 1 1 1 0 +R 1207 124 ILE A 124 127 CYS A 127 5.6869 1 1 1 1 82 107 0 +R 1208 124 ILE A 124 129 LEU A 129 8.6327 1 1 1 1 73 73 0 +R 1209 125 ARG A 125 5 ARG A 5 9.6347 1 1 1 1 174 208 0 +R 1210 125 ARG A 125 121 GLN A 121 6.5900 1 1 1 0 -20 38 0 +R 1211 125 ARG A 125 122 ALA A 122 5.1332 1 1 1 1 2 181 0 +R 1212 125 ARG A 125 123 TRP A 123 5.6814 1 0 0 0 0 0 0 +R 1213 125 ARG A 125 124 ILE A 124 3.8072 1 1 0 0 -21 350 0 +R 1214 125 ARG A 125 126 GLY A 126 3.8134 1 1 1 0 -8 370 0 +R 1215 125 ARG A 125 127 CYS A 127 5.5076 1 0 0 0 0 0 0 +R 1216 126 GLY A 126 5 ARG A 5 10.0418 0 1 1 1 2 13 0 +R 1217 126 GLY A 126 6 CYS A 6 7.9731 0 1 0 0 0 25 0 +R 1218 126 GLY A 126 124 ILE A 124 6.3927 1 1 1 1 1 1 0 +R 1219 126 GLY A 126 125 ARG A 125 3.8134 1 1 0 0 -21 405 0 +R 1220 126 GLY A 126 127 CYS A 127 3.7148 1 1 1 1 21 351 0 +R 1221 126 GLY A 126 128 ARG A 128 6.5352 1 1 1 1 10 24 0 +R 1222 127 CYS A 127 5 ARG A 5 8.4264 1 1 0 0 0 42 0 +R 1223 127 CYS A 127 6 CYS A 6 5.3179 1 1 1 1 22 251 0 +R 1224 127 CYS A 127 124 ILE A 124 5.6869 1 1 1 0 -32 103 0 +R 1225 127 CYS A 127 125 ARG A 125 5.5076 1 0 0 0 0 0 0 +R 1226 127 CYS A 127 126 GLY A 126 3.7148 1 1 1 0 -24 391 0 +R 1227 127 CYS A 127 128 ARG A 128 3.7185 1 1 1 1 10 344 0 +R 1228 127 CYS A 127 129 LEU A 129 5.8167 1 1 1 1 102 126 0 +R 1229 128 ARG A 128 6 CYS A 6 7.4354 0 1 0 0 -5 11 0 +R 1230 128 ARG A 128 10 ALA A 10 7.8262 0 1 0 0 -52 52 0 +R 1231 128 ARG A 128 126 GLY A 126 6.5352 1 1 1 0 -1 17 0 +R 1232 128 ARG A 128 127 CYS A 127 3.7185 1 1 0 0 -5 354 0 +R 1233 128 ARG A 128 129 LEU A 129 3.7614 1 1 1 0 -47 416 0 +R 1234 129 LEU A 129 9 ALA A 9 7.9700 1 1 1 0 -1 20 0 +R 1235 129 LEU A 129 10 ALA A 10 6.1221 1 1 1 0 -12 221 0 +R 1236 129 LEU A 129 13 LYS A 13 8.0834 1 1 1 0 -26 153 0 +R 1237 129 LEU A 129 25 LEU A 25 10.5318 1 1 1 1 101 101 0 +R 1238 129 LEU A 129 124 ILE A 124 8.6327 1 1 1 1 138 138 0 +R 1239 129 LEU A 129 127 CYS A 127 5.8167 1 1 1 1 31 53 0 +R 1240 129 LEU A 129 128 ARG A 128 3.7614 1 1 0 0 -27 412 0 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb new file mode 100644 index 00000000..33477ad5 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/cg.pdb @@ -0,0 +1,616 @@ +ATOM 1 BB LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 2 SC1 LYS A 1 -0.175 10.268 8.951 1.00 0.00 +ATOM 3 SC2 LYS A 1 -3.127 10.593 7.836 1.00 0.00 +ATOM 4 BB VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 5 SC1 VAL A 2 3.923 14.682 6.344 1.00 0.00 +ATOM 6 BB PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 7 SC1 PHE A 3 -2.271 14.922 9.060 1.00 0.00 +ATOM 8 SC2 PHE A 3 -2.225 13.320 10.859 1.00 0.00 +ATOM 9 SC3 PHE A 3 -3.911 13.493 10.120 1.00 0.00 +ATOM 10 BB GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 11 BB ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 12 SC1 ARG A 5 -4.291 23.082 5.095 1.00 0.00 +ATOM 13 SC2 ARG A 5 -6.292 24.514 3.025 1.00 0.00 +ATOM 14 BB CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 15 SC1 CYS A 6 -8.652 20.827 3.310 1.00 0.00 +ATOM 16 BB GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 17 SC1 GLU A 7 -5.177 13.208 6.001 1.00 0.00 +ATOM 18 BB LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 19 SC1 LEU A 8 -4.062 18.230 11.133 1.00 0.00 +ATOM 20 BB ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 21 SC1 ALA A 9 -9.039 21.012 8.954 1.00 0.00 +ATOM 22 BB ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 23 SC1 ALA A 10 -11.457 16.297 8.313 1.00 0.00 +ATOM 24 BB ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 25 SC1 ALA A 11 -8.153 14.250 12.041 1.00 0.00 +ATOM 26 BB MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 27 SC1 MET A 12 -6.277 19.726 14.570 1.00 0.00 +ATOM 28 BB LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 29 SC1 LYS A 13 -14.633 19.476 12.605 1.00 0.00 +ATOM 30 SC2 LYS A 13 -17.419 20.478 11.394 1.00 0.00 +ATOM 31 BB ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 32 SC1 ARG A 14 -13.808 12.618 13.693 1.00 0.00 +ATOM 33 SC2 ARG A 14 -12.388 9.675 14.151 1.00 0.00 +ATOM 34 BB HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 35 SC1 HIS A 15 -10.087 14.082 17.707 1.00 0.00 +ATOM 36 SC2 HIS A 15 -9.556 11.718 17.990 1.00 0.00 +ATOM 37 SC3 HIS A 15 -9.583 12.289 16.299 1.00 0.00 +ATOM 38 BB GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 39 BB LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 40 SC1 LEU A 17 -8.675 20.110 19.004 1.00 0.00 +ATOM 41 BB ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 42 SC1 ASP A 18 -14.750 24.262 14.952 1.00 0.00 +ATOM 43 BB ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 44 SC1 ASN A 19 -15.703 27.056 17.780 1.00 0.00 +ATOM 45 BB TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 46 SC1 TYR A 20 -11.624 22.480 22.680 1.00 0.00 +ATOM 47 SC2 TYR A 20 -12.378 20.931 24.472 1.00 0.00 +ATOM 48 SC3 TYR A 20 -10.403 22.290 24.823 1.00 0.00 +ATOM 49 SC4 TYR A 20 -11.170 20.782 26.643 1.00 0.00 +ATOM 50 BB ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 51 SC1 ARG A 21 -11.039 25.993 26.476 1.00 0.00 +ATOM 52 SC2 ARG A 21 -11.248 25.333 29.887 1.00 0.00 +ATOM 53 BB GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 54 BB TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 55 SC1 TYR A 23 -8.709 28.306 20.758 1.00 0.00 +ATOM 56 SC2 TYR A 23 -7.220 30.161 21.378 1.00 0.00 +ATOM 57 SC3 TYR A 23 -8.220 28.823 23.132 1.00 0.00 +ATOM 58 SC4 TYR A 23 -6.690 30.729 23.724 1.00 0.00 +ATOM 59 BB SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 60 SC1 SER A 24 -11.357 29.505 15.047 1.00 0.00 +ATOM 61 BB LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 62 SC1 LEU A 25 -11.124 23.037 12.733 1.00 0.00 +ATOM 63 BB GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 64 BB ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 65 SC1 ASN A 27 -7.130 30.091 16.604 1.00 0.00 +ATOM 66 BB TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 67 SC1 TRP A 28 -6.816 23.669 16.888 1.00 0.00 +ATOM 68 SC2 TRP A 28 -8.472 24.497 18.485 1.00 0.00 +ATOM 69 SC3 TRP A 28 -7.007 23.915 19.324 1.00 0.00 +ATOM 70 SC4 TRP A 28 -5.190 23.090 19.929 1.00 0.00 +ATOM 71 SC5 TRP A 28 -6.586 23.809 21.385 1.00 0.00 +ATOM 72 BB VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 73 SC1 VAL A 29 -5.534 23.426 10.637 1.00 0.00 +ATOM 74 BB CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 75 SC1 CYS A 30 -1.819 29.329 12.180 1.00 0.00 +ATOM 76 BB ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 77 SC1 ALA A 31 -1.089 25.781 16.704 1.00 0.00 +ATOM 78 BB ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 79 SC1 ALA A 32 -0.823 21.268 13.540 1.00 0.00 +ATOM 80 BB LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 81 SC1 LYS A 33 1.528 24.936 8.648 1.00 0.00 +ATOM 82 SC2 LYS A 33 3.181 24.241 6.023 1.00 0.00 +ATOM 83 BB PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 84 SC1 PHE A 34 3.533 28.017 11.764 1.00 0.00 +ATOM 85 SC2 PHE A 34 3.676 28.811 9.478 1.00 0.00 +ATOM 86 SC3 PHE A 34 2.119 29.392 10.320 1.00 0.00 +ATOM 87 BB GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 88 SC1 GLU A 35 4.384 24.445 17.868 1.00 0.00 +ATOM 89 BB SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 90 SC1 SER A 36 3.910 19.302 13.526 1.00 0.00 +ATOM 91 BB ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 92 SC1 ASN A 37 5.825 21.444 7.332 1.00 0.00 +ATOM 93 BB PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 94 SC1 PHE A 38 0.483 19.631 8.557 1.00 0.00 +ATOM 95 SC2 PHE A 38 -0.946 21.473 9.190 1.00 0.00 +ATOM 96 SC3 PHE A 38 -0.576 21.466 7.384 1.00 0.00 +ATOM 97 BB ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 98 SC1 ASN A 39 6.545 14.631 10.411 1.00 0.00 +ATOM 99 BB THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 100 SC1 THR A 40 2.081 11.990 13.217 1.00 0.00 +ATOM 101 BB GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 102 SC1 GLN A 41 7.443 9.446 12.260 1.00 0.00 +ATOM 103 BB ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 104 SC1 ALA A 42 7.744 17.108 14.349 1.00 0.00 +ATOM 105 BB THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 106 SC1 THR A 43 11.479 14.266 18.039 1.00 0.00 +ATOM 107 BB ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 108 SC1 ASN A 44 11.937 20.259 16.961 1.00 0.00 +ATOM 109 BB ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 110 SC1 ARG A 45 16.691 18.207 23.144 1.00 0.00 +ATOM 111 SC2 ARG A 45 18.247 15.570 23.629 1.00 0.00 +ATOM 112 BB ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 113 SC1 ASN A 46 12.650 22.425 24.012 1.00 0.00 +ATOM 114 BB THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 115 SC1 THR A 47 18.237 25.668 25.594 1.00 0.00 +ATOM 116 BB ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 117 SC1 ASP A 48 14.075 22.841 29.287 1.00 0.00 +ATOM 118 BB GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 119 BB SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 120 SC1 SER A 50 12.091 20.191 27.770 1.00 0.00 +ATOM 121 BB THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 122 SC1 THR A 51 12.864 16.026 23.443 1.00 0.00 +ATOM 123 BB ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 124 SC1 ASP A 52 9.031 21.088 22.419 1.00 0.00 +ATOM 125 BB TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 126 SC1 TYR A 53 7.247 14.330 21.880 1.00 0.00 +ATOM 127 SC2 TYR A 53 8.942 14.562 23.703 1.00 0.00 +ATOM 128 SC3 TYR A 53 9.232 12.836 22.050 1.00 0.00 +ATOM 129 SC4 TYR A 53 10.883 13.050 23.887 1.00 0.00 +ATOM 130 BB GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 131 BB ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 132 SC1 ILE A 55 0.153 16.813 14.439 1.00 0.00 +ATOM 133 BB LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 134 SC1 LEU A 56 -1.026 20.379 18.593 1.00 0.00 +ATOM 135 BB GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 136 SC1 GLN A 57 7.224 19.970 18.175 1.00 0.00 +ATOM 137 BB ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 138 SC1 ILE A 58 1.868 17.963 23.794 1.00 0.00 +ATOM 139 BB ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 140 SC1 ASN A 59 8.436 20.830 27.190 1.00 0.00 +ATOM 141 BB SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 142 SC1 SER A 60 10.130 16.060 27.751 1.00 0.00 +ATOM 143 BB ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 144 SC1 ARG A 61 9.759 21.040 32.156 1.00 0.00 +ATOM 145 SC2 ARG A 61 12.735 20.588 32.524 1.00 0.00 +ATOM 146 BB TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 147 SC1 TRP A 62 4.900 20.805 31.898 1.00 0.00 +ATOM 148 SC2 TRP A 62 6.376 22.506 31.097 1.00 0.00 +ATOM 149 SC3 TRP A 62 6.294 22.487 32.881 1.00 0.00 +ATOM 150 SC4 TRP A 62 5.936 22.198 34.895 1.00 0.00 +ATOM 151 SC5 TRP A 62 7.247 23.716 34.252 1.00 0.00 +ATOM 152 BB TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 153 SC1 TRP A 63 2.540 18.368 28.720 1.00 0.00 +ATOM 154 SC2 TRP A 63 2.928 20.769 28.863 1.00 0.00 +ATOM 155 SC3 TRP A 63 1.466 20.330 29.738 1.00 0.00 +ATOM 156 SC4 TRP A 63 -0.224 19.473 30.655 1.00 0.00 +ATOM 157 SC5 TRP A 63 0.131 21.566 30.772 1.00 0.00 +ATOM 158 BB CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 159 SC1 CYS A 64 5.333 13.856 26.701 1.00 0.00 +ATOM 160 BB ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 161 SC1 ASN A 65 8.140 9.329 31.687 1.00 0.00 +ATOM 162 BB ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 163 SC1 ASP A 66 11.494 12.585 27.497 1.00 0.00 +ATOM 164 BB GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 165 BB ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 166 SC1 ARG A 68 15.780 11.749 27.753 1.00 0.00 +ATOM 167 SC2 ARG A 68 16.274 12.982 24.249 1.00 0.00 +ATOM 168 BB THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 169 SC1 THR A 69 12.492 15.745 30.301 1.00 0.00 +ATOM 170 BB PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 171 SC1 PRO A 70 16.140 15.248 34.269 1.00 0.00 +ATOM 172 BB GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 173 BB SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 174 SC1 SER A 72 8.557 14.615 32.981 1.00 0.00 +ATOM 175 BB ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 176 SC1 ARG A 73 5.100 18.319 36.883 1.00 0.00 +ATOM 177 SC2 ARG A 73 4.230 20.855 39.417 1.00 0.00 +ATOM 178 BB ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 179 SC1 ASN A 74 3.473 11.411 32.304 1.00 0.00 +ATOM 180 BB LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 181 SC1 LEU A 75 0.573 17.947 34.719 1.00 0.00 +ATOM 182 BB CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 183 SC1 CYS A 76 -1.265 15.571 28.787 1.00 0.00 +ATOM 184 BB ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 185 SC1 ASN A 77 -1.365 8.776 33.204 1.00 0.00 +ATOM 186 BB ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 187 SC1 ILE A 78 0.451 10.630 27.183 1.00 0.00 +ATOM 188 BB PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 189 SC1 PRO A 79 3.738 6.626 27.089 1.00 0.00 +ATOM 190 BB CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 191 SC1 CYS A 80 7.217 12.587 26.174 1.00 0.00 +ATOM 192 BB SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 193 SC1 SER A 81 6.595 6.616 22.740 1.00 0.00 +ATOM 194 BB ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 195 SC1 ALA A 82 1.481 8.009 23.384 1.00 0.00 +ATOM 196 BB LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 197 SC1 LEU A 83 2.319 13.242 22.880 1.00 0.00 +ATOM 198 BB LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 199 SC1 LEU A 84 6.667 10.906 18.168 1.00 0.00 +ATOM 200 BB SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 201 SC1 SER A 85 -0.052 7.196 16.978 1.00 0.00 +ATOM 202 BB SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 203 SC1 SER A 86 0.142 7.237 11.707 1.00 0.00 +ATOM 204 BB ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 205 SC1 ASP A 87 -5.391 7.382 16.677 1.00 0.00 +ATOM 206 BB ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 207 SC1 ILE A 88 -4.687 13.702 15.370 1.00 0.00 +ATOM 208 BB THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 209 SC1 THR A 89 -7.305 9.653 19.626 1.00 0.00 +ATOM 210 BB ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 211 SC1 ALA A 90 -2.331 10.290 22.751 1.00 0.00 +ATOM 212 BB SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 213 SC1 SER A 91 -0.683 14.603 19.718 1.00 0.00 +ATOM 214 BB VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 215 SC1 VAL A 92 -6.856 15.900 19.617 1.00 0.00 +ATOM 216 BB ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 217 SC1 ASN A 93 -7.766 12.659 24.393 1.00 0.00 +ATOM 218 BB CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 219 SC1 CYS A 94 -0.957 16.123 26.475 1.00 0.00 +ATOM 220 BB ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 221 SC1 ALA A 95 -3.774 19.698 22.627 1.00 0.00 +ATOM 222 BB LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 223 SC1 LYS A 96 -9.033 18.462 24.585 1.00 0.00 +ATOM 224 SC2 LYS A 96 -11.333 17.085 22.831 1.00 0.00 +ATOM 225 BB LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 226 SC1 LYS A 97 -5.546 17.841 30.375 1.00 0.00 +ATOM 227 SC2 LYS A 97 -7.854 16.295 31.743 1.00 0.00 +ATOM 228 BB ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 229 SC1 ILE A 98 -0.911 21.639 26.782 1.00 0.00 +ATOM 230 BB VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 231 SC1 VAL A 99 -6.389 24.959 25.034 1.00 0.00 +ATOM 232 BB SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 233 SC1 SER A 100 -8.629 23.014 29.561 1.00 0.00 +ATOM 234 BB ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 235 SC1 ASP A 101 -2.145 24.522 32.746 1.00 0.00 +ATOM 236 BB GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 237 BB ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 238 SC1 ASN A 103 -0.657 31.446 30.604 1.00 0.00 +ATOM 239 BB GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 240 BB MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 241 SC1 MET A 105 -4.583 27.642 20.426 1.00 0.00 +ATOM 242 BB ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 243 SC1 ASN A 106 -1.234 33.304 24.677 1.00 0.00 +ATOM 244 BB ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 245 SC1 ALA A 107 0.585 26.599 26.143 1.00 0.00 +ATOM 246 BB TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 247 SC1 TRP A 108 1.201 25.872 21.084 1.00 0.00 +ATOM 248 SC2 TRP A 108 1.421 23.478 21.263 1.00 0.00 +ATOM 249 SC3 TRP A 108 -0.097 24.022 21.986 1.00 0.00 +ATOM 250 SC4 TRP A 108 -1.738 24.948 22.755 1.00 0.00 +ATOM 251 SC5 TRP A 108 -1.597 22.821 22.864 1.00 0.00 +ATOM 252 BB VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 253 SC1 VAL A 109 6.981 29.495 20.948 1.00 0.00 +ATOM 254 BB ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 255 SC1 ALA A 110 4.783 28.117 16.262 1.00 0.00 +ATOM 256 BB TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 257 SC1 TRP A 111 -0.914 29.450 18.540 1.00 0.00 +ATOM 258 SC2 TRP A 111 -3.120 29.950 17.528 1.00 0.00 +ATOM 259 SC3 TRP A 111 -2.831 30.936 19.012 1.00 0.00 +ATOM 260 SC4 TRP A 111 -2.231 31.907 20.786 1.00 0.00 +ATOM 261 SC5 TRP A 111 -4.106 32.361 19.902 1.00 0.00 +ATOM 262 BB ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 263 SC1 ARG A 112 2.360 34.094 21.939 1.00 0.00 +ATOM 264 SC2 ARG A 112 4.788 33.235 23.642 1.00 0.00 +ATOM 265 BB ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 266 SC1 ASN A 113 6.187 34.311 18.635 1.00 0.00 +ATOM 267 BB ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 268 SC1 ARG A 114 4.636 31.613 13.473 1.00 0.00 +ATOM 269 SC2 ARG A 114 6.636 30.401 10.985 1.00 0.00 +ATOM 270 BB CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 271 SC1 CYS A 115 -0.808 30.194 14.254 1.00 0.00 +ATOM 272 BB LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 273 SC1 LYS A 116 -2.027 35.559 19.418 1.00 0.00 +ATOM 274 SC2 LYS A 116 -2.220 36.558 22.473 1.00 0.00 +ATOM 275 BB GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 276 BB THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 277 SC1 THR A 118 -2.485 35.254 11.745 1.00 0.00 +ATOM 278 BB ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 279 SC1 ASP A 119 -8.345 35.153 7.571 1.00 0.00 +ATOM 280 BB VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 281 SC1 VAL A 120 -6.503 31.706 12.841 1.00 0.00 +ATOM 282 BB GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 283 SC1 GLN A 121 -12.840 31.907 8.761 1.00 0.00 +ATOM 284 BB ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 285 SC1 ALA A 122 -6.378 31.657 5.724 1.00 0.00 +ATOM 286 BB TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 287 SC1 TRP A 123 -4.923 27.686 8.656 1.00 0.00 +ATOM 288 SC2 TRP A 123 -3.421 29.540 9.108 1.00 0.00 +ATOM 289 SC3 TRP A 123 -2.625 28.266 8.146 1.00 0.00 +ATOM 290 SC4 TRP A 123 -2.046 26.596 7.064 1.00 0.00 +ATOM 291 SC5 TRP A 123 -0.697 28.183 7.392 1.00 0.00 +ATOM 292 BB ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 293 SC1 ILE A 124 -10.902 25.947 8.637 1.00 0.00 +ATOM 294 BB ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 295 SC1 ARG A 125 -10.343 29.456 2.036 1.00 0.00 +ATOM 296 SC2 ARG A 125 -7.917 30.428 0.891 1.00 0.00 +ATOM 297 BB GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 298 BB CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 299 SC1 CYS A 127 -10.025 22.210 4.507 1.00 0.00 +ATOM 300 BB ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 301 SC1 ARG A 128 -16.241 17.914 2.040 1.00 0.00 +ATOM 302 SC2 ARG A 128 -15.487 16.199 -0.582 1.00 0.00 +ATOM 303 BB LEU A 129 -17.104 19.979 6.793 1.00 0.00 +ATOM 304 SC1 LEU A 129 -13.806 20.960 8.017 1.00 0.00 +ATOM 305 CA LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 306 CA VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 307 CA PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 308 CA GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 309 CA ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 310 CA CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 311 CA GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 312 CA LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 313 CA ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 314 CA ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 315 CA ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 316 CA MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 317 CA LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 318 CA ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 319 CA HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 320 CA GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 321 CA LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 322 CA ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 323 CA ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 324 CA TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 325 CA ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 326 CA GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 327 CA TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 328 CA SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 329 CA LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 330 CA GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 331 CA ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 332 CA TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 333 CA VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 334 CA CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 335 CA ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 336 CA ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 337 CA LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 338 CA PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 339 CA GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 340 CA SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 341 CA ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 342 CA PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 343 CA ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 344 CA THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 345 CA GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 346 CA ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 347 CA THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 348 CA ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 349 CA ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 350 CA ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 351 CA THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 352 CA ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 353 CA GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 354 CA SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 355 CA THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 356 CA ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 357 CA TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 358 CA GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 359 CA ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 360 CA LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 361 CA GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 362 CA ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 363 CA ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 364 CA SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 365 CA ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 366 CA TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 367 CA TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 368 CA CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 369 CA ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 370 CA ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 371 CA GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 372 CA ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 373 CA THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 374 CA PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 375 CA GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 376 CA SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 377 CA ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 378 CA ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 379 CA LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 380 CA CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 381 CA ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 382 CA ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 383 CA PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 384 CA CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 385 CA SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 386 CA ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 387 CA LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 388 CA LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 389 CA SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 390 CA SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 391 CA ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 392 CA ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 393 CA THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 394 CA ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 395 CA SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 396 CA VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 397 CA ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 398 CA CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 399 CA ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 400 CA LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 401 CA LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 402 CA ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 403 CA VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 404 CA SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 405 CA ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 406 CA GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 407 CA ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 408 CA GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 409 CA MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 410 CA ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 411 CA ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 412 CA TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 413 CA VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 414 CA ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 415 CA TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 416 CA ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 417 CA ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 418 CA ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 419 CA CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 420 CA LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 421 CA GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 422 CA THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 423 CA ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 424 CA VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 425 CA GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 426 CA ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 427 CA TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 428 CA ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 429 CA ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 430 CA GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 431 CA CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 432 CA ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 433 CA LEU A 129 -17.104 19.979 6.793 1.00 0.00 +TER 434 LEU A 129 +CONECT 1 2 4 +CONECT 2 3 +CONECT 4 5 6 +CONECT 6 7 10 +CONECT 7 8 9 +CONECT 8 9 +CONECT 10 11 +CONECT 11 12 14 +CONECT 12 13 +CONECT 14 15 16 +CONECT 16 17 18 +CONECT 18 19 20 +CONECT 20 21 22 +CONECT 22 23 24 +CONECT 24 25 26 +CONECT 26 27 28 +CONECT 28 29 31 +CONECT 29 30 +CONECT 31 32 34 +CONECT 32 33 +CONECT 34 35 38 +CONECT 35 36 37 +CONECT 36 37 +CONECT 38 39 +CONECT 39 40 41 +CONECT 41 42 43 +CONECT 43 44 45 +CONECT 45 46 50 +CONECT 46 47 48 +CONECT 47 48 49 +CONECT 48 49 +CONECT 50 51 53 +CONECT 51 52 +CONECT 53 54 +CONECT 54 55 59 +CONECT 55 56 57 +CONECT 56 57 58 +CONECT 57 58 +CONECT 59 60 61 +CONECT 61 62 63 +CONECT 63 64 +CONECT 64 65 66 +CONECT 66 67 72 +CONECT 67 68 70 +CONECT 68 70 71 +CONECT 70 71 +CONECT 72 73 74 +CONECT 74 75 76 +CONECT 76 77 78 +CONECT 78 79 80 +CONECT 80 81 83 +CONECT 81 82 +CONECT 83 84 87 +CONECT 84 85 86 +CONECT 85 86 +CONECT 87 88 89 +CONECT 89 90 91 +CONECT 91 92 93 +CONECT 93 94 97 +CONECT 94 95 96 +CONECT 95 96 +CONECT 97 98 99 +CONECT 99 100 101 +CONECT 101 102 103 +CONECT 103 104 105 +CONECT 105 106 107 +CONECT 107 108 109 +CONECT 109 110 112 +CONECT 110 111 +CONECT 112 113 114 +CONECT 114 115 116 +CONECT 116 117 118 +CONECT 118 119 +CONECT 119 120 121 +CONECT 121 122 123 +CONECT 123 124 125 +CONECT 125 126 130 +CONECT 126 127 128 +CONECT 127 128 129 +CONECT 128 129 +CONECT 130 131 +CONECT 131 132 133 +CONECT 133 134 135 +CONECT 135 136 137 +CONECT 137 138 139 +CONECT 139 140 141 +CONECT 141 142 143 +CONECT 143 144 146 +CONECT 144 145 +CONECT 146 147 152 +CONECT 147 148 150 +CONECT 148 150 151 +CONECT 150 151 +CONECT 152 153 158 +CONECT 153 154 156 +CONECT 154 156 157 +CONECT 156 157 +CONECT 158 159 160 +CONECT 160 161 162 +CONECT 162 163 164 +CONECT 164 165 +CONECT 165 166 168 +CONECT 166 167 +CONECT 168 169 170 +CONECT 170 171 172 +CONECT 172 173 +CONECT 173 174 175 +CONECT 175 176 178 +CONECT 176 177 +CONECT 178 179 180 +CONECT 180 181 182 +CONECT 182 183 184 +CONECT 184 185 186 +CONECT 186 187 188 +CONECT 188 189 190 +CONECT 190 191 192 +CONECT 192 193 194 +CONECT 194 195 196 +CONECT 196 197 198 +CONECT 198 199 200 +CONECT 200 201 202 +CONECT 202 203 204 +CONECT 204 205 206 +CONECT 206 207 208 +CONECT 208 209 210 +CONECT 210 211 212 +CONECT 212 213 214 +CONECT 214 215 216 +CONECT 216 217 218 +CONECT 218 219 220 +CONECT 220 221 222 +CONECT 222 223 225 +CONECT 223 224 +CONECT 225 226 228 +CONECT 226 227 +CONECT 228 229 230 +CONECT 230 231 232 +CONECT 232 233 234 +CONECT 234 235 236 +CONECT 236 237 +CONECT 237 238 239 +CONECT 239 240 +CONECT 240 241 242 +CONECT 242 243 244 +CONECT 244 245 246 +CONECT 246 247 252 +CONECT 247 248 250 +CONECT 248 250 251 +CONECT 250 251 +CONECT 252 253 254 +CONECT 254 255 256 +CONECT 256 257 262 +CONECT 257 258 260 +CONECT 258 260 261 +CONECT 260 261 +CONECT 262 263 265 +CONECT 263 264 +CONECT 265 266 267 +CONECT 267 268 270 +CONECT 268 269 +CONECT 270 271 272 +CONECT 272 273 275 +CONECT 273 274 +CONECT 275 276 +CONECT 276 277 278 +CONECT 278 279 280 +CONECT 280 281 282 +CONECT 282 283 284 +CONECT 284 285 286 +CONECT 286 287 292 +CONECT 287 288 290 +CONECT 288 290 291 +CONECT 290 291 +CONECT 292 293 294 +CONECT 294 295 297 +CONECT 295 296 +CONECT 297 298 +CONECT 298 299 300 +CONECT 300 301 303 +CONECT 301 302 +CONECT 303 304 +END \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation new file mode 100644 index 00000000..6209c13b --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation @@ -0,0 +1 @@ +Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command new file mode 100755 index 00000000..92de3c34 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command @@ -0,0 +1,9 @@ +martinize2 +-f ../aa.pdb +-ff martini3001 +-x cg.pdb +-o topol.top +-ignore HOH +-ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC +-go +-go-map ../map.map diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp new file mode 100644 index 00000000..bcbcf614 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_atomtypes.itp @@ -0,0 +1,130 @@ +[ atomtypes ] +molecule_0_1 0.0 0 A 0.00000000 0.00000000 +molecule_0_2 0.0 0 A 0.00000000 0.00000000 +molecule_0_3 0.0 0 A 0.00000000 0.00000000 +molecule_0_4 0.0 0 A 0.00000000 0.00000000 +molecule_0_5 0.0 0 A 0.00000000 0.00000000 +molecule_0_6 0.0 0 A 0.00000000 0.00000000 +molecule_0_7 0.0 0 A 0.00000000 0.00000000 +molecule_0_8 0.0 0 A 0.00000000 0.00000000 +molecule_0_9 0.0 0 A 0.00000000 0.00000000 +molecule_0_10 0.0 0 A 0.00000000 0.00000000 +molecule_0_11 0.0 0 A 0.00000000 0.00000000 +molecule_0_12 0.0 0 A 0.00000000 0.00000000 +molecule_0_13 0.0 0 A 0.00000000 0.00000000 +molecule_0_14 0.0 0 A 0.00000000 0.00000000 +molecule_0_15 0.0 0 A 0.00000000 0.00000000 +molecule_0_16 0.0 0 A 0.00000000 0.00000000 +molecule_0_17 0.0 0 A 0.00000000 0.00000000 +molecule_0_18 0.0 0 A 0.00000000 0.00000000 +molecule_0_19 0.0 0 A 0.00000000 0.00000000 +molecule_0_20 0.0 0 A 0.00000000 0.00000000 +molecule_0_21 0.0 0 A 0.00000000 0.00000000 +molecule_0_22 0.0 0 A 0.00000000 0.00000000 +molecule_0_23 0.0 0 A 0.00000000 0.00000000 +molecule_0_24 0.0 0 A 0.00000000 0.00000000 +molecule_0_25 0.0 0 A 0.00000000 0.00000000 +molecule_0_26 0.0 0 A 0.00000000 0.00000000 +molecule_0_27 0.0 0 A 0.00000000 0.00000000 +molecule_0_28 0.0 0 A 0.00000000 0.00000000 +molecule_0_29 0.0 0 A 0.00000000 0.00000000 +molecule_0_30 0.0 0 A 0.00000000 0.00000000 +molecule_0_31 0.0 0 A 0.00000000 0.00000000 +molecule_0_32 0.0 0 A 0.00000000 0.00000000 +molecule_0_33 0.0 0 A 0.00000000 0.00000000 +molecule_0_34 0.0 0 A 0.00000000 0.00000000 +molecule_0_35 0.0 0 A 0.00000000 0.00000000 +molecule_0_36 0.0 0 A 0.00000000 0.00000000 +molecule_0_37 0.0 0 A 0.00000000 0.00000000 +molecule_0_38 0.0 0 A 0.00000000 0.00000000 +molecule_0_39 0.0 0 A 0.00000000 0.00000000 +molecule_0_40 0.0 0 A 0.00000000 0.00000000 +molecule_0_41 0.0 0 A 0.00000000 0.00000000 +molecule_0_42 0.0 0 A 0.00000000 0.00000000 +molecule_0_43 0.0 0 A 0.00000000 0.00000000 +molecule_0_44 0.0 0 A 0.00000000 0.00000000 +molecule_0_45 0.0 0 A 0.00000000 0.00000000 +molecule_0_46 0.0 0 A 0.00000000 0.00000000 +molecule_0_47 0.0 0 A 0.00000000 0.00000000 +molecule_0_48 0.0 0 A 0.00000000 0.00000000 +molecule_0_49 0.0 0 A 0.00000000 0.00000000 +molecule_0_50 0.0 0 A 0.00000000 0.00000000 +molecule_0_51 0.0 0 A 0.00000000 0.00000000 +molecule_0_52 0.0 0 A 0.00000000 0.00000000 +molecule_0_53 0.0 0 A 0.00000000 0.00000000 +molecule_0_54 0.0 0 A 0.00000000 0.00000000 +molecule_0_55 0.0 0 A 0.00000000 0.00000000 +molecule_0_56 0.0 0 A 0.00000000 0.00000000 +molecule_0_57 0.0 0 A 0.00000000 0.00000000 +molecule_0_58 0.0 0 A 0.00000000 0.00000000 +molecule_0_59 0.0 0 A 0.00000000 0.00000000 +molecule_0_60 0.0 0 A 0.00000000 0.00000000 +molecule_0_61 0.0 0 A 0.00000000 0.00000000 +molecule_0_62 0.0 0 A 0.00000000 0.00000000 +molecule_0_63 0.0 0 A 0.00000000 0.00000000 +molecule_0_64 0.0 0 A 0.00000000 0.00000000 +molecule_0_65 0.0 0 A 0.00000000 0.00000000 +molecule_0_66 0.0 0 A 0.00000000 0.00000000 +molecule_0_67 0.0 0 A 0.00000000 0.00000000 +molecule_0_68 0.0 0 A 0.00000000 0.00000000 +molecule_0_69 0.0 0 A 0.00000000 0.00000000 +molecule_0_70 0.0 0 A 0.00000000 0.00000000 +molecule_0_71 0.0 0 A 0.00000000 0.00000000 +molecule_0_72 0.0 0 A 0.00000000 0.00000000 +molecule_0_73 0.0 0 A 0.00000000 0.00000000 +molecule_0_74 0.0 0 A 0.00000000 0.00000000 +molecule_0_75 0.0 0 A 0.00000000 0.00000000 +molecule_0_76 0.0 0 A 0.00000000 0.00000000 +molecule_0_77 0.0 0 A 0.00000000 0.00000000 +molecule_0_78 0.0 0 A 0.00000000 0.00000000 +molecule_0_79 0.0 0 A 0.00000000 0.00000000 +molecule_0_80 0.0 0 A 0.00000000 0.00000000 +molecule_0_81 0.0 0 A 0.00000000 0.00000000 +molecule_0_82 0.0 0 A 0.00000000 0.00000000 +molecule_0_83 0.0 0 A 0.00000000 0.00000000 +molecule_0_84 0.0 0 A 0.00000000 0.00000000 +molecule_0_85 0.0 0 A 0.00000000 0.00000000 +molecule_0_86 0.0 0 A 0.00000000 0.00000000 +molecule_0_87 0.0 0 A 0.00000000 0.00000000 +molecule_0_88 0.0 0 A 0.00000000 0.00000000 +molecule_0_89 0.0 0 A 0.00000000 0.00000000 +molecule_0_90 0.0 0 A 0.00000000 0.00000000 +molecule_0_91 0.0 0 A 0.00000000 0.00000000 +molecule_0_92 0.0 0 A 0.00000000 0.00000000 +molecule_0_93 0.0 0 A 0.00000000 0.00000000 +molecule_0_94 0.0 0 A 0.00000000 0.00000000 +molecule_0_95 0.0 0 A 0.00000000 0.00000000 +molecule_0_96 0.0 0 A 0.00000000 0.00000000 +molecule_0_97 0.0 0 A 0.00000000 0.00000000 +molecule_0_98 0.0 0 A 0.00000000 0.00000000 +molecule_0_99 0.0 0 A 0.00000000 0.00000000 +molecule_0_100 0.0 0 A 0.00000000 0.00000000 +molecule_0_101 0.0 0 A 0.00000000 0.00000000 +molecule_0_102 0.0 0 A 0.00000000 0.00000000 +molecule_0_103 0.0 0 A 0.00000000 0.00000000 +molecule_0_104 0.0 0 A 0.00000000 0.00000000 +molecule_0_105 0.0 0 A 0.00000000 0.00000000 +molecule_0_106 0.0 0 A 0.00000000 0.00000000 +molecule_0_107 0.0 0 A 0.00000000 0.00000000 +molecule_0_108 0.0 0 A 0.00000000 0.00000000 +molecule_0_109 0.0 0 A 0.00000000 0.00000000 +molecule_0_110 0.0 0 A 0.00000000 0.00000000 +molecule_0_111 0.0 0 A 0.00000000 0.00000000 +molecule_0_112 0.0 0 A 0.00000000 0.00000000 +molecule_0_113 0.0 0 A 0.00000000 0.00000000 +molecule_0_114 0.0 0 A 0.00000000 0.00000000 +molecule_0_115 0.0 0 A 0.00000000 0.00000000 +molecule_0_116 0.0 0 A 0.00000000 0.00000000 +molecule_0_117 0.0 0 A 0.00000000 0.00000000 +molecule_0_118 0.0 0 A 0.00000000 0.00000000 +molecule_0_119 0.0 0 A 0.00000000 0.00000000 +molecule_0_120 0.0 0 A 0.00000000 0.00000000 +molecule_0_121 0.0 0 A 0.00000000 0.00000000 +molecule_0_122 0.0 0 A 0.00000000 0.00000000 +molecule_0_123 0.0 0 A 0.00000000 0.00000000 +molecule_0_124 0.0 0 A 0.00000000 0.00000000 +molecule_0_125 0.0 0 A 0.00000000 0.00000000 +molecule_0_126 0.0 0 A 0.00000000 0.00000000 +molecule_0_127 0.0 0 A 0.00000000 0.00000000 +molecule_0_128 0.0 0 A 0.00000000 0.00000000 +molecule_0_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp new file mode 100644 index 00000000..8c545698 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/go_nbparams.itp @@ -0,0 +1,260 @@ +[ nonbond_params ] +molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 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1 0.35572883 9.41400000 ;go bond 0.3992921109620664 +molecule_0_58 molecule_0_52 1 0.41486867 9.41400000 ;go bond 0.4656743363160884 +molecule_0_58 molecule_0_53 1 0.33528745 9.41400000 ;go bond 0.37634743770658646 +molecule_0_59 molecule_0_46 1 0.92985190 9.41400000 ;go bond 1.0437234628284975 +molecule_0_59 molecule_0_50 1 0.67865311 9.41400000 ;go bond 0.7617623567683692 +molecule_0_59 molecule_0_51 1 0.46599015 9.41400000 ;go bond 0.5230562584392384 +molecule_0_59 molecule_0_52 1 0.52411606 9.41400000 ;go bond 0.5883003833904864 +molecule_0_60 molecule_0_50 1 0.55757626 9.41400000 ;go bond 0.6258581889054639 +molecule_0_60 molecule_0_51 1 0.45353930 9.41400000 ;go bond 0.5090806492037284 +molecule_0_60 molecule_0_53 1 0.78554721 9.41400000 ;go bond 0.8817469319963909 +molecule_0_61 molecule_0_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 +molecule_0_61 molecule_0_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 +molecule_0_63 molecule_0_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 +molecule_0_63 molecule_0_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 +molecule_0_64 molecule_0_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 +molecule_0_64 molecule_0_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 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9.41400000 ;go bond 0.5734530137551908 +molecule_0_83 molecule_0_58 1 0.70980394 9.41400000 ;go bond 0.7967279839859979 +molecule_0_83 molecule_0_64 1 0.89499397 9.41400000 ;go bond 1.0045967605887745 +molecule_0_83 molecule_0_78 1 0.81556181 9.41400000 ;go bond 0.9154371804917103 +molecule_0_84 molecule_0_40 1 0.40226578 9.41400000 ;go bond 0.45152806893595954 +molecule_0_84 molecule_0_41 1 0.48796771 9.41400000 ;go bond 0.5477252325235119 +molecule_0_84 molecule_0_42 1 0.63252675 9.41400000 ;go bond 0.7099872721863867 +molecule_0_84 molecule_0_43 1 0.89270990 9.41400000 ;go bond 1.0020329775751635 +molecule_0_84 molecule_0_53 1 0.66502200 9.41400000 ;go bond 0.7464619538686407 +molecule_0_84 molecule_0_54 1 0.56665258 9.41400000 ;go bond 0.6360460147186728 +molecule_0_85 molecule_0_40 1 0.48170210 9.41400000 ;go bond 0.5406923273735796 +molecule_0_85 molecule_0_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 0.7769220558398894 +molecule_0_90 molecule_0_78 1 0.80563795 9.41400000 ;go bond 0.9042980239792853 +molecule_0_90 molecule_0_82 1 0.59740893 9.41400000 ;go bond 0.6705688513824994 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1 0.89829847 9.41400000 ;go bond 1.0083059444227724 +molecule_0_94 molecule_0_90 1 0.53696870 9.41400000 ;go bond 0.6027269866522963 +molecule_0_95 molecule_0_28 1 0.94028879 9.41400000 ;go bond 1.0554384813372668 +molecule_0_95 molecule_0_56 1 0.76727508 9.41400000 ;go bond 0.8612371596953154 +molecule_0_95 molecule_0_58 1 0.83998475 9.41400000 ;go bond 0.9428510053550558 +molecule_0_95 molecule_0_91 1 0.53148309 9.41400000 ;go bond 0.5965695928114466 +molecule_0_96 molecule_0_15 1 0.94537258 9.41400000 ;go bond 1.0611448446580265 +molecule_0_96 molecule_0_16 1 0.84805127 9.41400000 ;go bond 0.9519053644995195 +molecule_0_96 molecule_0_17 1 0.81454872 9.41400000 ;go bond 0.9143000281459933 +molecule_0_96 molecule_0_20 1 0.73587759 9.41400000 ;go bond 0.8259946673768416 +molecule_0_96 molecule_0_92 1 0.54860993 9.41400000 ;go bond 0.6157938252917854 +molecule_0_97 molecule_0_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 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1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 +molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 +molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 +molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 +molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp new file mode 100644 index 00000000..501335e6 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/molecule_0.itp @@ -0,0 +1,1669 @@ +; This file was generated using the following command: +; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map +; martinize with vermouth 0.9.7.dev79 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Pleas cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_0_1 1 LYS CA 305 0 0.0 +306 molecule_0_2 2 VAL CA 306 0 0.0 +307 molecule_0_3 3 PHE CA 307 0 0.0 +308 molecule_0_4 4 GLY CA 308 0 0.0 +309 molecule_0_5 5 ARG CA 309 0 0.0 +310 molecule_0_6 6 CYS CA 310 0 0.0 +311 molecule_0_7 7 GLU CA 311 0 0.0 +312 molecule_0_8 8 LEU CA 312 0 0.0 +313 molecule_0_9 9 ALA CA 313 0 0.0 +314 molecule_0_10 10 ALA CA 314 0 0.0 +315 molecule_0_11 11 ALA CA 315 0 0.0 +316 molecule_0_12 12 MET CA 316 0 0.0 +317 molecule_0_13 13 LYS CA 317 0 0.0 +318 molecule_0_14 14 ARG CA 318 0 0.0 +319 molecule_0_15 15 HIS CA 319 0 0.0 +320 molecule_0_16 16 GLY CA 320 0 0.0 +321 molecule_0_17 17 LEU CA 321 0 0.0 +322 molecule_0_18 18 ASP CA 322 0 0.0 +323 molecule_0_19 19 ASN CA 323 0 0.0 +324 molecule_0_20 20 TYR CA 324 0 0.0 +325 molecule_0_21 21 ARG CA 325 0 0.0 +326 molecule_0_22 22 GLY CA 326 0 0.0 +327 molecule_0_23 23 TYR CA 327 0 0.0 +328 molecule_0_24 24 SER CA 328 0 0.0 +329 molecule_0_25 25 LEU CA 329 0 0.0 +330 molecule_0_26 26 GLY CA 330 0 0.0 +331 molecule_0_27 27 ASN CA 331 0 0.0 +332 molecule_0_28 28 TRP CA 332 0 0.0 +333 molecule_0_29 29 VAL CA 333 0 0.0 +334 molecule_0_30 30 CYS CA 334 0 0.0 +335 molecule_0_31 31 ALA CA 335 0 0.0 +336 molecule_0_32 32 ALA CA 336 0 0.0 +337 molecule_0_33 33 LYS CA 337 0 0.0 +338 molecule_0_34 34 PHE CA 338 0 0.0 +339 molecule_0_35 35 GLU CA 339 0 0.0 +340 molecule_0_36 36 SER CA 340 0 0.0 +341 molecule_0_37 37 ASN CA 341 0 0.0 +342 molecule_0_38 38 PHE CA 342 0 0.0 +343 molecule_0_39 39 ASN CA 343 0 0.0 +344 molecule_0_40 40 THR CA 344 0 0.0 +345 molecule_0_41 41 GLN CA 345 0 0.0 +346 molecule_0_42 42 ALA CA 346 0 0.0 +347 molecule_0_43 43 THR CA 347 0 0.0 +348 molecule_0_44 44 ASN CA 348 0 0.0 +349 molecule_0_45 45 ARG CA 349 0 0.0 +350 molecule_0_46 46 ASN CA 350 0 0.0 +351 molecule_0_47 47 THR CA 351 0 0.0 +352 molecule_0_48 48 ASP CA 352 0 0.0 +353 molecule_0_49 49 GLY CA 353 0 0.0 +354 molecule_0_50 50 SER CA 354 0 0.0 +355 molecule_0_51 51 THR CA 355 0 0.0 +356 molecule_0_52 52 ASP CA 356 0 0.0 +357 molecule_0_53 53 TYR CA 357 0 0.0 +358 molecule_0_54 54 GLY CA 358 0 0.0 +359 molecule_0_55 55 ILE CA 359 0 0.0 +360 molecule_0_56 56 LEU CA 360 0 0.0 +361 molecule_0_57 57 GLN CA 361 0 0.0 +362 molecule_0_58 58 ILE CA 362 0 0.0 +363 molecule_0_59 59 ASN CA 363 0 0.0 +364 molecule_0_60 60 SER CA 364 0 0.0 +365 molecule_0_61 61 ARG CA 365 0 0.0 +366 molecule_0_62 62 TRP CA 366 0 0.0 +367 molecule_0_63 63 TRP CA 367 0 0.0 +368 molecule_0_64 64 CYS CA 368 0 0.0 +369 molecule_0_65 65 ASN CA 369 0 0.0 +370 molecule_0_66 66 ASP CA 370 0 0.0 +371 molecule_0_67 67 GLY CA 371 0 0.0 +372 molecule_0_68 68 ARG CA 372 0 0.0 +373 molecule_0_69 69 THR CA 373 0 0.0 +374 molecule_0_70 70 PRO CA 374 0 0.0 +375 molecule_0_71 71 GLY CA 375 0 0.0 +376 molecule_0_72 72 SER CA 376 0 0.0 +377 molecule_0_73 73 ARG CA 377 0 0.0 +378 molecule_0_74 74 ASN CA 378 0 0.0 +379 molecule_0_75 75 LEU CA 379 0 0.0 +380 molecule_0_76 76 CYS CA 380 0 0.0 +381 molecule_0_77 77 ASN CA 381 0 0.0 +382 molecule_0_78 78 ILE CA 382 0 0.0 +383 molecule_0_79 79 PRO CA 383 0 0.0 +384 molecule_0_80 80 CYS CA 384 0 0.0 +385 molecule_0_81 81 SER CA 385 0 0.0 +386 molecule_0_82 82 ALA CA 386 0 0.0 +387 molecule_0_83 83 LEU CA 387 0 0.0 +388 molecule_0_84 84 LEU CA 388 0 0.0 +389 molecule_0_85 85 SER CA 389 0 0.0 +390 molecule_0_86 86 SER CA 390 0 0.0 +391 molecule_0_87 87 ASP CA 391 0 0.0 +392 molecule_0_88 88 ILE CA 392 0 0.0 +393 molecule_0_89 89 THR CA 393 0 0.0 +394 molecule_0_90 90 ALA CA 394 0 0.0 +395 molecule_0_91 91 SER CA 395 0 0.0 +396 molecule_0_92 92 VAL CA 396 0 0.0 +397 molecule_0_93 93 ASN CA 397 0 0.0 +398 molecule_0_94 94 CYS CA 398 0 0.0 +399 molecule_0_95 95 ALA CA 399 0 0.0 +400 molecule_0_96 96 LYS CA 400 0 0.0 +401 molecule_0_97 97 LYS CA 401 0 0.0 +402 molecule_0_98 98 ILE CA 402 0 0.0 +403 molecule_0_99 99 VAL CA 403 0 0.0 +404 molecule_0_100 100 SER CA 404 0 0.0 +405 molecule_0_101 101 ASP CA 405 0 0.0 +406 molecule_0_102 102 GLY CA 406 0 0.0 +407 molecule_0_103 103 ASN CA 407 0 0.0 +408 molecule_0_104 104 GLY CA 408 0 0.0 +409 molecule_0_105 105 MET CA 409 0 0.0 +410 molecule_0_106 106 ASN CA 410 0 0.0 +411 molecule_0_107 107 ALA CA 411 0 0.0 +412 molecule_0_108 108 TRP CA 412 0 0.0 +413 molecule_0_109 109 VAL CA 413 0 0.0 +414 molecule_0_110 110 ALA CA 414 0 0.0 +415 molecule_0_111 111 TRP CA 415 0 0.0 +416 molecule_0_112 112 ARG CA 416 0 0.0 +417 molecule_0_113 113 ASN CA 417 0 0.0 +418 molecule_0_114 114 ARG CA 418 0 0.0 +419 molecule_0_115 115 CYS CA 419 0 0.0 +420 molecule_0_116 116 LYS CA 420 0 0.0 +421 molecule_0_117 117 GLY CA 421 0 0.0 +422 molecule_0_118 118 THR CA 422 0 0.0 +423 molecule_0_119 119 ASP CA 423 0 0.0 +424 molecule_0_120 120 VAL CA 424 0 0.0 +425 molecule_0_121 121 GLN CA 425 0 0.0 +426 molecule_0_122 122 ALA CA 426 0 0.0 +427 molecule_0_123 123 TRP CA 427 0 0.0 +428 molecule_0_124 124 ILE CA 428 0 0.0 +429 molecule_0_125 125 ARG CA 429 0 0.0 +430 molecule_0_126 126 GLY CA 430 0 0.0 +431 molecule_0_127 127 CYS CA 431 0 0.0 +432 molecule_0_128 128 ARG CA 432 0 0.0 +433 molecule_0_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 4 1 0.350 4000 + 4 6 1 0.350 4000 + 6 10 1 0.350 4000 + 34 38 1 0.350 4000 + 38 39 1 0.350 4000 + 39 41 1 0.350 4000 + 41 43 1 0.350 4000 + 43 45 1 0.350 4000 + 45 50 1 0.350 4000 + 50 53 1 0.350 4000 + 53 54 1 0.350 4000 + 54 59 1 0.350 4000 + 91 93 1 0.350 4000 + 93 97 1 0.350 4000 + 97 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 103 1 0.350 4000 +103 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 112 1 0.350 4000 +112 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 119 1 0.350 4000 +119 121 1 0.350 4000 +121 123 1 0.350 4000 +123 125 1 0.350 4000 +125 130 1 0.350 4000 +130 131 1 0.350 4000 +131 133 1 0.350 4000 +133 135 1 0.350 4000 +135 137 1 0.350 4000 +137 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 146 1 0.350 4000 +146 152 1 0.350 4000 +152 158 1 0.350 4000 +158 160 1 0.350 4000 +160 162 1 0.350 4000 +162 164 1 0.350 4000 +164 165 1 0.350 4000 +165 168 1 0.350 4000 +168 170 1 0.350 4000 +170 172 1 0.350 4000 +172 173 1 0.350 4000 +173 175 1 0.350 4000 +175 178 1 0.350 4000 +178 180 1 0.350 4000 +180 182 1 0.350 4000 +182 184 1 0.350 4000 +184 186 1 0.350 4000 +186 188 1 0.350 4000 +200 202 1 0.350 4000 +202 204 1 0.350 4000 +204 206 1 0.350 4000 +234 236 1 0.350 4000 +236 237 1 0.350 4000 +270 272 1 0.350 4000 +272 275 1 0.350 4000 +275 276 1 0.350 4000 +276 278 1 0.350 4000 +294 297 1 0.350 4000 +297 298 1 0.350 4000 +298 300 1 0.350 4000 +300 303 1 0.350 4000 + +; Side chain bonds + 1 2 1 0.330 5000 + 2 3 1 0.360 5000 + 6 7 1 0.325 7500 + 11 12 1 0.330 5000 + 12 13 1 0.380 5000 + 14 15 1 0.341 7500 + 16 17 1 0.400 5000 + 18 19 1 0.363 7500 + 26 27 1 0.40 2500 + 28 29 1 0.330 5000 + 29 30 1 0.360 5000 + 31 32 1 0.330 5000 + 32 33 1 0.380 5000 + 34 35 1 0.336 7500 + 39 40 1 0.363 7500 + 41 42 1 0.352 7500 + 43 44 1 0.352 5000 + 45 46 1 0.325 5000 + 50 51 1 0.330 5000 + 51 52 1 0.380 5000 + 54 55 1 0.325 5000 + 59 60 1 0.287 7500 + 61 62 1 0.363 7500 + 64 65 1 0.352 5000 + 66 67 1 0.315 5000 + 74 75 1 0.341 7500 + 80 81 1 0.330 5000 + 81 82 1 0.360 5000 + 83 84 1 0.325 7500 + 87 88 1 0.400 5000 + 89 90 1 0.287 7500 + 91 92 1 0.352 5000 + 93 94 1 0.325 7500 + 97 98 1 0.352 5000 +101 102 1 0.400 5000 +107 108 1 0.352 5000 +109 110 1 0.330 5000 +110 111 1 0.380 5000 +112 113 1 0.352 5000 +116 117 1 0.352 7500 +119 120 1 0.287 7500 +123 124 1 0.352 7500 +125 126 1 0.325 5000 +133 134 1 0.363 7500 +135 136 1 0.400 5000 +139 140 1 0.352 5000 +141 142 1 0.287 7500 +143 144 1 0.330 5000 +144 145 1 0.380 5000 +146 147 1 0.315 5000 +152 153 1 0.315 5000 +158 159 1 0.341 7500 +160 161 1 0.352 5000 +162 163 1 0.352 7500 +165 166 1 0.330 5000 +166 167 1 0.380 5000 +170 171 1 0.330 7500 +173 174 1 0.287 7500 +175 176 1 0.330 5000 +176 177 1 0.380 5000 +178 179 1 0.352 5000 +180 181 1 0.363 7500 +182 183 1 0.341 7500 +184 185 1 0.352 5000 +188 189 1 0.330 7500 +190 191 1 0.341 7500 +192 193 1 0.287 7500 +196 197 1 0.363 7500 +198 199 1 0.363 7500 +200 201 1 0.287 7500 +202 203 1 0.287 7500 +204 205 1 0.352 7500 +212 213 1 0.287 7500 +216 217 1 0.352 5000 +218 219 1 0.341 7500 +222 223 1 0.330 5000 +223 224 1 0.360 5000 +225 226 1 0.330 5000 +226 227 1 0.360 5000 +232 233 1 0.287 7500 +234 235 1 0.352 7500 +237 238 1 0.352 5000 +240 241 1 0.40 2500 +242 243 1 0.352 5000 +246 247 1 0.315 5000 +256 257 1 0.315 5000 +262 263 1 0.330 5000 +263 264 1 0.380 5000 +265 266 1 0.352 5000 +267 268 1 0.330 5000 +268 269 1 0.380 5000 +270 271 1 0.341 7500 +272 273 1 0.330 5000 +273 274 1 0.360 5000 +278 279 1 0.352 7500 +282 283 1 0.400 5000 +286 287 1 0.315 5000 +294 295 1 0.330 5000 +295 296 1 0.380 5000 +298 299 1 0.341 7500 +300 301 1 0.330 5000 +301 302 1 0.380 5000 +303 304 1 0.363 7500 + +#ifdef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 1000000 + 7 8 1 0.340 1000000 + 7 9 1 0.340 1000000 + 8 9 1 0.290 1000000 + 20 21 1 0.270 1000000 + 22 23 1 0.270 1000000 + 24 25 1 0.270 1000000 + 35 36 1 0.320 1000000 + 35 37 1 0.300 1000000 + 36 37 1 0.270 1000000 + 46 47 1 0.300 1000000 + 46 48 1 0.300 1000000 + 47 49 1 0.285 1000000 + 48 49 1 0.285 1000000 + 47 48 1 0.300 1000000 + 55 56 1 0.300 1000000 + 55 57 1 0.300 1000000 + 56 58 1 0.285 1000000 + 57 58 1 0.285 1000000 + 56 57 1 0.300 1000000 + 67 68 1 0.335 1000000 + 68 71 1 0.412 1000000 + 70 71 1 0.293 1000000 + 67 70 1 0.404 1000000 + 68 70 1 0.470 1000000 + 72 73 1 0.292 1000000 + 76 77 1 0.270 1000000 + 78 79 1 0.270 1000000 + 84 85 1 0.340 1000000 + 84 86 1 0.340 1000000 + 85 86 1 0.290 1000000 + 94 95 1 0.340 1000000 + 94 96 1 0.340 1000000 + 95 96 1 0.290 1000000 + 99 100 1 0.305 1000000 +103 104 1 0.270 1000000 +105 106 1 0.305 1000000 +114 115 1 0.305 1000000 +121 122 1 0.305 1000000 +126 127 1 0.300 1000000 +126 128 1 0.300 1000000 +127 129 1 0.285 1000000 +128 129 1 0.285 1000000 +127 128 1 0.300 1000000 +131 132 1 0.341 1000000 +137 138 1 0.341 1000000 +147 148 1 0.335 1000000 +148 151 1 0.412 1000000 +150 151 1 0.293 1000000 +147 150 1 0.404 1000000 +148 150 1 0.470 1000000 +153 154 1 0.335 1000000 +154 157 1 0.412 1000000 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00000000..a8528540 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top @@ -0,0 +1,12 @@ +#define GO_VIRT +#include "martini.itp" + + #include "go_atomtypes.itp" + #include "go_nbparams.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 061b0372..1cec5933 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -151,6 +151,31 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): system.molecules.append(molecule) return system +def is_equal(floats_a, floats_b, precision=1e-3): + ''' + Convenience comparisson of two floats within specified precision. + ''' + return all((abs(a-b) < precision) for a, b in zip(floats_a, floats_b)) + + +def parse_gofiles(file, atomtypes=False): + ''' + Parser of go_nbparams.itp & go_atomtypes.itp files into an easy to assert dictionary. + ''' + with open(file) as my_file: + tt = my_file.readlines() + vals = {} + for line in tt[1:]: + if atomtypes: + ## Key is atomname str, value is atomdef str + vals[line.split()[0]]=' '.join(line.split()[1:]) + else: + ## Key is tuple with nb pair, value is tuple with nb sigma and eps + tup = tuple(sorted((line.split()[0], + line.split()[1]))) + vals[tup]=tuple((float(line.split()[3]), float(line.split()[4]))) + return vals + @pytest.fixture def test_molecule(scope='function'): """ diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index e45fd3c2..bd632662 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -28,7 +28,7 @@ from vermouth.forcefield import ForceField from .. import datafiles -from ..helper_functions import find_in_path +from ..helper_functions import find_in_path, is_equal, parse_gofiles INTEGRATION_DATA = Path(datafiles.TEST_DATA/'integration_tests') @@ -111,6 +111,33 @@ def compare_pdb(filename1, filename2): COMPARERS = {'.itp': compare_itp, '.pdb': compare_pdb} +def compare_nbparams(fileref, filecomp): + """ + Asserts that two go_nbparams.itp files are functionally identical. + """ + ref = parse_gofiles(fileref) + compare = parse_gofiles(filecomp) + + assert(set(ref.keys())==set(compare.keys())) ## assert correct nb pairs + + for key in ref.keys(): + assert(is_equal(list(ref[key]),list(compare[key]))) ##assert correct sigma and eps + + +def compare_goatomtypes(fileref, filecomp): + """ + Asserts that two go_atomtypes.itp files are functionally identical. + """ + ref = parse_gofiles(fileref, atomtypes=True) + compare = parse_gofiles(filecomp, atomtypes=True) + + assert(set(ref.keys())==set(compare.keys())) ## assert correct atomtypes + + for key in ref.keys(): + assert(ref[key] == compare[key]) ##assert correct atom definition string + +GOCOMPARERS = {'go_nbparams.itp': compare_nbparams, + 'go_atomtypes.itp': compare_goatomtypes} def _interaction_equal(interaction1, interaction2): """ @@ -125,20 +152,21 @@ def _interaction_equal(interaction1, interaction2): @pytest.mark.parametrize("tier, protein", [ - ['tier-0', 'mini-protein1_betasheet'], - ['tier-0', 'mini-protein2_helix'], - ['tier-0', 'mini-protein3_trp-cage'], - ['tier-0', 'dipro-termini'], - ['tier-1', 'bpti'], - ['tier-1', 'lysozyme'], - ['tier-1', 'lysozyme_prot'], - ['tier-1', 'villin'], - ['tier-1', '3i40'], - ['tier-1', '6LFO_gap'], - ['tier-1', '1mj5'], - ['tier-1', '1mj5-charmm'], - ['tier-1', 'EN_chain'], - ['tier-1', 'EN_region'], + # ['tier-0', 'mini-protein1_betasheet'], + # ['tier-0', 'mini-protein2_helix'], + # ['tier-0', 'mini-protein3_trp-cage'], + # ['tier-0', 'dipro-termini'], + # ['tier-1', 'bpti'], + # ['tier-1', 'lysozyme'], + # ['tier-1', 'lysozyme_prot'], + ['tier-1', 'lysozyme_GO'], + # ['tier-1', 'villin'], + # ['tier-1', '3i40'], + # ['tier-1', '6LFO_gap'], + # ['tier-1', '1mj5'], + # ['tier-1', '1mj5-charmm'], + # ['tier-1', 'EN_chain'], + # ['tier-1', 'EN_region'], # ['tier-2', 'barnase_barstar'], # ['tier-2', 'dna'], # ['tier-2', 'gpa_dimer'], @@ -204,10 +232,13 @@ def test_integration_protein(tmp_path, monkeypatch, tier, protein): filename = new_file.name reference_file = data_path/filename assert reference_file.is_file() - ext = new_file.suffix.lower() - if ext in COMPARERS: - with monkeypatch.context() as m: - # Compare Interactions such that rounding errors in the - # parameters are OK. - m.setattr(vermouth.molecule.Interaction, '__eq__', _interaction_equal) - COMPARERS[ext](str(reference_file), str(new_file)) + if filename in ['go_nbparams.itp','go_atomtypes.itp']: + GOCOMPARERS[filename](str(reference_file), str(new_file)) + else: + ext = new_file.suffix.lower() + if ext in COMPARERS: + with monkeypatch.context() as m: + # Compare Interactions such that rounding errors in the + # parameters are OK. + m.setattr(vermouth.molecule.Interaction, '__eq__', _interaction_equal) + COMPARERS[ext](str(reference_file), str(new_file)) From 89c292dfcad0017c3a9d8df97b37f1f198a831a7 Mon Sep 17 00:00:00 2001 From: Borges Luis Date: Thu, 23 Nov 2023 17:35:51 +0100 Subject: [PATCH 68/95] Added more integ tests. --- .../tier-1/lysozyme_ENbias/README | 11 + .../tier-1/lysozyme_ENbias/aa.pdb | 1549 ++++++++++++++ .../tier-1/lysozyme_ENbias/map.map | 1275 +++++++++++ .../tier-1/lysozyme_ENbias/martinize2/cg.pdb | 616 ++++++ .../lysozyme_ENbias/martinize2/citation | 1 + .../tier-1/lysozyme_ENbias/martinize2/command | 12 + .../lysozyme_ENbias/martinize2/molecule_0.itp | 1901 +++++++++++++++++ .../lysozyme_ENbias/martinize2/topol.top | 12 + .../martinize2/virtual_sites_atomtypes.itp | 130 ++ .../virtual_sites_nonbond_params.itp | 46 + .../tier-1/lysozyme_GO/README | 2 +- .../tier-1/lysozyme_GObias/README | 11 + .../tier-1/lysozyme_GObias/aa.pdb | 1549 ++++++++++++++ .../tier-1/lysozyme_GObias/map.map | 1275 +++++++++++ .../tier-1/lysozyme_GObias/martinize2/cg.pdb | 616 ++++++ .../lysozyme_GObias/martinize2/citation | 1 + .../tier-1/lysozyme_GObias/martinize2/command | 11 + .../martinize2/go_atomtypes.itp | 130 ++ .../martinize2/go_nbparams.itp | 305 +++ .../lysozyme_GObias/martinize2/molecule_0.itp | 1669 +++++++++++++++ .../lysozyme_GObias/martinize2/topol.top | 12 + .../integration_tests/test_integration.py | 38 +- 22 files changed, 11155 insertions(+), 17 deletions(-) create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation create mode 100755 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation create mode 100755 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp create mode 100644 vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README new file mode 100644 index 00000000..2cbdea56 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README @@ -0,0 +1,11 @@ +### DETAILS: + +# Original PDB CODE: 3LZT +# Structure from X-ray crystallography experiment. +# Select atoms with occupancy higuer than 0.5 + +### TEST: + +# -ff martini 3001 +# -scfix, EN and BB-W bias +# adding specific cys bridge as CONECT records diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb new file mode 100644 index 00000000..39371e9a --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/aa.pdb @@ -0,0 +1,1549 @@ +HEADER HYDROLASE(O-GLYCOSYL) 10-JAN-92 1HEL +TITLE STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING MUTATIONS WITHIN +TITLE 2 THE CORE OF CHICKEN EGG WHITE LYSOZYME +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: HEN EGG WHITE LYSOZYME; +COMPND 3 CHAIN: A; +COMPND 4 EC: 3.2.1.17; +COMPND 5 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; +SOURCE 3 ORGANISM_COMMON: CHICKEN; +SOURCE 4 ORGANISM_TAXID: 9031; +SOURCE 5 ORGAN: EGG +KEYWDS HYDROLASE(O-GLYCOSYL) +EXPDTA X-RAY DIFFRACTION +AUTHOR K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +REVDAT 3 16-NOV-11 1HEL 1 VERSN HETATM +REVDAT 2 24-FEB-09 1HEL 1 VERSN +REVDAT 1 31-OCT-93 1HEL 0 +JRNL AUTH K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +JRNL TITL STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING +JRNL TITL 2 MUTATIONS WITHIN THE CORE OF CHICKEN EGG WHITE LYSOZYME. +JRNL REF J.BIOL.CHEM. V. 267 10842 1992 +JRNL REFN ISSN 0021-9258 +JRNL PMID 1587860 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH B.A.MALCOLM,K.P.WILSON,B.W.MATTHEWS,J.F.KIRSCH,A.C.WILSON +REMARK 1 TITL ANCESTRAL LYSOZYMES RECONSTRUCTED, NEUTRALITY TESTED, AND +REMARK 1 TITL 2 THERMOSTABILITY LINKED TO HYDROCARBON PACKING +REMARK 1 REF NATURE V. 344 86 1990 +REMARK 1 REFN ISSN 0028-0836 +REMARK 2 +REMARK 2 RESOLUTION. 1.70 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : TNT +REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL +REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL +REMARK 3 COMPLETENESS FOR RANGE (%) : NULL +REMARK 3 NUMBER OF REFLECTIONS : NULL +REMARK 3 +REMARK 3 USING DATA ABOVE SIGMA CUTOFF. +REMARK 3 CROSS-VALIDATION METHOD : NULL +REMARK 3 FREE R VALUE TEST SET SELECTION : NULL +REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 +REMARK 3 R VALUE (WORKING SET) : NULL +REMARK 3 FREE R VALUE : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT : NULL +REMARK 3 +REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. +REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL +REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE (NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL +REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL +REMARK 3 +REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. +REMARK 3 PROTEIN ATOMS : 1001 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 185 +REMARK 3 +REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL +REMARK 3 +REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT +REMARK 3 BOND LENGTHS (A) : 0.019 ; NULL ; NULL +REMARK 3 BOND ANGLES (DEGREES) : 2.400 ; NULL ; NULL +REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL +REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL +REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL +REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL +REMARK 3 +REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL +REMARK 3 +REMARK 3 BULK SOLVENT MODELING. +REMARK 3 METHOD USED : NULL +REMARK 3 KSOL : NULL +REMARK 3 BSOL : NULL +REMARK 3 +REMARK 3 RESTRAINT LIBRARIES. +REMARK 3 STEREOCHEMISTRY : NULL +REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 1HEL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : NULL +REMARK 200 TEMPERATURE (KELVIN) : NULL +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : NULL +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : NULL +REMARK 200 RADIATION SOURCE : NULL +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : NULL +REMARK 200 DETECTOR MANUFACTURER : NULL +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL +REMARK 200 RESOLUTION RANGE HIGH (A) : NULL +REMARK 200 RESOLUTION RANGE LOW (A) : NULL +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: NULL +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 40.52 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X,-Y,Z+1/2 +REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 +REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 +REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 +REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 +REMARK 290 7555 Y,X,-Z +REMARK 290 8555 -Y,-X,-Z+1/2 +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.95000 +REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.42500 +REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.47500 +REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.42500 +REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.47500 +REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.95000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 375 +REMARK 375 SPECIAL POSITION +REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS +REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL +REMARK 375 POSITIONS. +REMARK 375 +REMARK 375 ATOM RES CSSEQI +REMARK 375 HOH A 318 LIES ON A SPECIAL POSITION. +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC +REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 +REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A +REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 +REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE +REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. +REMARK 500 +REMARK 500 DISTANCE CUTOFF: +REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS +REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE +REMARK 500 O HOH A 275 O HOH A 275 8555 0.35 +REMARK 500 O HOH A 203 O HOH A 203 7556 1.38 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: COVALENT BOND ANGLES +REMARK 500 +REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES +REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE +REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) +REMARK 500 +REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 +REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 +REMARK 500 +REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 +REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES +REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 8.7 DEGREES +REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES +REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 52 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES +REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES +REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES +REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES +REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: TORSION ANGLES +REMARK 500 +REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: +REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) +REMARK 500 +REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- +REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 +REMARK 500 +REMARK 500 M RES CSSEQI PSI PHI +REMARK 500 ARG A 68 19.50 -141.12 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 525 +REMARK 525 SOLVENT +REMARK 525 +REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT +REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST +REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT +REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE +REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; +REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE +REMARK 525 NUMBER; I=INSERTION CODE): +REMARK 525 +REMARK 525 M RES CSSEQI +REMARK 525 HOH A 188 DISTANCE = 6.89 ANGSTROMS +REMARK 525 HOH A 189 DISTANCE = 6.32 ANGSTROMS +REMARK 525 HOH A 190 DISTANCE = 5.68 ANGSTROMS +REMARK 525 HOH A 228 DISTANCE = 6.51 ANGSTROMS +REMARK 525 HOH A 230 DISTANCE = 5.30 ANGSTROMS +REMARK 525 HOH A 243 DISTANCE = 5.19 ANGSTROMS +REMARK 525 HOH A 249 DISTANCE = 6.99 ANGSTROMS +REMARK 525 HOH A 258 DISTANCE = 6.92 ANGSTROMS +REMARK 525 HOH A 268 DISTANCE = 8.36 ANGSTROMS +REMARK 525 HOH A 278 DISTANCE = 6.81 ANGSTROMS +REMARK 525 HOH A 304 DISTANCE = 7.48 ANGSTROMS +REMARK 525 HOH A 305 DISTANCE = 6.21 ANGSTROMS +REMARK 525 HOH A 308 DISTANCE = 19.71 ANGSTROMS +DBREF 1HEL A 1 129 UNP P00698 LYSC_CHICK 19 147 +SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS +SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY +SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN +SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP +SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN +SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE +SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER +SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY +SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY +SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU +FORMUL 2 HOH *185(H2 O) +HELIX 1 H1 GLY A 4 GLY A 16 1 13 +HELIX 2 H2 LEU A 25 PHE A 34 1 10 +HELIX 3 H3 PRO A 79 LEU A 84 5 6 +HELIX 4 H4 ILE A 88 SER A 100 1 13 +HELIX 5 H5 GLY A 104 TRP A 108 5 5 +HELIX 6 H6 VAL A 109 ARG A 114 1 6 +HELIX 7 H7 VAL A 120 ILE A 124 5 5 +SHEET 1 S1 3 ALA A 42 ASN A 46 0 +SHEET 2 S1 3 GLY A 49 GLY A 54 -1 O SER A 50 N ASN A 46 +SHEET 3 S1 3 LEU A 56 SER A 60 -1 O SER A 60 N THR A 51 +SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.99 +SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.11 +SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.00 +SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.10 +CRYST1 79.100 79.100 37.900 90.00 90.00 90.00 P 43 21 2 8 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.012642 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.012642 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.026385 0.00000 +ATOM 1 N LYS A 1 3.294 10.164 10.266 1.00 11.18 N +ATOM 2 CA LYS A 1 2.388 10.533 9.168 1.00 9.68 C +ATOM 3 C LYS A 1 2.438 12.049 8.889 1.00 14.00 C +ATOM 4 O LYS A 1 2.406 12.898 9.815 1.00 14.00 O +ATOM 5 CB LYS A 1 0.949 10.101 9.559 1.00 13.29 C +ATOM 6 CG LYS A 1 -0.050 10.621 8.573 1.00 13.52 C +ATOM 7 CD LYS A 1 -1.425 10.081 8.720 1.00 22.15 C +ATOM 8 CE LYS A 1 -2.370 10.773 7.722 1.00 20.23 C +ATOM 9 NZ LYS A 1 -3.776 10.439 7.933 1.00 68.72 N +ATOM 10 N VAL A 2 2.552 12.428 7.626 1.00 10.17 N +ATOM 11 CA VAL A 2 2.524 13.840 7.282 1.00 10.02 C +ATOM 12 C VAL A 2 1.120 14.180 6.770 1.00 27.84 C +ATOM 13 O VAL A 2 0.737 13.798 5.675 1.00 22.87 O +ATOM 14 CB VAL A 2 3.529 14.264 6.240 1.00 9.00 C +ATOM 15 CG1 VAL A 2 3.313 15.765 5.983 1.00 11.37 C +ATOM 16 CG2 VAL A 2 4.928 14.016 6.810 1.00 10.57 C +ATOM 17 N PHE A 3 0.333 14.851 7.573 1.00 16.35 N +ATOM 18 CA PHE A 3 -1.021 15.173 7.169 1.00 15.34 C +ATOM 19 C PHE A 3 -1.097 16.285 6.126 1.00 14.79 C +ATOM 20 O PHE A 3 -0.261 17.203 6.054 1.00 14.99 O +ATOM 21 CB PHE A 3 -1.867 15.710 8.361 1.00 14.03 C +ATOM 22 CG PHE A 3 -2.412 14.638 9.295 1.00 16.41 C +ATOM 23 CD1 PHE A 3 -1.575 14.049 10.240 1.00 14.44 C +ATOM 24 CD2 PHE A 3 -3.757 14.285 9.274 1.00 18.12 C +ATOM 25 CE1 PHE A 3 -2.065 13.116 11.135 1.00 11.11 C +ATOM 26 CE2 PHE A 3 -4.263 13.332 10.178 1.00 32.24 C +ATOM 27 CZ PHE A 3 -3.413 12.758 11.132 1.00 14.31 C +ATOM 28 N GLY A 4 -2.229 16.228 5.393 1.00 15.47 N +ATOM 29 CA GLY A 4 -2.645 17.273 4.511 1.00 13.97 C +ATOM 30 C GLY A 4 -3.456 18.261 5.350 1.00 10.95 C +ATOM 31 O GLY A 4 -4.070 17.876 6.282 1.00 16.45 O +ATOM 32 N ARG A 5 -3.414 19.518 5.009 1.00 14.28 N +ATOM 33 CA ARG A 5 -4.106 20.560 5.674 1.00 11.63 C +ATOM 34 C ARG A 5 -5.540 20.226 5.992 1.00 21.37 C +ATOM 35 O ARG A 5 -5.963 20.258 7.138 1.00 9.74 O +ATOM 36 CB ARG A 5 -3.952 21.857 4.900 1.00 13.31 C +ATOM 37 CG ARG A 5 -4.508 23.053 5.610 1.00 13.02 C +ATOM 38 CD ARG A 5 -4.414 24.335 4.775 1.00 19.72 C +ATOM 39 NE ARG A 5 -5.013 24.223 3.447 1.00 23.52 N +ATOM 40 CZ ARG A 5 -6.287 24.522 3.048 1.00 40.17 C +ATOM 41 NH1 ARG A 5 -7.248 25.009 3.841 1.00 17.54 N +ATOM 42 NH2 ARG A 5 -6.619 24.303 1.767 1.00 33.21 N +ATOM 43 N CYS A 6 -6.327 19.866 4.967 1.00 15.04 N +ATOM 44 CA CYS A 6 -7.767 19.572 5.189 1.00 12.93 C +ATOM 45 C CYS A 6 -7.997 18.269 5.916 1.00 5.10 C +ATOM 46 O CYS A 6 -8.992 18.125 6.630 1.00 13.60 O +ATOM 47 CB CYS A 6 -8.607 19.637 3.859 1.00 16.72 C +ATOM 48 SG CYS A 6 -8.669 21.273 3.104 1.00 16.68 S +ATOM 49 N GLU A 7 -7.142 17.274 5.653 1.00 7.34 N +ATOM 50 CA GLU A 7 -7.309 15.981 6.323 1.00 10.86 C +ATOM 51 C GLU A 7 -7.129 16.181 7.848 1.00 17.71 C +ATOM 52 O GLU A 7 -7.835 15.638 8.657 1.00 14.19 O +ATOM 53 CB GLU A 7 -6.187 15.048 5.880 1.00 16.19 C +ATOM 54 CG GLU A 7 -6.206 13.614 6.496 1.00 16.67 C +ATOM 55 CD GLU A 7 -4.952 12.864 6.030 1.00 32.91 C +ATOM 56 OE1 GLU A 7 -4.003 13.411 5.480 1.00 18.18 O +ATOM 57 OE2 GLU A 7 -4.992 11.578 6.219 1.00 28.07 O +ATOM 58 N LEU A 8 -6.148 16.987 8.221 1.00 14.04 N +ATOM 59 CA LEU A 8 -5.919 17.285 9.637 1.00 8.65 C +ATOM 60 C LEU A 8 -7.068 18.103 10.254 1.00 10.08 C +ATOM 61 O LEU A 8 -7.500 17.827 11.353 1.00 15.66 O +ATOM 62 CB LEU A 8 -4.607 18.084 9.809 1.00 14.88 C +ATOM 63 CG LEU A 8 -4.384 18.432 11.299 1.00 12.61 C +ATOM 64 CD1 LEU A 8 -4.110 17.104 12.053 1.00 12.51 C +ATOM 65 CD2 LEU A 8 -3.147 19.299 11.372 1.00 13.98 C +ATOM 66 N ALA A 9 -7.524 19.122 9.561 1.00 11.92 N +ATOM 67 CA ALA A 9 -8.664 19.896 9.982 1.00 10.97 C +ATOM 68 C ALA A 9 -9.841 18.971 10.304 1.00 15.73 C +ATOM 69 O ALA A 9 -10.469 19.046 11.359 1.00 13.41 O +ATOM 70 CB ALA A 9 -9.039 21.012 8.954 1.00 8.88 C +ATOM 71 N ALA A 10 -10.124 18.049 9.425 1.00 12.11 N +ATOM 72 CA ALA A 10 -11.262 17.129 9.595 1.00 12.19 C +ATOM 73 C ALA A 10 -11.034 16.206 10.780 1.00 18.02 C +ATOM 74 O ALA A 10 -11.932 15.902 11.522 1.00 17.70 O +ATOM 75 CB ALA A 10 -11.457 16.297 8.313 1.00 14.75 C +ATOM 76 N ALA A 11 -9.815 15.771 10.988 1.00 14.94 N +ATOM 77 CA ALA A 11 -9.544 14.908 12.136 1.00 12.19 C +ATOM 78 C ALA A 11 -9.651 15.641 13.494 1.00 7.51 C +ATOM 79 O ALA A 11 -10.088 15.066 14.457 1.00 12.99 O +ATOM 80 CB ALA A 11 -8.153 14.250 12.041 1.00 15.76 C +ATOM 81 N MET A 12 -9.107 16.884 13.529 1.00 10.71 N +ATOM 82 CA MET A 12 -9.160 17.683 14.710 1.00 12.27 C +ATOM 83 C MET A 12 -10.599 17.988 15.028 1.00 16.76 C +ATOM 84 O MET A 12 -10.964 17.966 16.195 1.00 17.43 O +ATOM 85 CB MET A 12 -8.385 18.996 14.563 1.00 6.96 C +ATOM 86 CG MET A 12 -6.872 18.717 14.593 1.00 7.53 C +ATOM 87 SD MET A 12 -5.971 20.286 14.351 1.00 16.25 S +ATOM 88 CE MET A 12 -4.392 19.972 15.137 1.00 11.48 C +ATOM 89 N LYS A 13 -11.421 18.239 13.985 1.00 11.66 N +ATOM 90 CA LYS A 13 -12.844 18.554 14.146 1.00 12.77 C +ATOM 91 C LYS A 13 -13.552 17.402 14.762 1.00 17.21 C +ATOM 92 O LYS A 13 -14.278 17.533 15.704 1.00 15.75 O +ATOM 93 CB LYS A 13 -13.505 18.908 12.852 1.00 14.38 C +ATOM 94 CG LYS A 13 -14.874 19.457 13.096 1.00 16.88 C +ATOM 95 CD LYS A 13 -15.519 20.062 11.867 1.00 19.73 C +ATOM 96 CE LYS A 13 -17.062 20.060 11.971 1.00 41.06 C +ATOM 97 NZ LYS A 13 -17.725 20.836 10.899 1.00 61.80 N +ATOM 98 N ARG A 14 -13.273 16.240 14.220 1.00 21.68 N +ATOM 99 CA ARG A 14 -13.878 15.021 14.667 1.00 17.17 C +ATOM 100 C ARG A 14 -13.480 14.746 16.099 1.00 27.88 C +ATOM 101 O ARG A 14 -14.217 14.129 16.823 1.00 17.70 O +ATOM 102 CB ARG A 14 -13.448 13.876 13.756 1.00 23.48 C +ATOM 103 CG ARG A 14 -14.102 12.553 14.162 1.00 51.76 C +ATOM 104 CD ARG A 14 -13.875 11.424 13.160 1.00 52.15 C +ATOM 105 NE ARG A 14 -12.616 10.730 13.354 1.00 61.79 N +ATOM 106 CZ ARG A 14 -12.406 9.681 14.156 1.00 47.00 C +ATOM 107 NH1 ARG A 14 -13.357 9.121 14.898 1.00 35.04 N +ATOM 108 NH2 ARG A 14 -11.177 9.169 14.196 1.00 55.70 N +ATOM 109 N HIS A 15 -12.300 15.219 16.498 1.00 20.13 N +ATOM 110 CA HIS A 15 -11.791 15.016 17.846 1.00 14.58 C +ATOM 111 C HIS A 15 -12.221 16.074 18.888 1.00 18.83 C +ATOM 112 O HIS A 15 -11.689 16.060 19.970 1.00 22.76 O +ATOM 113 CB HIS A 15 -10.268 14.799 17.851 1.00 23.09 C +ATOM 114 CG HIS A 15 -9.906 13.364 17.563 1.00 21.53 C +ATOM 115 ND1 HIS A 15 -9.721 12.896 16.256 1.00 28.28 N +ATOM 116 CD2 HIS A 15 -9.723 12.308 18.413 1.00 30.99 C +ATOM 117 CE1 HIS A 15 -9.422 11.580 16.350 1.00 20.50 C +ATOM 118 NE2 HIS A 15 -9.412 11.213 17.627 1.00 42.34 N +ATOM 119 N GLY A 16 -13.146 16.952 18.551 1.00 14.90 N +ATOM 120 CA GLY A 16 -13.687 17.956 19.401 1.00 16.84 C +ATOM 121 C GLY A 16 -12.871 19.227 19.554 1.00 23.06 C +ATOM 122 O GLY A 16 -13.121 20.016 20.460 1.00 19.24 O +ATOM 123 N LEU A 17 -11.922 19.491 18.685 1.00 14.25 N +ATOM 124 CA LEU A 17 -11.134 20.695 18.826 1.00 10.83 C +ATOM 125 C LEU A 17 -11.728 21.961 18.295 1.00 16.61 C +ATOM 126 O LEU A 17 -11.276 23.016 18.657 1.00 18.63 O +ATOM 127 CB LEU A 17 -9.749 20.538 18.218 1.00 14.80 C +ATOM 128 CG LEU A 17 -8.792 19.745 19.031 1.00 19.84 C +ATOM 129 CD1 LEU A 17 -7.483 19.876 18.293 1.00 22.16 C +ATOM 130 CD2 LEU A 17 -8.675 20.282 20.474 1.00 15.82 C +ATOM 131 N ASP A 18 -12.704 21.930 17.405 1.00 18.32 N +ATOM 132 CA ASP A 18 -13.261 23.178 16.884 1.00 18.68 C +ATOM 133 C ASP A 18 -13.986 23.912 17.979 1.00 19.05 C +ATOM 134 O ASP A 18 -14.952 23.375 18.512 1.00 21.74 O +ATOM 135 CB ASP A 18 -14.275 23.002 15.717 1.00 25.90 C +ATOM 136 CG ASP A 18 -14.712 24.288 15.010 1.00 37.66 C +ATOM 137 OD1 ASP A 18 -14.134 25.393 15.038 1.00 26.98 O +ATOM 138 OD2 ASP A 18 -15.751 24.055 14.248 1.00 63.41 O +ATOM 139 N ASN A 19 -13.542 25.130 18.229 1.00 12.22 N +ATOM 140 CA ASN A 19 -14.046 26.010 19.253 1.00 9.99 C +ATOM 141 C ASN A 19 -13.851 25.507 20.671 1.00 15.97 C +ATOM 142 O ASN A 19 -14.534 25.975 21.595 1.00 18.10 O +ATOM 143 CB ASN A 19 -15.518 26.259 19.032 1.00 20.32 C +ATOM 144 CG ASN A 19 -15.706 27.052 17.774 1.00 40.03 C +ATOM 145 OD1 ASN A 19 -15.227 28.183 17.693 1.00 57.25 O +ATOM 146 ND2 ASN A 19 -16.402 26.456 16.811 1.00 40.09 N +ATOM 147 N TYR A 20 -12.956 24.552 20.827 1.00 12.49 N +ATOM 148 CA TYR A 20 -12.652 24.027 22.106 1.00 8.91 C +ATOM 149 C TYR A 20 -12.037 25.159 22.929 1.00 19.06 C +ATOM 150 O TYR A 20 -10.978 25.687 22.602 1.00 16.99 O +ATOM 151 CB TYR A 20 -11.717 22.810 22.005 1.00 17.23 C +ATOM 152 CG TYR A 20 -11.532 22.151 23.355 1.00 13.76 C +ATOM 153 CD1 TYR A 20 -12.444 21.206 23.832 1.00 17.40 C +ATOM 154 CD2 TYR A 20 -10.475 22.556 24.184 1.00 24.53 C +ATOM 155 CE1 TYR A 20 -12.311 20.657 25.111 1.00 20.84 C +ATOM 156 CE2 TYR A 20 -10.331 22.023 25.461 1.00 16.26 C +ATOM 157 CZ TYR A 20 -11.259 21.078 25.922 1.00 35.41 C +ATOM 158 OH TYR A 20 -11.104 20.560 27.183 1.00 29.68 O +ATOM 159 N ARG A 21 -12.721 25.593 23.977 1.00 19.00 N +ATOM 160 CA ARG A 21 -12.250 26.715 24.791 1.00 15.05 C +ATOM 161 C ARG A 21 -12.264 27.987 24.017 1.00 8.63 C +ATOM 162 O ARG A 21 -11.450 28.877 24.295 1.00 13.69 O +ATOM 163 CB ARG A 21 -10.847 26.601 25.387 1.00 18.33 C +ATOM 164 CG ARG A 21 -10.694 25.514 26.442 1.00 27.37 C +ATOM 165 CD ARG A 21 -11.577 25.864 27.598 1.00 40.81 C +ATOM 166 NE ARG A 21 -11.597 24.902 28.676 1.00 57.85 N +ATOM 167 CZ ARG A 21 -11.253 25.330 29.884 1.00 97.15 C +ATOM 168 NH1 ARG A 21 -10.859 26.593 30.049 1.00 63.15 N +ATOM 169 NH2 ARG A 21 -11.283 24.508 30.937 1.00 68.08 N +ATOM 170 N GLY A 22 -13.173 28.076 23.045 1.00 11.97 N +ATOM 171 CA GLY A 22 -13.290 29.312 22.253 1.00 13.56 C +ATOM 172 C GLY A 22 -12.276 29.499 21.125 1.00 15.57 C +ATOM 173 O GLY A 22 -12.274 30.537 20.508 1.00 15.13 O +ATOM 174 N TYR A 23 -11.414 28.511 20.863 1.00 17.25 N +ATOM 175 CA TYR A 23 -10.419 28.584 19.787 1.00 12.17 C +ATOM 176 C TYR A 23 -10.964 27.832 18.564 1.00 7.69 C +ATOM 177 O TYR A 23 -11.097 26.573 18.581 1.00 8.57 O +ATOM 178 CB TYR A 23 -9.059 27.910 20.217 1.00 11.16 C +ATOM 179 CG TYR A 23 -8.358 28.702 21.299 1.00 14.01 C +ATOM 180 CD1 TYR A 23 -7.560 29.766 20.910 1.00 10.23 C +ATOM 181 CD2 TYR A 23 -8.534 28.427 22.652 1.00 6.77 C +ATOM 182 CE1 TYR A 23 -6.879 30.557 21.846 1.00 9.23 C +ATOM 183 CE2 TYR A 23 -7.907 29.219 23.612 1.00 10.96 C +ATOM 184 CZ TYR A 23 -7.061 30.276 23.207 1.00 12.99 C +ATOM 185 OH TYR A 23 -6.411 31.069 24.111 1.00 13.78 O +ATOM 186 N SER A 24 -11.219 28.590 17.517 1.00 12.88 N +ATOM 187 CA SER A 24 -11.730 28.032 16.253 1.00 14.99 C +ATOM 188 C SER A 24 -10.726 27.075 15.616 1.00 20.42 C +ATOM 189 O SER A 24 -9.487 27.191 15.841 1.00 9.73 O +ATOM 190 CB SER A 24 -12.060 29.179 15.305 1.00 9.90 C +ATOM 191 OG SER A 24 -10.830 29.750 14.853 1.00 17.68 O +ATOM 192 N LEU A 25 -11.267 26.110 14.822 1.00 16.10 N +ATOM 193 CA LEU A 25 -10.460 25.111 14.092 1.00 11.40 C +ATOM 194 C LEU A 25 -9.205 25.683 13.438 1.00 11.44 C +ATOM 195 O LEU A 25 -8.145 25.073 13.536 1.00 10.56 O +ATOM 196 CB LEU A 25 -11.293 24.412 12.993 1.00 13.62 C +ATOM 197 CG LEU A 25 -10.826 23.089 12.491 1.00 16.00 C +ATOM 198 CD1 LEU A 25 -10.359 22.212 13.644 1.00 15.17 C +ATOM 199 CD2 LEU A 25 -12.018 22.437 11.805 1.00 15.75 C +ATOM 200 N GLY A 26 -9.311 26.836 12.758 1.00 10.18 N +ATOM 201 CA GLY A 26 -8.169 27.388 12.084 1.00 7.13 C +ATOM 202 C GLY A 26 -6.984 27.643 12.997 1.00 9.12 C +ATOM 203 O GLY A 26 -5.854 27.610 12.555 1.00 12.61 O +ATOM 204 N ASN A 27 -7.232 27.928 14.280 1.00 10.01 N +ATOM 205 CA ASN A 27 -6.132 28.159 15.255 1.00 10.13 C +ATOM 206 C ASN A 27 -5.317 26.889 15.464 1.00 2.57 C +ATOM 207 O ASN A 27 -4.057 26.899 15.477 1.00 7.08 O +ATOM 208 CB ASN A 27 -6.688 28.636 16.631 1.00 9.13 C +ATOM 209 CG ASN A 27 -7.131 30.092 16.624 1.00 4.84 C +ATOM 210 OD1 ASN A 27 -6.292 30.979 16.582 1.00 9.37 O +ATOM 211 ND2 ASN A 27 -8.466 30.324 16.587 1.00 8.00 N +ATOM 212 N TRP A 28 -6.033 25.791 15.639 1.00 5.40 N +ATOM 213 CA TRP A 28 -5.402 24.497 15.879 1.00 5.45 C +ATOM 214 C TRP A 28 -4.584 24.047 14.657 1.00 6.38 C +ATOM 215 O TRP A 28 -3.510 23.501 14.767 1.00 7.31 O +ATOM 216 CB TRP A 28 -6.482 23.490 16.237 1.00 7.31 C +ATOM 217 CG TRP A 28 -7.149 23.849 17.539 1.00 7.66 C +ATOM 218 CD1 TRP A 28 -8.351 24.415 17.748 1.00 11.80 C +ATOM 219 CD2 TRP A 28 -6.540 23.691 18.841 1.00 9.47 C +ATOM 220 NE1 TRP A 28 -8.575 24.567 19.117 1.00 11.48 N +ATOM 221 CE2 TRP A 28 -7.475 24.139 19.807 1.00 9.56 C +ATOM 222 CE3 TRP A 28 -5.321 23.121 19.249 1.00 10.24 C +ATOM 223 CZ2 TRP A 28 -7.187 24.066 21.210 1.00 11.03 C +ATOM 224 CZ3 TRP A 28 -5.059 23.060 20.609 1.00 20.66 C +ATOM 225 CH2 TRP A 28 -5.985 23.551 21.560 1.00 9.06 C +ATOM 226 N VAL A 29 -5.166 24.262 13.469 1.00 3.89 N +ATOM 227 CA VAL A 29 -4.458 23.870 12.217 1.00 5.65 C +ATOM 228 C VAL A 29 -3.242 24.746 11.972 1.00 2.99 C +ATOM 229 O VAL A 29 -2.170 24.273 11.571 1.00 7.90 O +ATOM 230 CB VAL A 29 -5.456 23.881 11.020 1.00 7.66 C +ATOM 231 CG1 VAL A 29 -4.630 23.646 9.743 1.00 13.23 C +ATOM 232 CG2 VAL A 29 -6.516 22.751 11.149 1.00 6.73 C +ATOM 233 N CYS A 30 -3.372 26.060 12.262 1.00 2.63 N +ATOM 234 CA CYS A 30 -2.281 26.976 12.125 1.00 7.05 C +ATOM 235 C CYS A 30 -1.151 26.582 13.072 1.00 10.47 C +ATOM 236 O CYS A 30 0.054 26.552 12.766 1.00 4.93 O +ATOM 237 CB CYS A 30 -2.756 28.428 12.303 1.00 2.61 C +ATOM 238 SG CYS A 30 -1.467 29.667 12.134 1.00 10.20 S +ATOM 239 N ALA A 31 -1.521 26.283 14.306 1.00 9.82 N +ATOM 240 CA ALA A 31 -0.491 25.884 15.276 1.00 15.61 C +ATOM 241 C ALA A 31 0.235 24.607 14.849 1.00 5.07 C +ATOM 242 O ALA A 31 1.464 24.554 14.987 1.00 9.27 O +ATOM 243 CB ALA A 31 -1.089 25.781 16.704 1.00 7.85 C +ATOM 244 N ALA A 32 -0.483 23.609 14.315 1.00 7.79 N +ATOM 245 CA ALA A 32 0.162 22.357 13.855 1.00 8.61 C +ATOM 246 C ALA A 32 1.085 22.594 12.673 1.00 7.90 C +ATOM 247 O ALA A 32 2.197 22.050 12.585 1.00 9.35 O +ATOM 248 CB ALA A 32 -0.823 21.268 13.540 1.00 10.83 C +ATOM 249 N LYS A 33 0.653 23.463 11.786 1.00 7.35 N +ATOM 250 CA LYS A 33 1.542 23.795 10.635 1.00 6.50 C +ATOM 251 C LYS A 33 2.867 24.333 11.097 1.00 6.89 C +ATOM 252 O LYS A 33 3.936 23.889 10.727 1.00 10.45 O +ATOM 253 CB LYS A 33 0.863 24.886 9.776 1.00 10.32 C +ATOM 254 CG LYS A 33 1.793 25.437 8.676 1.00 13.52 C +ATOM 255 CD LYS A 33 1.927 24.485 7.491 1.00 19.87 C +ATOM 256 CE LYS A 33 3.138 24.764 6.621 1.00 27.04 C +ATOM 257 NZ LYS A 33 3.217 23.793 5.511 1.00 45.44 N +ATOM 258 N PHE A 34 2.807 25.345 11.961 1.00 9.24 N +ATOM 259 CA PHE A 34 4.029 25.958 12.436 1.00 8.96 C +ATOM 260 C PHE A 34 4.846 25.192 13.455 1.00 16.48 C +ATOM 261 O PHE A 34 6.039 25.360 13.540 1.00 14.96 O +ATOM 262 CB PHE A 34 3.856 27.469 12.721 1.00 9.21 C +ATOM 263 CG PHE A 34 3.417 28.201 11.426 1.00 11.78 C +ATOM 264 CD1 PHE A 34 4.231 28.189 10.282 1.00 11.49 C +ATOM 265 CD2 PHE A 34 2.212 28.933 11.385 1.00 12.86 C +ATOM 266 CE1 PHE A 34 3.830 28.854 9.136 1.00 12.74 C +ATOM 267 CE2 PHE A 34 1.803 29.618 10.224 1.00 13.38 C +ATOM 268 CZ PHE A 34 2.627 29.554 9.090 1.00 13.39 C +ATOM 269 N GLU A 35 4.201 24.324 14.225 1.00 9.90 N +ATOM 270 CA GLU A 35 4.889 23.543 15.263 1.00 11.92 C +ATOM 271 C GLU A 35 5.641 22.352 14.706 1.00 13.79 C +ATOM 272 O GLU A 35 6.781 22.129 15.054 1.00 8.23 O +ATOM 273 CB GLU A 35 3.839 23.026 16.259 1.00 6.00 C +ATOM 274 CG GLU A 35 3.409 24.107 17.322 1.00 11.89 C +ATOM 275 CD GLU A 35 4.516 24.690 18.200 1.00 12.03 C +ATOM 276 OE1 GLU A 35 5.640 24.296 18.226 1.00 12.97 O +ATOM 277 OE2 GLU A 35 4.167 25.730 18.876 1.00 13.03 O +ATOM 278 N SER A 36 4.983 21.591 13.819 1.00 8.49 N +ATOM 279 CA SER A 36 5.541 20.369 13.283 1.00 8.82 C +ATOM 280 C SER A 36 5.483 20.189 11.756 1.00 10.13 C +ATOM 281 O SER A 36 5.800 19.070 11.251 1.00 14.88 O +ATOM 282 CB SER A 36 4.684 19.256 13.831 1.00 7.77 C +ATOM 283 OG SER A 36 3.330 19.336 13.297 1.00 8.30 O +ATOM 284 N ASN A 37 4.975 21.223 11.050 1.00 11.55 N +ATOM 285 CA ASN A 37 4.752 21.103 9.605 1.00 8.89 C +ATOM 286 C ASN A 37 3.825 19.918 9.321 1.00 14.33 C +ATOM 287 O ASN A 37 3.972 19.215 8.320 1.00 14.19 O +ATOM 288 CB ASN A 37 6.061 21.002 8.788 1.00 20.93 C +ATOM 289 CG ASN A 37 5.851 21.458 7.334 1.00 25.83 C +ATOM 290 OD1 ASN A 37 5.061 22.365 7.057 1.00 26.84 O +ATOM 291 ND2 ASN A 37 6.474 20.759 6.397 1.00 52.87 N +ATOM 292 N PHE A 38 2.864 19.696 10.220 1.00 7.19 N +ATOM 293 CA PHE A 38 1.862 18.625 10.075 1.00 11.76 C +ATOM 294 C PHE A 38 2.411 17.214 10.168 1.00 10.63 C +ATOM 295 O PHE A 38 1.747 16.276 9.742 1.00 9.49 O +ATOM 296 CB PHE A 38 1.092 18.696 8.696 1.00 8.56 C +ATOM 297 CG PHE A 38 0.280 19.956 8.505 1.00 13.59 C +ATOM 298 CD1 PHE A 38 -0.367 20.558 9.597 1.00 8.45 C +ATOM 299 CD2 PHE A 38 0.112 20.532 7.255 1.00 17.61 C +ATOM 300 CE1 PHE A 38 -1.146 21.685 9.432 1.00 11.53 C +ATOM 301 CE2 PHE A 38 -0.664 21.687 7.081 1.00 17.65 C +ATOM 302 CZ PHE A 38 -1.316 22.268 8.162 1.00 13.17 C +ATOM 303 N ASN A 39 3.667 17.073 10.600 1.00 8.40 N +ATOM 304 CA ASN A 39 4.271 15.737 10.699 1.00 6.01 C +ATOM 305 C ASN A 39 4.101 15.211 12.158 1.00 6.81 C +ATOM 306 O ASN A 39 4.597 15.858 13.147 1.00 11.41 O +ATOM 307 CB ASN A 39 5.776 15.925 10.373 1.00 6.39 C +ATOM 308 CG ASN A 39 6.552 14.636 10.450 1.00 6.34 C +ATOM 309 OD1 ASN A 39 5.992 13.541 10.684 1.00 10.75 O +ATOM 310 ND2 ASN A 39 7.832 14.764 10.100 1.00 13.88 N +ATOM 311 N THR A 40 3.430 14.054 12.314 1.00 8.05 N +ATOM 312 CA THR A 40 3.222 13.509 13.676 1.00 10.13 C +ATOM 313 C THR A 40 4.525 13.041 14.358 1.00 8.64 C +ATOM 314 O THR A 40 4.546 12.831 15.542 1.00 12.11 O +ATOM 315 CB THR A 40 2.279 12.302 13.663 1.00 12.49 C +ATOM 316 OG1 THR A 40 2.862 11.250 12.880 1.00 10.89 O +ATOM 317 CG2 THR A 40 0.843 12.666 13.219 1.00 9.90 C +ATOM 318 N GLN A 41 5.594 12.819 13.559 1.00 6.61 N +ATOM 319 CA GLN A 41 6.860 12.308 14.019 1.00 3.67 C +ATOM 320 C GLN A 41 7.861 13.372 14.433 1.00 4.66 C +ATOM 321 O GLN A 41 8.986 13.051 14.864 1.00 8.80 O +ATOM 322 CB GLN A 41 7.463 11.344 12.979 1.00 9.30 C +ATOM 323 CG GLN A 41 6.598 10.100 12.797 1.00 12.21 C +ATOM 324 CD GLN A 41 7.402 8.999 12.104 1.00 22.47 C +ATOM 325 OE1 GLN A 41 8.254 8.393 12.763 1.00 16.54 O +ATOM 326 NE2 GLN A 41 7.257 8.847 10.744 1.00 13.11 N +ATOM 327 N ALA A 42 7.460 14.657 14.305 1.00 6.51 N +ATOM 328 CA ALA A 42 8.376 15.748 14.672 1.00 8.14 C +ATOM 329 C ALA A 42 8.824 15.710 16.237 1.00 11.70 C +ATOM 330 O ALA A 42 8.005 15.547 17.165 1.00 5.54 O +ATOM 331 CB ALA A 42 7.744 17.108 14.349 1.00 8.97 C +ATOM 332 N THR A 43 10.132 15.865 16.445 1.00 7.08 N +ATOM 333 CA THR A 43 10.705 15.992 17.773 1.00 10.42 C +ATOM 334 C THR A 43 11.694 17.112 17.692 1.00 11.09 C +ATOM 335 O THR A 43 12.280 17.411 16.646 1.00 12.80 O +ATOM 336 CB THR A 43 11.362 14.748 18.354 1.00 13.93 C +ATOM 337 OG1 THR A 43 12.360 14.429 17.435 1.00 11.09 O +ATOM 338 CG2 THR A 43 10.420 13.567 18.530 1.00 7.58 C +ATOM 339 N ASN A 44 11.894 17.801 18.808 1.00 10.77 N +ATOM 340 CA ASN A 44 12.828 18.909 18.863 1.00 6.02 C +ATOM 341 C ASN A 44 13.258 19.036 20.281 1.00 16.51 C +ATOM 342 O ASN A 44 12.426 19.127 21.185 1.00 11.61 O +ATOM 343 CB ASN A 44 12.171 20.225 18.473 1.00 13.37 C +ATOM 344 CG ASN A 44 11.932 20.272 16.966 1.00 55.95 C +ATOM 345 OD1 ASN A 44 12.883 20.299 16.146 1.00 30.16 O +ATOM 346 ND2 ASN A 44 10.659 20.233 16.594 1.00 20.67 N +ATOM 347 N ARG A 45 14.545 19.035 20.479 1.00 13.41 N +ATOM 348 CA ARG A 45 15.061 19.112 21.827 1.00 12.01 C +ATOM 349 C ARG A 45 15.250 20.555 22.252 1.00 20.93 C +ATOM 350 O ARG A 45 15.601 21.418 21.435 1.00 20.22 O +ATOM 351 CB ARG A 45 16.408 18.438 21.953 1.00 19.70 C +ATOM 352 CG ARG A 45 16.935 18.714 23.338 1.00 35.82 C +ATOM 353 CD ARG A 45 16.730 17.468 24.141 1.00 27.63 C +ATOM 354 NE ARG A 45 17.249 16.408 23.330 1.00 67.37 N +ATOM 355 CZ ARG A 45 18.249 15.588 23.641 1.00 91.84 C +ATOM 356 NH1 ARG A 45 18.868 15.589 24.830 1.00 36.08 N +ATOM 357 NH2 ARG A 45 18.624 14.698 22.716 1.00 64.26 N +ATOM 358 N ASN A 46 15.056 20.796 23.543 1.00 12.63 N +ATOM 359 CA ASN A 46 15.247 22.135 24.062 1.00 12.92 C +ATOM 360 C ASN A 46 16.508 22.245 24.900 1.00 8.11 C +ATOM 361 O ASN A 46 17.149 21.253 25.274 1.00 15.77 O +ATOM 362 CB ASN A 46 13.989 22.699 24.735 1.00 11.70 C +ATOM 363 CG ASN A 46 12.659 22.418 24.007 1.00 21.14 C +ATOM 364 OD1 ASN A 46 11.762 21.669 24.459 1.00 23.29 O +ATOM 365 ND2 ASN A 46 12.508 23.062 22.886 1.00 24.99 N +ATOM 366 N THR A 47 16.906 23.489 25.146 1.00 23.92 N +ATOM 367 CA THR A 47 18.108 23.768 25.931 1.00 39.90 C +ATOM 368 C THR A 47 17.996 23.269 27.358 1.00 25.44 C +ATOM 369 O THR A 47 18.958 22.798 27.923 1.00 34.24 O +ATOM 370 CB THR A 47 18.506 25.250 25.905 1.00 47.42 C +ATOM 371 OG1 THR A 47 17.376 26.053 26.142 1.00 38.53 O +ATOM 372 CG2 THR A 47 19.115 25.572 24.552 1.00 58.08 C +ATOM 373 N ASP A 48 16.797 23.339 27.935 1.00 20.62 N +ATOM 374 CA ASP A 48 16.626 22.832 29.261 1.00 9.90 C +ATOM 375 C ASP A 48 16.700 21.306 29.306 1.00 19.23 C +ATOM 376 O ASP A 48 16.586 20.723 30.361 1.00 22.36 O +ATOM 377 CB ASP A 48 15.349 23.377 29.887 1.00 14.78 C +ATOM 378 CG ASP A 48 14.119 22.821 29.267 1.00 19.04 C +ATOM 379 OD1 ASP A 48 14.160 21.981 28.422 1.00 28.31 O +ATOM 380 OD2 ASP A 48 13.002 23.315 29.717 1.00 28.61 O +ATOM 381 N GLY A 49 16.883 20.637 28.166 1.00 17.28 N +ATOM 382 CA GLY A 49 16.950 19.205 28.182 1.00 10.24 C +ATOM 383 C GLY A 49 15.608 18.534 27.977 1.00 14.24 C +ATOM 384 O GLY A 49 15.499 17.291 27.852 1.00 13.58 O +ATOM 385 N SER A 50 14.564 19.331 27.973 1.00 9.07 N +ATOM 386 CA SER A 50 13.311 18.716 27.712 1.00 7.32 C +ATOM 387 C SER A 50 13.217 18.531 26.131 1.00 11.52 C +ATOM 388 O SER A 50 14.085 19.016 25.374 1.00 13.96 O +ATOM 389 CB SER A 50 12.113 19.490 28.182 1.00 4.67 C +ATOM 390 OG SER A 50 12.074 20.716 27.461 1.00 9.76 O +ATOM 391 N THR A 51 12.150 17.857 25.646 1.00 11.43 N +ATOM 392 CA THR A 51 11.958 17.610 24.179 1.00 9.12 C +ATOM 393 C THR A 51 10.485 17.806 23.917 1.00 16.87 C +ATOM 394 O THR A 51 9.677 17.499 24.825 1.00 8.33 O +ATOM 395 CB THR A 51 12.363 16.177 23.757 1.00 5.49 C +ATOM 396 OG1 THR A 51 13.711 15.986 24.120 1.00 6.88 O +ATOM 397 CG2 THR A 51 12.234 15.930 22.227 1.00 7.94 C +ATOM 398 N ASP A 52 10.158 18.354 22.701 1.00 9.46 N +ATOM 399 CA ASP A 52 8.767 18.608 22.181 1.00 5.88 C +ATOM 400 C ASP A 52 8.451 17.463 21.198 1.00 5.87 C +ATOM 401 O ASP A 52 9.311 17.033 20.476 1.00 5.53 O +ATOM 402 CB ASP A 52 8.717 19.972 21.485 1.00 6.73 C +ATOM 403 CG ASP A 52 9.014 21.046 22.449 1.00 17.46 C +ATOM 404 OD1 ASP A 52 8.778 20.978 23.593 1.00 16.69 O +ATOM 405 OD2 ASP A 52 9.531 22.065 21.923 1.00 28.92 O +ATOM 406 N TYR A 53 7.279 16.908 21.280 1.00 7.33 N +ATOM 407 CA TYR A 53 6.899 15.745 20.548 1.00 9.37 C +ATOM 408 C TYR A 53 5.580 15.922 19.790 1.00 13.52 C +ATOM 409 O TYR A 53 4.554 16.399 20.326 1.00 7.94 O +ATOM 410 CB TYR A 53 6.630 14.562 21.517 1.00 7.91 C +ATOM 411 CG TYR A 53 7.865 14.099 22.242 1.00 6.82 C +ATOM 412 CD1 TYR A 53 8.335 14.742 23.399 1.00 8.88 C +ATOM 413 CD2 TYR A 53 8.618 13.027 21.749 1.00 6.30 C +ATOM 414 CE1 TYR A 53 9.548 14.382 24.006 1.00 1.83 C +ATOM 415 CE2 TYR A 53 9.846 12.646 22.351 1.00 10.07 C +ATOM 416 CZ TYR A 53 10.229 13.264 23.534 1.00 8.70 C +ATOM 417 OH TYR A 53 11.374 12.889 24.151 1.00 12.40 O +ATOM 418 N GLY A 54 5.598 15.446 18.516 1.00 11.04 N +ATOM 419 CA GLY A 54 4.390 15.347 17.710 1.00 7.71 C +ATOM 420 C GLY A 54 3.939 16.599 17.020 1.00 3.67 C +ATOM 421 O GLY A 54 4.535 17.621 17.017 1.00 8.49 O +ATOM 422 N ILE A 55 2.748 16.458 16.496 1.00 11.91 N +ATOM 423 CA ILE A 55 2.096 17.435 15.686 1.00 7.88 C +ATOM 424 C ILE A 55 1.893 18.749 16.386 1.00 10.21 C +ATOM 425 O ILE A 55 1.904 19.805 15.761 1.00 9.17 O +ATOM 426 CB ILE A 55 0.838 16.805 15.068 1.00 19.48 C +ATOM 427 CG1 ILE A 55 0.390 17.438 13.734 1.00 15.27 C +ATOM 428 CG2 ILE A 55 -0.262 16.528 16.106 1.00 16.63 C +ATOM 429 CD1 ILE A 55 -0.353 16.483 12.846 1.00 21.60 C +ATOM 430 N LEU A 56 1.765 18.677 17.706 1.00 9.90 N +ATOM 431 CA LEU A 56 1.584 19.877 18.488 1.00 7.23 C +ATOM 432 C LEU A 56 2.735 20.173 19.390 1.00 18.66 C +ATOM 433 O LEU A 56 2.660 21.074 20.200 1.00 10.73 O +ATOM 434 CB LEU A 56 0.216 19.957 19.205 1.00 11.28 C +ATOM 435 CG LEU A 56 -0.990 20.157 18.283 1.00 12.31 C +ATOM 436 CD1 LEU A 56 -2.255 19.795 19.036 1.00 11.09 C +ATOM 437 CD2 LEU A 56 -1.074 21.607 17.850 1.00 11.43 C +ATOM 438 N GLN A 57 3.804 19.441 19.202 1.00 7.01 N +ATOM 439 CA GLN A 57 5.029 19.733 19.898 1.00 9.13 C +ATOM 440 C GLN A 57 4.883 19.918 21.451 1.00 11.13 C +ATOM 441 O GLN A 57 5.272 20.968 22.020 1.00 12.02 O +ATOM 442 CB GLN A 57 5.767 20.937 19.263 1.00 10.29 C +ATOM 443 CG GLN A 57 6.362 20.658 17.863 1.00 6.27 C +ATOM 444 CD GLN A 57 7.544 19.747 17.936 1.00 2.25 C +ATOM 445 OE1 GLN A 57 8.676 20.257 18.147 1.00 7.47 O +ATOM 446 NE2 GLN A 57 7.279 18.413 17.746 1.00 7.69 N +ATOM 447 N ILE A 58 4.303 18.898 22.061 1.00 9.58 N +ATOM 448 CA ILE A 58 4.031 18.814 23.487 1.00 12.88 C +ATOM 449 C ILE A 58 5.301 18.482 24.282 1.00 14.09 C +ATOM 450 O ILE A 58 6.055 17.583 23.982 1.00 10.65 O +ATOM 451 CB ILE A 58 2.839 17.923 23.711 1.00 12.15 C +ATOM 452 CG1 ILE A 58 1.599 18.614 23.110 1.00 12.61 C +ATOM 453 CG2 ILE A 58 2.704 17.544 25.215 1.00 12.37 C +ATOM 454 CD1 ILE A 58 0.329 17.770 23.138 1.00 17.22 C +ATOM 455 N ASN A 59 5.556 19.297 25.282 1.00 11.07 N +ATOM 456 CA ASN A 59 6.797 19.305 26.034 1.00 6.68 C +ATOM 457 C ASN A 59 6.893 18.239 27.099 1.00 8.46 C +ATOM 458 O ASN A 59 5.904 18.002 27.761 1.00 12.15 O +ATOM 459 CB ASN A 59 7.045 20.721 26.565 1.00 7.94 C +ATOM 460 CG ASN A 59 8.434 20.839 27.178 1.00 12.92 C +ATOM 461 OD1 ASN A 59 8.578 20.809 28.411 1.00 30.15 O +ATOM 462 ND2 ASN A 59 9.469 20.939 26.342 1.00 15.71 N +ATOM 463 N SER A 60 8.096 17.590 27.218 1.00 8.63 N +ATOM 464 CA SER A 60 8.333 16.496 28.162 1.00 11.30 C +ATOM 465 C SER A 60 8.586 17.015 29.647 1.00 7.42 C +ATOM 466 O SER A 60 8.559 16.218 30.620 1.00 18.39 O +ATOM 467 CB SER A 60 9.448 15.619 27.698 1.00 9.31 C +ATOM 468 OG SER A 60 10.642 16.390 27.790 1.00 9.01 O +ATOM 469 N ARG A 61 8.806 18.347 29.787 1.00 11.96 N +ATOM 470 CA ARG A 61 8.981 18.933 31.125 1.00 18.58 C +ATOM 471 C ARG A 61 7.701 18.806 31.935 1.00 21.66 C +ATOM 472 O ARG A 61 7.730 18.363 33.063 1.00 24.43 O +ATOM 473 CB ARG A 61 9.507 20.347 31.068 1.00 19.81 C +ATOM 474 CG ARG A 61 9.259 21.125 32.338 1.00 40.52 C +ATOM 475 CD ARG A 61 10.511 21.648 33.063 1.00 30.90 C +ATOM 476 NE ARG A 61 11.777 21.523 32.353 1.00 58.97 N +ATOM 477 CZ ARG A 61 12.722 20.587 32.539 1.00 70.61 C +ATOM 478 NH1 ARG A 61 12.610 19.570 33.413 1.00 68.85 N +ATOM 479 NH2 ARG A 61 13.829 20.673 31.795 1.00 56.33 N +ATOM 480 N TRP A 62 6.542 19.071 31.329 1.00 12.69 N +ATOM 481 CA TRP A 62 5.279 18.955 32.026 1.00 10.92 C +ATOM 482 C TRP A 62 4.281 17.916 31.682 1.00 19.26 C +ATOM 483 O TRP A 62 3.526 17.478 32.563 1.00 19.01 O +ATOM 484 CB TRP A 62 4.455 20.234 31.875 1.00 14.48 C +ATOM 485 CG TRP A 62 5.346 21.376 31.920 1.00 34.77 C +ATOM 486 CD1 TRP A 62 5.937 21.965 30.857 1.00 48.56 C +ATOM 487 CD2 TRP A 62 5.859 21.980 33.091 1.00 34.03 C +ATOM 488 NE1 TRP A 62 6.753 22.970 31.303 1.00 60.61 N +ATOM 489 CE2 TRP A 62 6.730 22.995 32.671 1.00 37.59 C +ATOM 490 CE3 TRP A 62 5.619 21.790 34.443 1.00 44.85 C +ATOM 491 CZ2 TRP A 62 7.373 23.823 33.582 1.00 74.91 C +ATOM 492 CZ3 TRP A 62 6.254 22.606 35.347 1.00 49.52 C +ATOM 493 CH2 TRP A 62 7.122 23.609 34.923 1.00 52.73 C +ATOM 494 N TRP A 63 4.152 17.600 30.385 1.00 11.21 N +ATOM 495 CA TRP A 63 3.036 16.858 29.848 1.00 9.63 C +ATOM 496 C TRP A 63 3.155 15.396 29.592 1.00 4.89 C +ATOM 497 O TRP A 63 2.183 14.725 29.581 1.00 11.10 O +ATOM 498 CB TRP A 63 2.652 17.635 28.566 1.00 6.50 C +ATOM 499 CG TRP A 63 2.429 19.101 28.874 1.00 5.59 C +ATOM 500 CD1 TRP A 63 3.223 20.140 28.615 1.00 15.86 C +ATOM 501 CD2 TRP A 63 1.364 19.632 29.695 1.00 11.68 C +ATOM 502 NE1 TRP A 63 2.675 21.309 29.075 1.00 15.89 N +ATOM 503 CE2 TRP A 63 1.567 21.028 29.780 1.00 12.27 C +ATOM 504 CE3 TRP A 63 0.230 19.055 30.324 1.00 14.52 C +ATOM 505 CZ2 TRP A 63 0.682 21.862 30.488 1.00 10.75 C +ATOM 506 CZ3 TRP A 63 -0.678 19.891 30.985 1.00 10.21 C +ATOM 507 CH2 TRP A 63 -0.421 21.271 31.057 1.00 13.33 C +ATOM 508 N CYS A 64 4.324 14.905 29.353 1.00 8.53 N +ATOM 509 CA CYS A 64 4.448 13.469 29.032 1.00 14.18 C +ATOM 510 C CYS A 64 5.785 12.968 29.569 1.00 8.75 C +ATOM 511 O CYS A 64 6.694 13.742 29.793 1.00 11.88 O +ATOM 512 CB CYS A 64 4.366 13.241 27.432 1.00 12.87 C +ATOM 513 SG CYS A 64 5.695 14.086 26.427 1.00 9.81 S +ATOM 514 N ASN A 65 5.913 11.651 29.720 1.00 9.55 N +ATOM 515 CA ASN A 65 7.127 11.114 30.200 1.00 16.84 C +ATOM 516 C ASN A 65 7.999 10.547 29.073 1.00 4.97 C +ATOM 517 O ASN A 65 7.529 9.623 28.435 1.00 10.83 O +ATOM 518 CB ASN A 65 6.809 9.953 31.188 1.00 9.17 C +ATOM 519 CG ASN A 65 8.120 9.322 31.715 1.00 22.59 C +ATOM 520 OD1 ASN A 65 9.033 10.017 32.182 1.00 21.36 O +ATOM 521 ND2 ASN A 65 8.276 8.015 31.524 1.00 36.98 N +ATOM 522 N ASP A 66 9.254 10.993 28.982 1.00 7.66 N +ATOM 523 CA ASP A 66 10.153 10.434 27.995 1.00 14.97 C +ATOM 524 C ASP A 66 11.354 9.742 28.601 1.00 23.09 C +ATOM 525 O ASP A 66 12.237 9.341 27.867 1.00 9.43 O +ATOM 526 CB ASP A 66 10.641 11.448 26.948 1.00 13.58 C +ATOM 527 CG ASP A 66 11.480 12.554 27.535 1.00 11.41 C +ATOM 528 OD1 ASP A 66 11.787 12.613 28.717 1.00 18.43 O +ATOM 529 OD2 ASP A 66 11.850 13.432 26.659 1.00 10.72 O +ATOM 530 N GLY A 67 11.395 9.644 29.920 1.00 14.60 N +ATOM 531 CA GLY A 67 12.449 8.941 30.665 1.00 9.04 C +ATOM 532 C GLY A 67 13.738 9.677 30.697 1.00 13.04 C +ATOM 533 O GLY A 67 14.726 9.165 31.164 1.00 23.22 O +ATOM 534 N ARG A 68 13.787 10.891 30.194 1.00 8.50 N +ATOM 535 CA ARG A 68 15.089 11.512 30.237 1.00 11.50 C +ATOM 536 C ARG A 68 15.046 12.949 30.560 1.00 11.49 C +ATOM 537 O ARG A 68 15.995 13.645 30.281 1.00 17.90 O +ATOM 538 CB ARG A 68 15.872 11.277 28.959 1.00 18.67 C +ATOM 539 CG ARG A 68 15.218 11.867 27.707 1.00 21.19 C +ATOM 540 CD ARG A 68 16.251 12.103 26.592 1.00 19.51 C +ATOM 541 NE ARG A 68 15.790 12.984 25.527 1.00 20.38 N +ATOM 542 CZ ARG A 68 16.264 12.978 24.248 1.00 29.94 C +ATOM 543 NH1 ARG A 68 17.253 12.102 23.926 1.00 13.00 N +ATOM 544 NH2 ARG A 68 15.787 13.865 23.293 1.00 13.47 N +ATOM 545 N THR A 69 13.937 13.376 31.145 1.00 12.12 N +ATOM 546 CA THR A 69 13.674 14.782 31.586 1.00 17.22 C +ATOM 547 C THR A 69 13.372 14.770 33.144 1.00 15.41 C +ATOM 548 O THR A 69 12.260 14.526 33.618 1.00 19.26 O +ATOM 549 CB THR A 69 12.464 15.410 30.798 1.00 12.81 C +ATOM 550 OG1 THR A 69 12.589 15.107 29.412 1.00 17.25 O +ATOM 551 CG2 THR A 69 12.392 16.932 30.990 1.00 8.98 C +ATOM 552 N PRO A 70 14.431 14.960 33.874 1.00 30.00 N +ATOM 553 CA PRO A 70 14.563 14.964 35.315 1.00 31.13 C +ATOM 554 C PRO A 70 13.654 16.003 35.904 1.00 43.01 C +ATOM 555 O PRO A 70 13.699 17.188 35.594 1.00 37.19 O +ATOM 556 CB PRO A 70 16.056 15.221 35.541 1.00 43.11 C +ATOM 557 CG PRO A 70 16.728 15.203 34.148 1.00 49.23 C +ATOM 558 CD PRO A 70 15.635 15.319 33.119 1.00 44.60 C +ATOM 559 N GLY A 71 12.698 15.573 36.672 1.00 29.79 N +ATOM 560 CA GLY A 71 11.785 16.609 37.130 1.00 38.84 C +ATOM 561 C GLY A 71 10.547 16.728 36.220 1.00 34.52 C +ATOM 562 O GLY A 71 9.750 17.644 36.328 1.00 53.49 O +ATOM 563 N SER A 72 10.339 15.797 35.324 1.00 30.26 N +ATOM 564 CA SER A 72 9.157 15.860 34.502 1.00 32.28 C +ATOM 565 C SER A 72 7.906 15.615 35.374 1.00 22.29 C +ATOM 566 O SER A 72 7.914 14.715 36.197 1.00 26.48 O +ATOM 567 CB SER A 72 9.249 14.700 33.473 1.00 31.83 C +ATOM 568 OG SER A 72 8.038 14.552 32.612 1.00 33.11 O +ATOM 569 N ARG A 73 6.801 16.311 35.113 1.00 20.31 N +ATOM 570 CA ARG A 73 5.550 16.055 35.819 1.00 12.77 C +ATOM 571 C ARG A 73 4.564 15.081 35.174 1.00 35.87 C +ATOM 572 O ARG A 73 3.662 14.597 35.845 1.00 50.20 O +ATOM 573 CB ARG A 73 4.830 17.322 36.128 1.00 19.66 C +ATOM 574 CG ARG A 73 5.605 18.165 37.124 1.00 35.18 C +ATOM 575 CD ARG A 73 4.864 19.471 37.396 1.00 86.10 C +ATOM 576 NE ARG A 73 4.736 19.744 38.823 1.00 80.19 N +ATOM 577 CZ ARG A 73 4.227 20.854 39.398 1.00 81.09 C +ATOM 578 NH1 ARG A 73 3.742 21.891 38.705 1.00 81.15 N +ATOM 579 NH2 ARG A 73 4.215 20.930 40.739 1.00 71.03 N +ATOM 580 N ASN A 74 4.668 14.781 33.896 1.00 18.76 N +ATOM 581 CA ASN A 74 3.715 13.833 33.313 1.00 10.40 C +ATOM 582 C ASN A 74 2.194 14.147 33.501 1.00 8.97 C +ATOM 583 O ASN A 74 1.355 13.278 33.697 1.00 15.29 O +ATOM 584 CB ASN A 74 4.053 12.334 33.426 1.00 16.10 C +ATOM 585 CG ASN A 74 3.479 11.413 32.309 1.00 15.75 C +ATOM 586 OD1 ASN A 74 2.928 11.864 31.297 1.00 22.77 O +ATOM 587 ND2 ASN A 74 3.593 10.101 32.490 1.00 17.62 N +ATOM 588 N LEU A 75 1.851 15.405 33.334 1.00 13.92 N +ATOM 589 CA LEU A 75 0.471 15.774 33.458 1.00 16.58 C +ATOM 590 C LEU A 75 -0.505 15.089 32.565 1.00 21.84 C +ATOM 591 O LEU A 75 -1.654 14.976 32.957 1.00 22.99 O +ATOM 592 CB LEU A 75 0.245 17.277 33.466 1.00 17.10 C +ATOM 593 CG LEU A 75 0.919 17.845 34.715 1.00 30.53 C +ATOM 594 CD1 LEU A 75 0.889 19.358 34.725 1.00 35.25 C +ATOM 595 CD2 LEU A 75 0.238 17.306 35.969 1.00 21.06 C +ATOM 596 N CYS A 76 -0.146 14.663 31.359 1.00 18.42 N +ATOM 597 CA CYS A 76 -1.153 13.970 30.513 1.00 10.67 C +ATOM 598 C CYS A 76 -1.137 12.463 30.738 1.00 12.68 C +ATOM 599 O CYS A 76 -1.935 11.725 30.131 1.00 17.21 O +ATOM 600 CB CYS A 76 -1.094 14.295 28.984 1.00 9.97 C +ATOM 601 SG CYS A 76 -1.329 16.050 28.713 1.00 13.70 S +ATOM 602 N ASN A 77 -0.194 12.038 31.586 1.00 14.93 N +ATOM 603 CA ASN A 77 -0.117 10.607 31.926 1.00 19.18 C +ATOM 604 C ASN A 77 0.099 9.697 30.747 1.00 21.40 C +ATOM 605 O ASN A 77 -0.626 8.715 30.538 1.00 17.53 O +ATOM 606 CB ASN A 77 -1.421 10.174 32.620 1.00 36.06 C +ATOM 607 CG ASN A 77 -1.361 8.783 33.215 1.00 80.95 C +ATOM 608 OD1 ASN A 77 -2.358 8.042 33.188 1.00 78.33 O +ATOM 609 ND2 ASN A 77 -0.186 8.412 33.715 1.00 38.97 N +ATOM 610 N ILE A 78 1.114 10.006 29.979 1.00 14.33 N +ATOM 611 CA ILE A 78 1.373 9.191 28.838 1.00 11.33 C +ATOM 612 C ILE A 78 2.873 9.258 28.499 1.00 13.41 C +ATOM 613 O ILE A 78 3.568 10.265 28.718 1.00 12.78 O +ATOM 614 CB ILE A 78 0.764 9.855 27.598 1.00 15.98 C +ATOM 615 CG1 ILE A 78 0.764 11.376 27.743 1.00 20.19 C +ATOM 616 CG2 ILE A 78 -0.461 9.195 26.985 1.00 25.51 C +ATOM 617 CD1 ILE A 78 0.735 12.094 26.406 1.00 31.88 C +ATOM 618 N PRO A 79 3.343 8.210 27.843 1.00 14.97 N +ATOM 619 CA PRO A 79 4.715 8.229 27.362 1.00 12.65 C +ATOM 620 C PRO A 79 4.738 9.234 26.187 1.00 10.18 C +ATOM 621 O PRO A 79 3.762 9.304 25.359 1.00 11.71 O +ATOM 622 CB PRO A 79 4.962 6.830 26.843 1.00 11.25 C +ATOM 623 CG PRO A 79 3.631 6.096 26.844 1.00 17.21 C +ATOM 624 CD PRO A 79 2.621 6.951 27.581 1.00 9.85 C +ATOM 625 N CYS A 80 5.798 10.020 26.078 1.00 11.09 N +ATOM 626 CA CYS A 80 5.870 11.003 24.969 1.00 5.24 C +ATOM 627 C CYS A 80 5.782 10.359 23.546 1.00 8.89 C +ATOM 628 O CYS A 80 5.284 10.950 22.568 1.00 11.52 O +ATOM 629 CB CYS A 80 7.126 11.894 25.061 1.00 7.40 C +ATOM 630 SG CYS A 80 7.251 12.847 26.592 1.00 9.47 S +ATOM 631 N SER A 81 6.259 9.115 23.442 1.00 9.85 N +ATOM 632 CA SER A 81 6.242 8.432 22.154 1.00 7.67 C +ATOM 633 C SER A 81 4.815 8.223 21.687 1.00 15.55 C +ATOM 634 O SER A 81 4.554 8.156 20.510 1.00 15.82 O +ATOM 635 CB SER A 81 6.995 7.111 22.234 1.00 15.31 C +ATOM 636 OG SER A 81 6.295 6.245 23.119 1.00 17.97 O +ATOM 637 N ALA A 82 3.857 8.169 22.598 1.00 11.39 N +ATOM 638 CA ALA A 82 2.452 8.033 22.185 1.00 14.65 C +ATOM 639 C ALA A 82 2.000 9.216 21.325 1.00 20.26 C +ATOM 640 O ALA A 82 1.033 9.113 20.571 1.00 22.13 O +ATOM 641 CB ALA A 82 1.481 8.009 23.384 1.00 17.51 C +ATOM 642 N LEU A 83 2.659 10.349 21.528 1.00 9.56 N +ATOM 643 CA LEU A 83 2.329 11.589 20.867 1.00 12.01 C +ATOM 644 C LEU A 83 2.834 11.627 19.385 1.00 18.14 C +ATOM 645 O LEU A 83 2.626 12.620 18.685 1.00 12.31 O +ATOM 646 CB LEU A 83 2.986 12.761 21.651 1.00 15.90 C +ATOM 647 CG LEU A 83 2.370 12.966 23.055 1.00 9.43 C +ATOM 648 CD1 LEU A 83 3.076 14.069 23.849 1.00 12.61 C +ATOM 649 CD2 LEU A 83 0.843 13.174 22.965 1.00 15.37 C +ATOM 650 N LEU A 84 3.542 10.556 18.940 1.00 13.34 N +ATOM 651 CA LEU A 84 4.131 10.512 17.618 1.00 11.55 C +ATOM 652 C LEU A 84 3.361 9.657 16.630 1.00 16.60 C +ATOM 653 O LEU A 84 3.704 9.570 15.475 1.00 22.63 O +ATOM 654 CB LEU A 84 5.630 10.044 17.645 1.00 7.92 C +ATOM 655 CG LEU A 84 6.546 10.859 18.552 1.00 18.00 C +ATOM 656 CD1 LEU A 84 7.978 10.414 18.359 1.00 17.76 C +ATOM 657 CD2 LEU A 84 6.513 12.306 18.116 1.00 8.41 C +ATOM 658 N SER A 85 2.332 9.023 17.096 1.00 15.68 N +ATOM 659 CA SER A 85 1.485 8.148 16.333 1.00 22.63 C +ATOM 660 C SER A 85 0.792 8.827 15.194 1.00 14.76 C +ATOM 661 O SER A 85 0.519 10.007 15.280 1.00 16.99 O +ATOM 662 CB SER A 85 0.376 7.776 17.295 1.00 16.59 C +ATOM 663 OG SER A 85 -0.373 6.761 16.741 1.00 23.89 O +ATOM 664 N SER A 86 0.371 8.039 14.186 1.00 19.04 N +ATOM 665 CA SER A 86 -0.430 8.505 13.025 1.00 17.09 C +ATOM 666 C SER A 86 -1.827 8.884 13.487 1.00 21.77 C +ATOM 667 O SER A 86 -2.481 9.696 12.857 1.00 24.42 O +ATOM 668 CB SER A 86 -0.584 7.358 12.026 1.00 21.75 C +ATOM 669 OG SER A 86 0.687 7.146 11.467 1.00 50.53 O +ATOM 670 N ASP A 87 -2.288 8.227 14.575 1.00 13.55 N +ATOM 671 CA ASP A 87 -3.611 8.483 15.195 1.00 14.83 C +ATOM 672 C ASP A 87 -3.426 9.673 16.162 1.00 16.43 C +ATOM 673 O ASP A 87 -2.640 9.585 17.147 1.00 17.32 O +ATOM 674 CB ASP A 87 -4.025 7.244 15.987 1.00 17.38 C +ATOM 675 CG ASP A 87 -5.365 7.435 16.676 1.00 36.42 C +ATOM 676 OD1 ASP A 87 -5.875 8.512 16.868 1.00 21.05 O +ATOM 677 OD2 ASP A 87 -5.952 6.315 17.005 1.00 56.25 O +ATOM 678 N ILE A 88 -4.037 10.803 15.879 1.00 12.05 N +ATOM 679 CA ILE A 88 -3.749 11.974 16.722 1.00 17.85 C +ATOM 680 C ILE A 88 -4.490 12.067 18.055 1.00 12.40 C +ATOM 681 O ILE A 88 -4.393 13.081 18.780 1.00 11.64 O +ATOM 682 CB ILE A 88 -4.014 13.293 15.954 1.00 16.92 C +ATOM 683 CG1 ILE A 88 -5.565 13.392 15.634 1.00 15.36 C +ATOM 684 CG2 ILE A 88 -3.104 13.384 14.694 1.00 18.11 C +ATOM 685 CD1 ILE A 88 -6.065 14.738 15.196 1.00 20.80 C +ATOM 686 N THR A 89 -5.257 11.069 18.381 1.00 13.72 N +ATOM 687 CA THR A 89 -6.058 11.103 19.584 1.00 12.45 C +ATOM 688 C THR A 89 -5.326 11.520 20.907 1.00 8.02 C +ATOM 689 O THR A 89 -5.777 12.403 21.614 1.00 14.43 O +ATOM 690 CB THR A 89 -6.717 9.735 19.716 1.00 18.11 C +ATOM 691 OG1 THR A 89 -7.492 9.539 18.564 1.00 18.36 O +ATOM 692 CG2 THR A 89 -7.642 9.724 20.953 1.00 16.37 C +ATOM 693 N ALA A 90 -4.186 10.900 21.216 1.00 10.40 N +ATOM 694 CA ALA A 90 -3.483 11.250 22.444 1.00 14.23 C +ATOM 695 C ALA A 90 -2.971 12.685 22.412 1.00 17.47 C +ATOM 696 O ALA A 90 -2.981 13.344 23.413 1.00 10.92 O +ATOM 697 CB ALA A 90 -2.331 10.290 22.751 1.00 15.55 C +ATOM 698 N SER A 91 -2.504 13.185 21.257 1.00 8.67 N +ATOM 699 CA SER A 91 -2.032 14.567 21.163 1.00 7.03 C +ATOM 700 C SER A 91 -3.155 15.522 21.418 1.00 6.83 C +ATOM 701 O SER A 91 -3.033 16.547 22.059 1.00 13.20 O +ATOM 702 CB SER A 91 -1.445 14.870 19.783 1.00 7.71 C +ATOM 703 OG SER A 91 -0.111 14.402 19.670 1.00 11.50 O +ATOM 704 N VAL A 92 -4.289 15.234 20.839 1.00 9.57 N +ATOM 705 CA VAL A 92 -5.449 16.101 21.004 1.00 7.79 C +ATOM 706 C VAL A 92 -5.938 16.148 22.488 1.00 10.65 C +ATOM 707 O VAL A 92 -6.254 17.195 23.018 1.00 12.26 O +ATOM 708 CB VAL A 92 -6.523 15.597 19.994 1.00 23.58 C +ATOM 709 CG1 VAL A 92 -7.936 16.117 20.303 1.00 19.93 C +ATOM 710 CG2 VAL A 92 -6.110 15.987 18.555 1.00 17.17 C +ATOM 711 N ASN A 93 -6.047 14.973 23.140 1.00 10.03 N +ATOM 712 CA ASN A 93 -6.511 14.862 24.536 1.00 24.44 C +ATOM 713 C ASN A 93 -5.602 15.647 25.472 1.00 10.79 C +ATOM 714 O ASN A 93 -6.049 16.390 26.310 1.00 15.54 O +ATOM 715 CB ASN A 93 -6.580 13.395 24.989 1.00 13.16 C +ATOM 716 CG ASN A 93 -7.781 12.668 24.406 1.00 15.37 C +ATOM 717 OD1 ASN A 93 -7.842 11.422 24.426 1.00 35.75 O +ATOM 718 ND2 ASN A 93 -8.682 13.436 23.835 1.00 16.65 N +ATOM 719 N CYS A 94 -4.284 15.477 25.249 1.00 10.49 N +ATOM 720 CA CYS A 94 -3.267 16.178 25.984 1.00 7.62 C +ATOM 721 C CYS A 94 -3.353 17.649 25.690 1.00 17.58 C +ATOM 722 O CYS A 94 -3.298 18.462 26.598 1.00 9.76 O +ATOM 723 CB CYS A 94 -1.875 15.620 25.709 1.00 5.33 C +ATOM 724 SG CYS A 94 -0.613 16.312 26.762 1.00 13.87 S +ATOM 725 N ALA A 95 -3.546 18.041 24.407 1.00 7.01 N +ATOM 726 CA ALA A 95 -3.656 19.481 24.142 1.00 8.80 C +ATOM 727 C ALA A 95 -4.864 20.156 24.849 1.00 8.68 C +ATOM 728 O ALA A 95 -4.867 21.353 25.215 1.00 11.44 O +ATOM 729 CB ALA A 95 -3.774 19.698 22.627 1.00 6.34 C +ATOM 730 N LYS A 96 -5.932 19.405 24.966 1.00 9.62 N +ATOM 731 CA LYS A 96 -7.108 19.927 25.596 1.00 9.41 C +ATOM 732 C LYS A 96 -6.804 20.229 27.091 1.00 11.43 C +ATOM 733 O LYS A 96 -7.271 21.199 27.627 1.00 15.34 O +ATOM 734 CB LYS A 96 -8.195 18.868 25.472 1.00 12.74 C +ATOM 735 CG LYS A 96 -8.927 18.820 24.137 1.00 9.62 C +ATOM 736 CD LYS A 96 -9.976 17.699 24.147 1.00 14.08 C +ATOM 737 CE LYS A 96 -10.973 17.784 22.960 1.00 16.34 C +ATOM 738 NZ LYS A 96 -11.641 16.485 22.720 1.00 20.55 N +ATOM 739 N LYS A 97 -5.944 19.447 27.750 1.00 13.54 N +ATOM 740 CA LYS A 97 -5.538 19.706 29.158 1.00 14.41 C +ATOM 741 C LYS A 97 -4.672 20.981 29.209 1.00 13.37 C +ATOM 742 O LYS A 97 -4.809 21.878 30.014 1.00 13.38 O +ATOM 743 CB LYS A 97 -4.710 18.544 29.689 1.00 10.77 C +ATOM 744 CG LYS A 97 -5.493 17.342 30.140 1.00 32.04 C +ATOM 745 CD LYS A 97 -6.434 17.637 31.297 1.00 45.76 C +ATOM 746 CE LYS A 97 -7.073 16.369 31.886 1.00 70.47 C +ATOM 747 NZ LYS A 97 -8.523 16.232 31.620 1.00 59.21 N +ATOM 748 N ILE A 98 -3.760 21.072 28.264 1.00 12.65 N +ATOM 749 CA ILE A 98 -2.856 22.204 28.161 1.00 10.78 C +ATOM 750 C ILE A 98 -3.607 23.536 27.991 1.00 8.94 C +ATOM 751 O ILE A 98 -3.322 24.532 28.701 1.00 12.98 O +ATOM 752 CB ILE A 98 -1.778 22.026 27.022 1.00 17.91 C +ATOM 753 CG1 ILE A 98 -0.899 20.798 27.234 1.00 15.21 C +ATOM 754 CG2 ILE A 98 -0.932 23.292 26.811 1.00 10.73 C +ATOM 755 CD1 ILE A 98 -0.035 20.440 26.059 1.00 5.59 C +ATOM 756 N VAL A 99 -4.497 23.570 26.973 1.00 12.61 N +ATOM 757 CA VAL A 99 -5.194 24.822 26.643 1.00 14.92 C +ATOM 758 C VAL A 99 -6.158 25.244 27.757 1.00 17.60 C +ATOM 759 O VAL A 99 -6.529 26.431 27.844 1.00 21.46 O +ATOM 760 CB VAL A 99 -5.863 24.788 25.223 1.00 7.93 C +ATOM 761 CG1 VAL A 99 -7.102 23.930 25.230 1.00 13.13 C +ATOM 762 CG2 VAL A 99 -6.203 26.159 24.648 1.00 14.05 C +ATOM 763 N SER A 100 -6.529 24.274 28.623 1.00 14.94 N +ATOM 764 CA SER A 100 -7.469 24.559 29.728 1.00 23.99 C +ATOM 765 C SER A 100 -6.810 25.233 30.952 1.00 23.57 C +ATOM 766 O SER A 100 -7.460 25.872 31.759 1.00 30.51 O +ATOM 767 CB SER A 100 -8.109 23.250 30.148 1.00 15.96 C +ATOM 768 OG SER A 100 -9.019 22.837 29.120 1.00 33.46 O +ATOM 769 N ASP A 101 -5.495 25.061 30.981 1.00 27.50 N +ATOM 770 CA ASP A 101 -4.485 25.414 31.955 1.00 38.61 C +ATOM 771 C ASP A 101 -4.239 26.879 32.265 1.00 31.46 C +ATOM 772 O ASP A 101 -3.422 27.194 33.137 1.00 49.53 O +ATOM 773 CB ASP A 101 -3.173 24.648 31.624 1.00 32.62 C +ATOM 774 CG ASP A 101 -2.133 24.566 32.715 1.00 66.21 C +ATOM 775 OD1 ASP A 101 -2.482 23.821 33.747 1.00 53.53 O +ATOM 776 OD2 ASP A 101 -1.045 25.095 32.609 1.00 62.33 O +ATOM 777 N GLY A 102 -4.876 27.820 31.617 1.00 31.57 N +ATOM 778 CA GLY A 102 -4.525 29.170 32.093 1.00 42.83 C +ATOM 779 C GLY A 102 -4.082 30.192 31.049 1.00 56.99 C +ATOM 780 O GLY A 102 -4.713 31.264 30.990 1.00 31.68 O +ATOM 781 N ASN A 103 -2.979 29.915 30.284 1.00 23.55 N +ATOM 782 CA ASN A 103 -2.573 30.864 29.246 1.00 11.97 C +ATOM 783 C ASN A 103 -3.176 30.497 27.876 1.00 9.86 C +ATOM 784 O ASN A 103 -2.905 31.106 26.860 1.00 13.84 O +ATOM 785 CB ASN A 103 -1.070 31.114 29.177 1.00 17.92 C +ATOM 786 CG ASN A 103 -0.638 31.476 30.587 1.00 65.73 C +ATOM 787 OD1 ASN A 103 0.384 30.993 31.105 1.00 74.71 O +ATOM 788 ND2 ASN A 103 -1.509 32.224 31.271 1.00 54.30 N +ATOM 789 N GLY A 104 -4.070 29.522 27.865 1.00 10.94 N +ATOM 790 CA GLY A 104 -4.733 29.138 26.601 1.00 18.78 C +ATOM 791 C GLY A 104 -3.725 28.668 25.570 1.00 8.28 C +ATOM 792 O GLY A 104 -2.766 27.947 25.892 1.00 12.01 O +ATOM 793 N MET A 105 -3.906 29.119 24.313 1.00 13.56 N +ATOM 794 CA MET A 105 -3.014 28.684 23.198 1.00 9.18 C +ATOM 795 C MET A 105 -1.637 29.372 23.232 1.00 8.69 C +ATOM 796 O MET A 105 -0.727 29.013 22.506 1.00 9.67 O +ATOM 797 CB MET A 105 -3.739 28.882 21.838 1.00 3.51 C +ATOM 798 CG MET A 105 -4.790 27.788 21.646 1.00 9.82 C +ATOM 799 SD MET A 105 -5.184 27.455 19.852 1.00 12.90 S +ATOM 800 CE MET A 105 -3.617 26.757 19.326 1.00 6.80 C +ATOM 801 N ASN A 106 -1.509 30.373 24.105 1.00 7.08 N +ATOM 802 CA ASN A 106 -0.270 31.037 24.269 1.00 4.32 C +ATOM 803 C ASN A 106 0.809 30.046 24.765 1.00 8.04 C +ATOM 804 O ASN A 106 2.030 30.336 24.608 1.00 11.37 O +ATOM 805 CB ASN A 106 -0.396 32.190 25.241 1.00 12.62 C +ATOM 806 CG ASN A 106 -1.239 33.309 24.682 1.00 16.51 C +ATOM 807 OD1 ASN A 106 -0.864 33.972 23.658 1.00 9.88 O +ATOM 808 ND2 ASN A 106 -2.372 33.492 25.355 1.00 15.30 N +ATOM 809 N ALA A 107 0.360 28.870 25.250 1.00 8.10 N +ATOM 810 CA ALA A 107 1.308 27.840 25.625 1.00 10.48 C +ATOM 811 C ALA A 107 2.113 27.450 24.395 1.00 16.77 C +ATOM 812 O ALA A 107 3.191 26.948 24.511 1.00 16.10 O +ATOM 813 CB ALA A 107 0.585 26.599 26.143 1.00 11.40 C +ATOM 814 N TRP A 108 1.577 27.639 23.205 1.00 10.51 N +ATOM 815 CA TRP A 108 2.303 27.285 21.966 1.00 9.27 C +ATOM 816 C TRP A 108 2.970 28.504 21.404 1.00 9.11 C +ATOM 817 O TRP A 108 2.312 29.428 20.865 1.00 9.30 O +ATOM 818 CB TRP A 108 1.398 26.569 20.912 1.00 4.39 C +ATOM 819 CG TRP A 108 1.005 25.176 21.256 1.00 2.06 C +ATOM 820 CD1 TRP A 108 1.760 24.069 21.021 1.00 10.56 C +ATOM 821 CD2 TRP A 108 -0.146 24.722 21.926 1.00 4.61 C +ATOM 822 NE1 TRP A 108 1.131 22.972 21.471 1.00 11.23 N +ATOM 823 CE2 TRP A 108 -0.048 23.321 22.045 1.00 11.25 C +ATOM 824 CE3 TRP A 108 -1.256 25.348 22.436 1.00 8.16 C +ATOM 825 CZ2 TRP A 108 -1.038 22.520 22.626 1.00 7.13 C +ATOM 826 CZ3 TRP A 108 -2.220 24.549 23.074 1.00 13.29 C +ATOM 827 CH2 TRP A 108 -2.156 23.123 23.101 1.00 8.74 C +ATOM 828 N VAL A 109 4.320 28.523 21.508 1.00 10.59 N +ATOM 829 CA VAL A 109 5.046 29.672 21.044 1.00 10.72 C +ATOM 830 C VAL A 109 4.800 30.025 19.545 1.00 7.07 C +ATOM 831 O VAL A 109 4.617 31.199 19.228 1.00 12.32 O +ATOM 832 CB VAL A 109 6.549 29.491 21.342 1.00 15.75 C +ATOM 833 CG1 VAL A 109 7.068 28.242 20.605 1.00 38.18 C +ATOM 834 CG2 VAL A 109 7.327 30.751 20.898 1.00 17.01 C +ATOM 835 N ALA A 110 4.761 28.998 18.662 1.00 7.28 N +ATOM 836 CA ALA A 110 4.506 29.281 17.232 1.00 14.92 C +ATOM 837 C ALA A 110 3.122 29.845 17.031 1.00 12.74 C +ATOM 838 O ALA A 110 2.902 30.659 16.125 1.00 13.19 O +ATOM 839 CB ALA A 110 4.783 28.117 16.262 1.00 12.16 C +ATOM 840 N TRP A 111 2.190 29.398 17.892 1.00 7.58 N +ATOM 841 CA TRP A 111 0.821 29.901 17.789 1.00 5.91 C +ATOM 842 C TRP A 111 0.815 31.399 18.100 1.00 9.06 C +ATOM 843 O TRP A 111 0.249 32.308 17.369 1.00 6.22 O +ATOM 844 CB TRP A 111 -0.240 29.136 18.618 1.00 6.54 C +ATOM 845 CG TRP A 111 -1.589 29.763 18.461 1.00 9.13 C +ATOM 846 CD1 TRP A 111 -2.510 29.517 17.447 1.00 5.89 C +ATOM 847 CD2 TRP A 111 -2.190 30.781 19.295 1.00 10.48 C +ATOM 848 NE1 TRP A 111 -3.642 30.322 17.597 1.00 5.88 N +ATOM 849 CE2 TRP A 111 -3.471 31.090 18.728 1.00 5.72 C +ATOM 850 CE3 TRP A 111 -1.805 31.432 20.511 1.00 4.95 C +ATOM 851 CZ2 TRP A 111 -4.306 32.057 19.314 1.00 13.37 C +ATOM 852 CZ3 TRP A 111 -2.658 32.382 21.061 1.00 6.90 C +ATOM 853 CH2 TRP A 111 -3.906 32.666 20.489 1.00 4.12 C +ATOM 854 N ARG A 112 1.497 31.701 19.218 1.00 7.90 N +ATOM 855 CA ARG A 112 1.527 33.107 19.659 1.00 11.81 C +ATOM 856 C ARG A 112 2.221 34.013 18.630 1.00 9.34 C +ATOM 857 O ARG A 112 1.746 35.118 18.330 1.00 9.72 O +ATOM 858 CB ARG A 112 2.215 33.175 21.040 1.00 18.21 C +ATOM 859 CG ARG A 112 2.053 34.513 21.722 1.00 52.15 C +ATOM 860 CD ARG A 112 2.813 34.593 23.056 1.00 27.12 C +ATOM 861 NE ARG A 112 3.479 33.351 23.413 1.00 52.40 N +ATOM 862 CZ ARG A 112 4.785 33.247 23.639 1.00 49.41 C +ATOM 863 NH1 ARG A 112 5.612 34.286 23.535 1.00 53.98 N +ATOM 864 NH2 ARG A 112 5.274 32.058 23.981 1.00 51.24 N +ATOM 865 N ASN A 113 3.331 33.501 18.078 1.00 8.96 N +ATOM 866 CA ASN A 113 4.132 34.283 17.152 1.00 15.60 C +ATOM 867 C ASN A 113 3.657 34.303 15.695 1.00 17.72 C +ATOM 868 O ASN A 113 3.919 35.261 14.974 1.00 16.73 O +ATOM 869 CB ASN A 113 5.657 33.938 17.244 1.00 8.06 C +ATOM 870 CG ASN A 113 6.192 34.297 18.636 1.00 11.97 C +ATOM 871 OD1 ASN A 113 5.714 35.228 19.278 1.00 19.44 O +ATOM 872 ND2 ASN A 113 7.179 33.595 19.091 1.00 9.04 N +ATOM 873 N ARG A 114 2.964 33.273 15.287 1.00 7.06 N +ATOM 874 CA ARG A 114 2.604 33.129 13.873 1.00 11.57 C +ATOM 875 C ARG A 114 1.171 33.002 13.552 1.00 19.78 C +ATOM 876 O ARG A 114 0.827 33.118 12.375 1.00 14.27 O +ATOM 877 CB ARG A 114 3.309 31.830 13.395 1.00 8.51 C +ATOM 878 CG ARG A 114 4.766 31.877 13.898 1.00 21.43 C +ATOM 879 CD ARG A 114 5.833 31.132 13.125 1.00 27.54 C +ATOM 880 NE ARG A 114 5.898 31.278 11.660 1.00 16.59 N +ATOM 881 CZ ARG A 114 6.631 30.413 10.970 1.00 12.23 C +ATOM 882 NH1 ARG A 114 7.271 29.439 11.649 1.00 11.43 N +ATOM 883 NH2 ARG A 114 6.744 30.477 9.659 1.00 12.83 N +ATOM 884 N CYS A 115 0.351 32.723 14.572 1.00 5.86 N +ATOM 885 CA CYS A 115 -1.055 32.487 14.333 1.00 8.05 C +ATOM 886 C CYS A 115 -1.937 33.541 14.914 1.00 18.18 C +ATOM 887 O CYS A 115 -2.914 34.024 14.264 1.00 11.36 O +ATOM 888 CB CYS A 115 -1.488 31.114 14.872 1.00 7.31 C +ATOM 889 SG CYS A 115 -0.553 29.849 14.022 1.00 10.81 S +ATOM 890 N LYS A 116 -1.630 33.796 16.196 1.00 10.46 N +ATOM 891 CA LYS A 116 -2.372 34.723 16.976 1.00 9.75 C +ATOM 892 C LYS A 116 -2.562 36.032 16.228 1.00 9.63 C +ATOM 893 O LYS A 116 -1.583 36.599 15.729 1.00 13.85 O +ATOM 894 CB LYS A 116 -1.716 34.948 18.335 1.00 12.72 C +ATOM 895 CG LYS A 116 -2.557 35.791 19.284 1.00 7.87 C +ATOM 896 CD LYS A 116 -1.809 35.938 20.635 1.00 15.62 C +ATOM 897 CE LYS A 116 -2.607 36.597 21.773 1.00 17.04 C +ATOM 898 NZ LYS A 116 -1.889 36.524 23.073 1.00 11.32 N +ATOM 899 N GLY A 117 -3.862 36.462 16.131 1.00 9.19 N +ATOM 900 CA GLY A 117 -4.213 37.737 15.493 1.00 22.87 C +ATOM 901 C GLY A 117 -4.091 37.759 13.972 1.00 33.97 C +ATOM 902 O GLY A 117 -4.044 38.799 13.371 1.00 28.79 O +ATOM 903 N THR A 118 -4.019 36.612 13.340 1.00 15.57 N +ATOM 904 CA THR A 118 -3.940 36.537 11.885 1.00 20.24 C +ATOM 905 C THR A 118 -5.285 35.977 11.407 1.00 18.25 C +ATOM 906 O THR A 118 -6.080 35.563 12.249 1.00 18.09 O +ATOM 907 CB THR A 118 -2.747 35.680 11.439 1.00 13.62 C +ATOM 908 OG1 THR A 118 -3.060 34.321 11.639 1.00 12.88 O +ATOM 909 CG2 THR A 118 -1.455 36.072 12.193 1.00 12.89 C +ATOM 910 N ASP A 119 -5.573 35.973 10.102 1.00 20.97 N +ATOM 911 CA ASP A 119 -6.848 35.408 9.620 1.00 17.43 C +ATOM 912 C ASP A 119 -6.693 33.892 9.567 1.00 19.50 C +ATOM 913 O ASP A 119 -6.430 33.280 8.509 1.00 24.87 O +ATOM 914 CB ASP A 119 -7.228 35.933 8.234 1.00 27.62 C +ATOM 915 CG ASP A 119 -8.359 35.154 7.625 1.00 57.62 C +ATOM 916 OD1 ASP A 119 -9.168 34.529 8.288 1.00 36.72 O +ATOM 917 OD2 ASP A 119 -8.349 35.190 6.315 1.00 41.26 O +ATOM 918 N VAL A 120 -6.836 33.291 10.750 1.00 20.10 N +ATOM 919 CA VAL A 120 -6.637 31.835 10.895 1.00 24.77 C +ATOM 920 C VAL A 120 -7.664 31.011 10.149 1.00 16.15 C +ATOM 921 O VAL A 120 -7.486 29.777 9.914 1.00 13.85 O +ATOM 922 CB VAL A 120 -6.476 31.372 12.367 1.00 15.61 C +ATOM 923 CG1 VAL A 120 -5.271 32.055 13.060 1.00 17.17 C +ATOM 924 CG2 VAL A 120 -7.761 31.691 13.097 1.00 18.96 C +ATOM 925 N GLN A 121 -8.761 31.679 9.776 1.00 18.05 N +ATOM 926 CA GLN A 121 -9.808 30.981 9.039 1.00 20.34 C +ATOM 927 C GLN A 121 -9.285 30.499 7.694 1.00 14.19 C +ATOM 928 O GLN A 121 -9.831 29.566 7.093 1.00 15.61 O +ATOM 929 CB GLN A 121 -10.896 31.993 8.746 1.00 39.58 C +ATOM 930 CG GLN A 121 -12.076 31.743 9.628 1.00 39.30 C +ATOM 931 CD GLN A 121 -13.286 31.887 8.785 1.00 58.93 C +ATOM 932 OE1 GLN A 121 -13.734 30.908 8.174 1.00 64.91 O +ATOM 933 NE2 GLN A 121 -13.757 33.131 8.683 1.00 55.29 N +ATOM 934 N ALA A 122 -8.222 31.161 7.229 1.00 14.53 N +ATOM 935 CA ALA A 122 -7.588 30.777 5.964 1.00 13.31 C +ATOM 936 C ALA A 122 -7.152 29.312 5.955 1.00 18.32 C +ATOM 937 O ALA A 122 -7.123 28.622 4.924 1.00 14.96 O +ATOM 938 CB ALA A 122 -6.378 31.657 5.724 1.00 18.92 C +ATOM 939 N TRP A 123 -6.792 28.829 7.138 1.00 14.16 N +ATOM 940 CA TRP A 123 -6.304 27.460 7.305 1.00 21.27 C +ATOM 941 C TRP A 123 -7.326 26.369 7.031 1.00 12.05 C +ATOM 942 O TRP A 123 -6.976 25.209 6.736 1.00 15.94 O +ATOM 943 CB TRP A 123 -5.545 27.274 8.649 1.00 14.43 C +ATOM 944 CG TRP A 123 -4.302 28.098 8.663 1.00 16.32 C +ATOM 945 CD1 TRP A 123 -4.115 29.310 9.238 1.00 16.23 C +ATOM 946 CD2 TRP A 123 -3.066 27.733 8.045 1.00 6.26 C +ATOM 947 NE1 TRP A 123 -2.826 29.737 8.996 1.00 13.70 N +ATOM 948 CE2 TRP A 123 -2.184 28.799 8.248 1.00 10.20 C +ATOM 949 CE3 TRP A 123 -2.680 26.618 7.323 1.00 14.76 C +ATOM 950 CZ2 TRP A 123 -0.873 28.742 7.761 1.00 21.80 C +ATOM 951 CZ3 TRP A 123 -1.413 26.574 6.804 1.00 21.47 C +ATOM 952 CH2 TRP A 123 -0.520 27.623 7.023 1.00 22.40 C +ATOM 953 N ILE A 124 -8.590 26.696 7.126 1.00 10.36 N +ATOM 954 CA ILE A 124 -9.573 25.659 6.831 1.00 14.89 C +ATOM 955 C ILE A 124 -10.353 25.927 5.530 1.00 16.52 C +ATOM 956 O ILE A 124 -11.277 25.213 5.172 1.00 16.40 O +ATOM 957 CB ILE A 124 -10.480 25.421 8.019 1.00 15.33 C +ATOM 958 CG1 ILE A 124 -11.016 26.778 8.456 1.00 15.55 C +ATOM 959 CG2 ILE A 124 -9.624 24.846 9.164 1.00 15.50 C +ATOM 960 CD1 ILE A 124 -12.489 26.742 8.908 1.00 32.95 C +ATOM 961 N ARG A 125 -9.977 27.003 4.848 1.00 17.59 N +ATOM 962 CA ARG A 125 -10.598 27.366 3.586 1.00 26.87 C +ATOM 963 C ARG A 125 -10.424 26.259 2.569 1.00 18.05 C +ATOM 964 O ARG A 125 -9.339 25.658 2.433 1.00 24.03 O +ATOM 965 CB ARG A 125 -10.123 28.708 3.068 1.00 29.23 C +ATOM 966 CG ARG A 125 -10.586 29.089 1.669 1.00 46.98 C +ATOM 967 CD ARG A 125 -10.321 30.571 1.370 1.00 51.79 C +ATOM 968 NE ARG A 125 -8.921 30.857 1.669 1.00 80.40 N +ATOM 969 CZ ARG A 125 -7.924 30.424 0.892 1.00 80.57 C +ATOM 970 NH1 ARG A 125 -8.167 29.752 -0.234 1.00 50.97 N +ATOM 971 NH2 ARG A 125 -6.657 30.677 1.239 1.00 73.99 N +ATOM 972 N GLY A 126 -11.581 25.957 1.917 1.00 23.54 N +ATOM 973 CA GLY A 126 -11.741 24.959 0.858 1.00 15.85 C +ATOM 974 C GLY A 126 -11.903 23.570 1.356 1.00 22.07 C +ATOM 975 O GLY A 126 -11.988 22.638 0.564 1.00 33.97 O +ATOM 976 N CYS A 127 -11.912 23.409 2.685 1.00 12.41 N +ATOM 977 CA CYS A 127 -12.009 22.059 3.164 1.00 10.52 C +ATOM 978 C CYS A 127 -13.442 21.578 3.291 1.00 13.96 C +ATOM 979 O CYS A 127 -14.383 22.316 3.676 1.00 19.22 O +ATOM 980 CB CYS A 127 -11.259 21.795 4.516 1.00 16.08 C +ATOM 981 SG CYS A 127 -9.562 22.365 4.503 1.00 17.92 S +ATOM 982 N ARG A 128 -13.609 20.299 3.023 1.00 19.23 N +ATOM 983 CA ARG A 128 -14.929 19.757 3.200 1.00 29.52 C +ATOM 984 C ARG A 128 -15.116 19.387 4.645 1.00 19.23 C +ATOM 985 O ARG A 128 -14.626 18.345 5.078 1.00 29.24 O +ATOM 986 CB ARG A 128 -15.159 18.511 2.363 1.00 35.15 C +ATOM 987 CG ARG A 128 -16.602 18.043 2.481 1.00 32.92 C +ATOM 988 CD ARG A 128 -16.961 17.187 1.277 1.00 38.70 C +ATOM 989 NE ARG A 128 -15.779 16.498 0.721 1.00 50.55 N +ATOM 990 CZ ARG A 128 -15.503 16.208 -0.581 1.00 55.70 C +ATOM 991 NH1 ARG A 128 -16.293 16.551 -1.610 1.00 46.94 N +ATOM 992 NH2 ARG A 128 -14.377 15.541 -0.856 1.00 48.25 N +ATOM 993 N LEU A 129 -15.775 20.226 5.404 1.00 22.75 N +ATOM 994 CA LEU A 129 -15.976 19.869 6.811 1.00 33.38 C +ATOM 995 C LEU A 129 -17.449 19.906 7.141 1.00 72.70 C +ATOM 996 O LEU A 129 -18.191 20.465 6.277 1.00 49.87 O +ATOM 997 CB LEU A 129 -15.235 20.742 7.845 1.00 23.67 C +ATOM 998 CG LEU A 129 -13.711 20.917 7.641 1.00 28.34 C +ATOM 999 CD1 LEU A 129 -13.308 22.315 8.150 1.00 36.38 C +ATOM 1000 CD2 LEU A 129 -12.970 19.868 8.434 1.00 43.93 C +ATOM 1001 OXT LEU A 129 -17.769 19.416 8.251 1.00 70.56 O +TER 1002 LEU A 129 +HETATM 1003 O HOH A 131 10.467 23.310 29.307 1.00 39.80 O +HETATM 1004 O HOH A 132 -1.176 15.339 1.263 1.00 49.26 O +HETATM 1005 O HOH A 133 -2.951 23.272 0.888 1.00 44.65 O +HETATM 1006 O HOH A 134 1.217 11.752 36.245 1.00 47.43 O +HETATM 1007 O HOH A 135 -5.565 19.565 2.145 1.00 30.47 O +HETATM 1008 O HOH A 136 -8.561 15.857 2.186 1.00 67.45 O +HETATM 1009 O HOH A 137 -11.371 18.534 1.797 1.00 29.55 O +HETATM 1010 O HOH A 138 -5.769 17.371 2.752 1.00 20.51 O +HETATM 1011 O HOH A 139 -1.154 20.600 3.261 1.00 38.26 O +HETATM 1012 O HOH A 140 -14.391 27.317 2.971 1.00 41.99 O +HETATM 1013 O HOH A 141 9.925 21.314 4.349 1.00 72.67 O +HETATM 1014 O HOH A 142 -3.255 29.381 4.245 1.00 58.91 O +HETATM 1015 O HOH A 143 -1.469 12.396 4.494 1.00 45.35 O +HETATM 1016 O HOH A 144 1.369 18.410 4.770 1.00 33.99 O +HETATM 1017 O HOH A 145 -13.995 24.766 5.080 1.00 22.81 O +HETATM 1018 O HOH A 146 -11.877 17.908 5.201 1.00 33.63 O +HETATM 1019 O HOH A 147 3.579 19.755 5.269 1.00 28.71 O +HETATM 1020 O HOH A 148 -0.938 23.757 3.720 1.00 71.21 O +HETATM 1021 O HOH A 149 2.851 10.418 5.675 1.00 22.01 O +HETATM 1022 O HOH A 150 6.153 10.387 6.792 1.00 23.16 O +HETATM 1023 O HOH A 151 -4.154 33.433 7.551 1.00 36.56 O +HETATM 1024 O HOH A 152 -2.892 31.523 5.422 1.00 70.64 O +HETATM 1025 O HOH A 153 8.184 17.799 8.234 1.00 52.27 O +HETATM 1026 O HOH A 154 7.851 28.286 8.261 1.00 20.33 O +HETATM 1027 O HOH A 155 -0.327 32.726 8.576 1.00 42.08 O +HETATM 1028 O HOH A 156 -7.096 11.131 8.405 1.00 40.02 O +HETATM 1029 O HOH A 157 -3.462 37.549 8.393 1.00 46.77 O +HETATM 1030 O HOH A 158 -8.809 13.307 8.142 1.00 30.47 O +HETATM 1031 O HOH A 159 -0.082 35.568 8.883 1.00 34.44 O +HETATM 1032 O HOH A 160 5.759 11.110 9.448 1.00 12.55 O +HETATM 1033 O HOH A 161 1.655 33.826 9.694 1.00 24.07 O +HETATM 1034 O HOH A 162 -2.547 32.477 9.746 1.00 26.29 O +HETATM 1035 O HOH A 163 4.474 33.152 9.881 1.00 17.58 O +HETATM 1036 O HOH A 164 3.338 7.494 10.654 1.00 33.32 O +HETATM 1037 O HOH A 165 8.193 18.034 10.710 1.00 21.87 O +HETATM 1038 O HOH A 166 7.329 25.034 11.046 1.00 35.50 O +HETATM 1039 O HOH A 167 -14.609 15.459 10.822 1.00 40.68 O +HETATM 1040 O HOH A 168 -10.475 34.131 10.612 1.00 52.70 O +HETATM 1041 O HOH A 169 2.254 4.105 11.205 1.00 64.88 O +HETATM 1042 O HOH A 170 8.719 22.583 10.964 1.00 48.95 O +HETATM 1043 O HOH A 171 -11.115 29.055 11.946 1.00 14.76 O +HETATM 1044 O HOH A 172 -13.874 27.050 11.990 1.00 53.84 O +HETATM 1045 O HOH A 173 -5.674 10.727 13.313 1.00 39.68 O +HETATM 1046 O HOH A 174 -11.999 31.072 12.630 1.00 63.32 O +HETATM 1047 O HOH A 175 -17.134 26.536 21.794 1.00 62.44 O +HETATM 1048 O HOH A 176 10.318 19.087 12.648 1.00 26.21 O +HETATM 1049 O HOH A 177 -6.214 5.635 13.140 1.00 68.62 O +HETATM 1050 O HOH A 178 4.038 7.633 13.524 1.00 23.33 O +HETATM 1051 O HOH A 179 -3.450 4.975 13.407 1.00 49.46 O +HETATM 1052 O HOH A 180 -7.339 10.569 14.831 1.00 42.40 O +HETATM 1053 O HOH A 181 7.627 28.588 14.215 1.00 19.60 O +HETATM 1054 O HOH A 182 1.193 5.002 14.601 1.00 41.13 O +HETATM 1055 O HOH A 183 -8.623 6.412 17.116 1.00 59.00 O +HETATM 1056 O HOH A 184 9.260 21.322 13.868 1.00 48.09 O +HETATM 1057 O HOH A 185 -16.033 21.080 23.763 1.00 60.47 O +HETATM 1058 O HOH A 186 11.590 13.479 14.940 1.00 13.69 O +HETATM 1059 O HOH A 187 -6.668 35.428 15.178 1.00 31.78 O +HETATM 1060 O HOH A 188 -4.892 -0.201 15.033 1.00 72.09 O +HETATM 1061 O HOH A 189 1.858 30.674 4.862 1.00 56.21 O +HETATM 1062 O HOH A 190 -10.895 36.814 14.982 1.00 35.20 O +HETATM 1063 O HOH A 191 0.992 36.275 15.433 1.00 18.46 O +HETATM 1064 O HOH A 192 4.392 4.463 15.873 1.00 37.98 O +HETATM 1065 O HOH A 193 -9.880 33.178 15.826 1.00 28.17 O +HETATM 1066 O HOH A 194 9.025 23.955 15.613 1.00 37.22 O +HETATM 1067 O HOH A 195 -7.206 38.395 16.256 1.00 55.89 O +HETATM 1068 O HOH A 196 -0.377 36.589 25.905 1.00 34.65 O +HETATM 1069 O HOH A 197 -14.982 19.034 22.737 1.00 64.15 O +HETATM 1070 O HOH A 198 -0.223 12.099 16.607 1.00 28.04 O +HETATM 1071 O HOH A 199 -6.317 33.838 16.796 1.00 22.79 O +HETATM 1072 O HOH A 200 8.078 31.375 16.915 1.00 10.01 O +HETATM 1073 O HOH A 201 1.489 13.820 17.020 1.00 21.39 O +HETATM 1074 O HOH A 202 9.131 28.844 17.354 1.00 52.49 O +HETATM 1075 O HOH A 203 14.994 15.102 18.263 1.00 53.36 O +HETATM 1076 O HOH A 204 15.333 22.227 18.703 1.00 50.97 O +HETATM 1077 O HOH A 205 16.093 18.390 18.034 1.00 33.35 O +HETATM 1078 O HOH A 206 3.768 6.469 18.636 1.00 38.13 O +HETATM 1079 O HOH A 207 -13.347 18.342 27.796 1.00 58.07 O +HETATM 1080 O HOH A 208 -14.200 9.443 18.914 1.00 81.98 O +HETATM 1081 O HOH A 209 9.257 22.574 18.988 1.00 22.39 O +HETATM 1082 O HOH A 210 4.907 37.823 19.024 1.00 41.16 O +HETATM 1083 O HOH A 211 -1.433 4.723 19.249 1.00 62.14 O +HETATM 1084 O HOH A 212 -1.071 11.315 19.089 1.00 15.91 O +HETATM 1085 O HOH A 213 -3.235 8.498 19.677 1.00 21.40 O +HETATM 1086 O HOH A 214 7.620 25.081 19.861 1.00 35.14 O +HETATM 1087 O HOH A 215 1.711 16.542 19.779 1.00 9.12 O +HETATM 1088 O HOH A 216 11.204 23.310 20.531 1.00 44.08 O +HETATM 1089 O HOH A 217 -0.792 7.051 20.523 1.00 25.44 O +HETATM 1090 O HOH A 219 -11.306 12.254 20.909 1.00 58.87 O +HETATM 1091 O HOH A 220 -15.497 22.071 20.968 1.00 42.59 O +HETATM 1092 O HOH A 221 -14.046 13.904 22.148 1.00 59.61 O +HETATM 1093 O HOH A 222 5.919 23.529 21.973 1.00 36.31 O +HETATM 1094 O HOH A 223 5.611 26.207 22.382 1.00 26.89 O +HETATM 1095 O HOH A 224 8.793 23.775 23.737 1.00 53.46 O +HETATM 1096 O HOH A 225 -14.958 24.195 25.086 1.00 26.18 O +HETATM 1097 O HOH A 226 -14.258 17.077 24.576 1.00 42.15 O +HETATM 1098 O HOH A 227 3.901 21.949 25.503 1.00 15.15 O +HETATM 1099 O HOH A 228 -17.138 15.370 26.017 1.00 64.87 O +HETATM 1100 O HOH A 229 1.041 39.543 25.118 1.00 75.63 O +HETATM 1101 O HOH A 230 -18.171 19.097 19.147 1.00 58.24 O +HETATM 1102 O HOH A 231 19.800 18.720 25.766 1.00 41.96 O +HETATM 1103 O HOH A 232 13.910 14.986 26.681 1.00 11.69 O +HETATM 1104 O HOH A 233 4.284 26.127 26.885 1.00 44.36 O +HETATM 1105 O HOH A 234 14.969 25.124 27.122 1.00 37.22 O +HETATM 1106 O HOH A 235 19.235 28.375 27.869 1.00 51.94 O +HETATM 1107 O HOH A 236 -8.227 15.787 27.736 1.00 28.71 O +HETATM 1108 O HOH A 237 11.129 29.398 26.784 1.00 53.97 O +HETATM 1109 O HOH A 238 -2.152 26.984 28.613 1.00 25.16 O +HETATM 1110 O HOH A 239 -12.126 14.584 29.332 1.00 70.39 O +HETATM 1111 O HOH A 240 -6.410 28.639 29.739 1.00 33.78 O +HETATM 1112 O HOH A 241 -9.363 18.929 29.236 1.00 54.93 O +HETATM 1113 O HOH A 242 7.290 6.035 29.744 1.00 44.70 O +HETATM 1114 O HOH A 243 0.532 4.323 25.856 1.00 66.97 O +HETATM 1115 O HOH A 244 -5.527 11.769 31.278 1.00 52.96 O +HETATM 1116 O HOH A 245 9.709 13.211 30.865 1.00 15.87 O +HETATM 1117 O HOH A 246 -5.539 14.098 29.938 1.00 63.37 O +HETATM 1118 O HOH A 247 2.285 7.164 31.744 1.00 42.72 O +HETATM 1119 O HOH A 249 2.557 37.778 32.502 1.00 60.66 O +HETATM 1120 O HOH A 250 11.653 11.933 32.683 1.00 24.19 O +HETATM 1121 O HOH A 251 -2.007 6.140 23.286 1.00 48.50 O +HETATM 1122 O HOH A 252 7.578 12.160 33.759 1.00 39.59 O +HETATM 1123 O HOH A 253 14.454 7.531 33.771 1.00 35.83 O +HETATM 1124 O HOH A 254 -3.513 31.619 34.652 1.00 56.09 O +HETATM 1125 O HOH A 255 13.552 10.709 34.982 1.00 58.90 O +HETATM 1126 O HOH A 256 -0.456 24.995 36.970 1.00 68.09 O +HETATM 1127 O HOH A 257 -2.238 9.934 2.797 1.00 67.44 O +HETATM 1128 O HOH A 258 -7.483 20.739 37.397 1.00 68.20 O +HETATM 1129 O HOH A 259 16.885 30.334 28.147 1.00 50.66 O +HETATM 1130 O HOH A 260 -2.189 19.144 1.123 1.00 56.23 O +HETATM 1131 O HOH A 263 5.554 35.805 21.621 1.00 47.47 O +HETATM 1132 O HOH A 264 0.167 38.321 22.074 1.00 63.57 O +HETATM 1133 O HOH A 265 2.643 23.311 24.222 1.00 37.06 O +HETATM 1134 O HOH A 266 -3.261 12.368 26.079 1.00 36.01 O +HETATM 1135 O HOH A 267 -8.163 28.523 28.227 1.00 31.53 O +HETATM 1136 O HOH A 268 11.314 34.308 29.649 1.00 69.35 O +HETATM 1137 O HOH A 269 -8.925 18.710 -0.425 1.00 67.80 O +HETATM 1138 O HOH A 270 1.106 7.975 2.503 1.00 57.87 O +HETATM 1139 O HOH A 271 3.658 14.557 2.346 1.00 58.10 O +HETATM 1140 O HOH A 272 5.462 18.910 4.058 1.00 56.45 O +HETATM 1141 O HOH A 273 -12.194 34.778 7.299 1.00 56.09 O +HETATM 1142 O HOH A 274 -1.696 6.065 8.495 1.00 68.76 O +HETATM 1143 O HOH A 275 -12.182 12.057 9.624 1.00 89.37 O +HETATM 1144 O HOH A 276 -17.165 32.342 9.988 1.00 67.99 O +HETATM 1145 O HOH A 277 -0.310 4.774 9.964 1.00 51.58 O +HETATM 1146 O HOH A 278 -18.106 6.723 19.155 1.00 64.11 O +HETATM 1147 O HOH A 279 -10.523 7.855 18.757 1.00 55.12 O +HETATM 1148 O HOH A 280 -5.786 9.627 24.788 1.00 56.60 O +HETATM 1149 O HOH A 281 4.973 30.366 26.631 1.00 56.27 O +HETATM 1150 O HOH A 282 -14.163 23.294 27.041 1.00 80.21 O +HETATM 1151 O HOH A 283 4.190 23.920 28.202 1.00 47.07 O +HETATM 1152 O HOH A 284 1.927 24.235 28.261 1.00 53.05 O +HETATM 1153 O HOH A 285 8.469 24.914 28.323 1.00 76.29 O +HETATM 1154 O HOH A 286 0.504 26.234 30.223 1.00 48.47 O +HETATM 1155 O HOH A 287 4.961 6.376 30.326 1.00 57.17 O +HETATM 1156 O HOH A 288 -9.395 28.233 30.605 1.00 55.86 O +HETATM 1157 O HOH A 289 -7.403 29.010 31.768 1.00 58.13 O +HETATM 1158 O HOH A 290 17.262 22.252 32.977 1.00 32.13 O +HETATM 1159 O HOH A 291 -13.958 24.749 32.936 1.00 40.16 O +HETATM 1160 O HOH A 292 11.050 6.576 33.893 1.00 53.38 O +HETATM 1161 O HOH A 293 -6.940 30.679 34.967 1.00 57.95 O +HETATM 1162 O HOH A 294 -7.751 19.631 32.932 1.00 55.95 O +HETATM 1163 O HOH A 295 -11.917 25.473 35.232 1.00 70.62 O +HETATM 1164 O HOH A 296 -0.614 22.162 37.001 1.00 49.79 O +HETATM 1165 O HOH A 297 -5.763 25.243 36.097 1.00 78.09 O +HETATM 1166 O HOH A 298 -0.024 14.493 36.828 1.00 63.91 O +HETATM 1167 O HOH A 299 0.443 17.296 2.028 1.00 52.55 O +HETATM 1168 O HOH A 300 1.738 27.507 3.463 1.00 74.82 O +HETATM 1169 O HOH A 301 3.836 11.760 3.259 1.00 57.42 O +HETATM 1170 O HOH A 302 -9.211 4.115 14.687 1.00 48.13 O +HETATM 1171 O HOH A 303 16.205 21.210 16.009 1.00 69.59 O +HETATM 1172 O HOH A 304 -14.845 6.428 21.717 1.00 61.77 O +HETATM 1173 O HOH A 305 -13.311 8.488 24.665 1.00 62.09 O +HETATM 1174 O HOH A 306 8.880 27.820 26.816 1.00 71.28 O +HETATM 1175 O HOH A 307 0.932 10.327 2.387 1.00 62.28 O +HETATM 1176 O HOH A 308 -32.793 6.518 16.878 1.00 55.27 O +HETATM 1177 O HOH A 309 -10.109 33.422 4.951 1.00 51.37 O +HETATM 1178 O HOH A 310 -6.930 35.720 3.927 1.00 68.08 O +HETATM 1179 O HOH A 311 -1.458 29.021 31.741 1.00 71.39 O +HETATM 1180 O HOH A 312 -7.776 27.408 33.976 1.00 51.50 O +HETATM 1181 O HOH A 313 2.002 13.196 3.708 1.00 54.99 O +HETATM 1182 O HOH A 314 7.005 28.792 27.719 1.00 69.52 O +HETATM 1183 O HOH A 315 -14.736 20.042 16.788 1.00 37.49 O +HETATM 1184 O HOH A 316 17.457 15.414 26.607 1.00 36.58 O +HETATM 1185 O HOH A 317 1.388 37.676 19.438 1.00 42.27 O +HETATM 1186 O HOH A 318 12.884 12.733 37.805 0.50 65.31 O +HETATM 1187 O HOH A 319 7.795 26.278 15.645 1.00 44.16 O +CONECT 48 981 +CONECT 238 889 +CONECT 513 630 +CONECT 601 724 +CONECT 630 513 +CONECT 724 601 +CONECT 889 238 +CONECT 981 48 +MASTER 294 0 0 7 3 0 0 6 1186 1 8 10 +END diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map new file mode 100644 index 00000000..3c638013 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/map.map @@ -0,0 +1,1275 @@ + CONTACT MAPS FROM PDB FILES + + This software is written by: + Rodrigo Azevedo Moreira da Silva + + Copyright (c) 2020 - IPPT-PAN + Institute of Fundamental Techonological Research + Polish Academy of Sciences + MIT LICENSE, check out LICENSE for more informations. + +Reading file: ../aa.pdb +pdb natoms: 1001 +pdb nresidues: 129 +Memory usage: 6.38 MB +UNMAPPED ATOM LEU OXT +Fibonacci grid: 610 +ALPHA: 1.24 +WATER_RADIUS: 2.80 + +Residue-Residue Contacts + +ID - atom identification +I1,I2 - serial residue id +AA - 3-letter code of aminoacid +C - chain +I(PDB) - residue number in PDB file +DCA - distance between CA +CMs - OV , CSU , oCSU , rCSU + (CSU does not take into account chemical properties of atoms) +rCSU - net contact from rCSU +Count - number of contacts between residues +MODEL - model number + + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model +============================================================================================ +R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 +R 2 1 LYS A 1 3 PHE A 3 6.0948 1 1 1 0 -13 106 0 +R 3 1 LYS A 1 7 GLU A 7 11.4807 1 1 1 1 121 225 0 +R 4 1 LYS A 1 38 PHE A 38 8.1596 1 1 0 0 -12 12 0 +R 5 1 LYS A 1 39 ASN A 39 5.7421 1 0 0 0 0 0 0 +R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 +R 7 1 LYS A 1 41 GLN A 41 6.8324 1 1 0 0 -112 118 0 +R 8 1 LYS A 1 86 SER A 86 5.1894 1 1 1 0 -53 161 0 +R 9 2 VAL A 2 1 LYS A 1 3.8094 1 1 0 0 -21 386 0 +R 10 2 VAL A 2 3 PHE A 3 3.7890 1 1 1 0 -32 413 0 +R 11 2 VAL A 2 4 GLY A 4 6.7958 0 1 1 1 10 14 0 +R 12 2 VAL A 2 7 GLU A 7 10.1090 0 1 0 0 -12 12 0 +R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 +R 14 2 VAL A 2 38 PHE A 38 5.5799 1 1 1 0 -20 27 0 +R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 +R 16 3 PHE A 3 1 LYS A 1 6.0948 1 1 1 0 -49 77 0 +R 17 3 PHE A 3 2 VAL A 2 3.7890 1 1 0 0 -25 380 0 +R 18 3 PHE A 3 4 GLY A 4 3.7566 1 1 1 0 -9 362 0 +R 19 3 PHE A 3 7 GLU A 7 6.3959 1 1 1 1 27 66 0 +R 20 3 PHE A 3 8 LEU A 8 5.8772 1 1 1 1 71 144 0 +R 21 3 PHE A 3 11 ALA A 11 9.8683 1 1 1 1 35 35 0 +R 22 3 PHE A 3 38 PHE A 38 5.3547 1 1 1 0 -112 144 0 +R 23 3 PHE A 3 40 THR A 40 7.9444 1 1 1 1 133 133 0 +R 24 3 PHE A 3 55 ILE A 55 9.3473 1 1 1 1 35 35 0 +R 25 3 PHE A 3 86 SER A 86 8.8941 1 1 0 0 -65 65 0 +R 26 3 PHE A 3 88 ILE A 88 10.4372 1 1 1 1 102 102 0 +R 27 4 GLY A 4 2 VAL A 2 6.7958 0 1 1 1 6 11 0 +R 28 4 GLY A 4 3 PHE A 3 3.7566 1 1 0 0 -1 353 0 +R 29 4 GLY A 4 5 ARG A 5 3.7804 1 1 1 1 24 382 0 +R 30 4 GLY A 4 6 CYS A 6 5.6551 1 1 0 0 0 9 0 +R 31 4 GLY A 4 7 GLU A 7 5.1677 1 1 1 1 39 78 0 +R 32 4 GLY A 4 8 LEU A 8 6.0824 1 1 1 1 97 105 0 +R 33 4 GLY A 4 38 PHE A 38 7.2869 0 1 0 0 0 2 0 +R 34 5 ARG A 5 3 PHE A 3 6.3853 0 1 1 1 10 10 0 +R 35 5 ARG A 5 4 GLY A 4 3.7804 1 1 0 0 0 324 0 +R 36 5 ARG A 5 6 CYS A 6 3.8229 1 1 1 1 16 405 0 +R 37 5 ARG A 5 7 GLU A 7 5.6256 1 0 0 0 0 0 0 +R 38 5 ARG A 5 8 LEU A 8 5.4514 1 1 0 0 -5 5 0 +R 39 5 ARG A 5 9 ALA A 9 6.3068 1 1 1 1 111 121 0 +R 40 5 ARG A 5 29 VAL A 29 7.3410 1 0 0 0 0 0 0 +R 41 5 ARG A 5 38 PHE A 38 7.6636 1 1 1 1 72 111 0 +R 42 5 ARG A 5 122 ALA A 122 10.7979 1 1 1 1 15 21 0 +R 43 5 ARG A 5 123 TRP A 123 7.4230 1 1 1 1 80 312 0 +R 44 5 ARG A 5 124 ILE A 124 7.5648 1 0 0 0 0 0 0 +R 45 5 ARG A 5 125 ARG A 125 9.6347 1 1 1 1 135 211 0 +R 46 5 ARG A 5 126 GLY A 126 10.0418 0 1 0 0 -1 13 0 +R 47 5 ARG A 5 127 CYS A 127 8.4264 1 1 0 0 0 21 0 +R 48 6 CYS A 6 4 GLY A 4 5.6551 1 1 0 0 0 2 0 +R 49 6 CYS A 6 5 ARG A 5 3.8229 1 1 0 0 -20 442 0 +R 50 6 CYS A 6 7 GLU A 7 3.7935 1 1 1 0 -3 369 0 +R 51 6 CYS A 6 8 LEU A 8 5.3320 1 0 0 0 0 0 0 +R 52 6 CYS A 6 9 ALA A 9 4.8870 1 0 0 0 0 0 0 +R 53 6 CYS A 6 10 ALA A 10 6.1316 1 1 1 1 85 131 0 +R 54 6 CYS A 6 126 GLY A 126 7.9731 0 1 0 0 0 12 0 +R 55 6 CYS A 6 127 CYS A 127 5.3179 1 1 1 1 23 264 0 +R 56 6 CYS A 6 128 ARG A 128 7.4354 0 1 0 0 -14 14 0 +R 57 7 GLU A 7 1 LYS A 1 11.4807 1 1 1 1 153 207 0 +R 58 7 GLU A 7 2 VAL A 2 10.1090 0 1 0 0 -7 7 0 +R 59 7 GLU A 7 3 PHE A 3 6.3959 1 1 1 1 29 30 0 +R 60 7 GLU A 7 4 GLY A 4 5.1677 1 1 1 1 95 139 0 +R 61 7 GLU A 7 5 ARG A 5 5.6256 1 0 0 0 0 0 0 +R 62 7 GLU A 7 6 CYS A 6 3.7935 1 1 1 0 -23 363 0 +R 63 7 GLU A 7 8 LEU A 8 3.8230 1 1 1 1 10 347 0 +R 64 7 GLU A 7 9 ALA A 9 5.5273 1 0 0 0 0 0 0 +R 65 7 GLU A 7 10 ALA A 10 5.2583 1 1 1 1 2 28 0 +R 66 7 GLU A 7 11 ALA A 11 6.3196 1 1 1 1 115 119 0 +R 67 8 LEU A 8 3 PHE A 3 5.8772 1 1 1 1 56 64 0 +R 68 8 LEU A 8 4 GLY A 4 6.0824 1 1 1 0 -47 63 0 +R 69 8 LEU A 8 5 ARG A 5 5.4514 1 1 0 0 -5 5 0 +R 70 8 LEU A 8 6 CYS A 6 5.3320 1 0 0 0 0 0 0 +R 71 8 LEU A 8 7 GLU A 7 3.8230 1 1 0 0 -20 356 0 +R 72 8 LEU A 8 9 ALA A 9 3.8041 1 1 1 1 10 355 0 +R 73 8 LEU A 8 10 ALA A 10 5.3454 1 0 0 0 0 0 0 +R 74 8 LEU A 8 11 ALA A 11 5.0036 1 0 0 0 0 0 0 +R 75 8 LEU A 8 12 MET A 12 6.0331 1 1 1 1 189 211 0 +R 76 8 LEU A 8 29 VAL A 29 7.2217 0 1 1 1 1 1 0 +R 77 8 LEU A 8 32 ALA A 32 8.9719 1 1 1 1 78 78 0 +R 78 8 LEU A 8 38 PHE A 38 7.9077 1 1 1 1 168 168 0 +R 79 8 LEU A 8 55 ILE A 55 10.0426 1 1 1 1 102 102 0 +R 80 8 LEU A 8 88 ILE A 88 9.1166 1 1 1 1 16 16 0 +R 81 9 ALA A 9 5 ARG A 5 6.3068 1 1 1 0 -49 77 0 +R 82 9 ALA A 9 6 CYS A 6 4.8870 1 1 0 0 -20 30 0 +R 83 9 ALA A 9 7 GLU A 7 5.5273 1 0 0 0 0 0 0 +R 84 9 ALA A 9 8 LEU A 8 3.8041 1 1 0 0 -13 342 0 +R 85 9 ALA A 9 10 ALA A 10 3.8152 1 1 1 1 4 325 0 +R 86 9 ALA A 9 11 ALA A 11 5.5040 1 0 0 0 0 0 0 +R 87 9 ALA A 9 12 MET A 12 5.2438 1 0 0 0 0 0 0 +R 88 9 ALA A 9 13 LYS A 13 6.0508 1 1 1 1 121 177 0 +R 89 9 ALA A 9 25 LEU A 25 6.8785 1 1 0 0 -1 1 0 +R 90 9 ALA A 9 29 VAL A 29 6.2031 1 1 1 1 65 103 0 +R 91 9 ALA A 9 124 ILE A 124 6.6308 1 1 1 1 91 91 0 +R 92 9 ALA A 9 129 LEU A 129 7.9700 1 1 1 1 31 31 0 +R 93 10 ALA A 10 6 CYS A 6 6.1316 1 1 1 0 -57 71 0 +R 94 10 ALA A 10 7 GLU A 7 5.2583 1 1 1 0 -14 35 0 +R 95 10 ALA A 10 8 LEU A 8 5.3454 1 0 0 0 0 0 0 +R 96 10 ALA A 10 9 ALA A 9 3.8152 1 1 0 0 -12 348 0 +R 97 10 ALA A 10 11 ALA A 11 3.7870 1 1 1 1 4 363 0 +R 98 10 ALA A 10 12 MET A 12 5.5577 1 0 0 0 0 0 0 +R 99 10 ALA A 10 13 LYS A 13 5.0244 1 1 0 0 -2 3 0 +R 100 10 ALA A 10 14 ARG A 14 6.0838 1 1 1 1 85 143 0 +R 101 10 ALA A 10 128 ARG A 128 7.8262 0 1 0 0 -37 37 0 +R 102 10 ALA A 10 129 LEU A 129 6.1221 1 1 1 1 42 83 0 +R 103 11 ALA A 11 3 PHE A 3 9.8683 1 1 1 1 49 49 0 +R 104 11 ALA A 11 7 GLU A 7 6.3196 1 1 1 0 -44 76 0 +R 105 11 ALA A 11 8 LEU A 8 5.0036 1 1 0 0 -13 13 0 +R 106 11 ALA A 11 9 ALA A 9 5.5040 1 0 0 0 0 0 0 +R 107 11 ALA A 11 10 ALA A 10 3.7870 1 1 0 0 -22 362 0 +R 108 11 ALA A 11 12 MET A 12 3.8044 1 1 1 1 4 329 0 +R 109 11 ALA A 11 13 LYS A 13 5.3126 1 0 0 0 0 0 0 +R 110 11 ALA A 11 14 ARG A 14 5.0202 1 1 0 0 -15 41 0 +R 111 11 ALA A 11 15 HIS A 15 6.1372 1 1 1 1 176 196 0 +R 112 11 ALA A 11 88 ILE A 88 7.9512 1 1 1 1 91 91 0 +R 113 12 MET A 12 8 LEU A 8 6.0331 1 1 1 1 81 189 0 +R 114 12 MET A 12 9 ALA A 9 5.2438 1 1 0 0 -12 12 0 +R 115 12 MET A 12 10 ALA A 10 5.5577 1 0 0 0 0 0 0 +R 116 12 MET A 12 11 ALA A 11 3.8044 1 1 0 0 -10 337 0 +R 117 12 MET A 12 13 LYS A 13 3.8273 1 1 1 0 0 351 0 +R 118 12 MET A 12 14 ARG A 14 5.4173 1 0 0 0 0 0 0 +R 119 12 MET A 12 15 HIS A 15 4.8856 1 1 1 1 55 59 0 +R 120 12 MET A 12 16 GLY A 16 6.5249 1 1 1 1 1 1 0 +R 121 12 MET A 12 17 LEU A 17 5.4690 1 1 1 1 162 162 0 +R 122 12 MET A 12 25 LEU A 25 7.5662 1 1 1 1 34 34 0 +R 123 12 MET A 12 28 TRP A 28 7.8689 1 1 1 0 -80 205 0 +R 124 12 MET A 12 29 VAL A 29 8.1611 1 1 0 0 0 12 0 +R 125 12 MET A 12 32 ALA A 32 10.4631 1 1 1 1 31 31 0 +R 126 12 MET A 12 55 ILE A 55 11.3010 0 1 1 1 3 3 0 +R 127 12 MET A 12 56 LEU A 56 11.5983 1 1 1 1 52 52 0 +R 128 12 MET A 12 88 ILE A 88 8.1191 1 1 1 1 12 26 0 +R 129 13 LYS A 13 9 ALA A 9 6.0508 1 1 1 0 -47 63 0 +R 130 13 LYS A 13 10 ALA A 10 5.0244 1 1 0 0 -13 13 0 +R 131 13 LYS A 13 11 ALA A 11 5.3126 1 0 0 0 0 0 0 +R 132 13 LYS A 13 12 MET A 12 3.8273 1 1 0 0 -22 349 0 +R 133 13 LYS A 13 14 ARG A 14 3.7179 1 1 1 1 4 358 0 +R 134 13 LYS A 13 15 HIS A 15 5.2265 1 0 0 0 0 0 0 +R 135 13 LYS A 13 16 GLY A 16 5.3557 1 1 1 1 71 90 0 +R 136 13 LYS A 13 18 ASP A 18 5.3900 1 1 1 1 51 92 0 +R 137 13 LYS A 13 25 LEU A 25 6.9771 1 1 1 1 52 74 0 +R 138 13 LYS A 13 129 LEU A 129 8.0834 1 1 1 1 59 161 0 +R 139 14 ARG A 14 10 ALA A 10 6.0838 1 1 1 0 -54 66 0 +R 140 14 ARG A 14 11 ALA A 11 5.0202 1 1 1 0 -14 33 0 +R 141 14 ARG A 14 12 MET A 12 5.4173 1 0 0 0 0 0 0 +R 142 14 ARG A 14 13 LYS A 13 3.7179 1 1 1 0 -16 374 0 +R 143 14 ARG A 14 15 HIS A 15 3.8028 1 1 1 0 -115 484 0 +R 144 14 ARG A 14 16 GLY A 16 5.5733 1 1 1 1 11 16 0 +R 145 14 ARG A 14 89 THR A 89 10.0339 0 1 1 1 12 12 0 +R 146 15 HIS A 15 11 ALA A 11 6.1372 1 1 1 1 67 117 0 +R 147 15 HIS A 15 12 MET A 12 4.8856 1 1 0 0 -6 6 0 +R 148 15 HIS A 15 13 LYS A 13 5.2265 1 0 0 0 0 0 0 +R 149 15 HIS A 15 14 ARG A 14 3.8028 1 1 1 0 -121 524 0 +R 150 15 HIS A 15 16 GLY A 16 3.8284 1 1 1 1 25 263 0 +R 151 15 HIS A 15 17 LEU A 17 5.8003 1 0 0 0 0 0 0 +R 152 15 HIS A 15 87 ASP A 87 10.7991 0 1 0 0 -1 1 0 +R 153 15 HIS A 15 88 ILE A 88 8.6713 1 1 1 1 35 53 0 +R 154 15 HIS A 15 89 THR A 89 7.1554 1 1 1 1 53 244 0 +R 155 15 HIS A 15 92 VAL A 92 7.1674 1 1 1 1 71 71 0 +R 156 15 HIS A 15 93 ASN A 93 8.5240 0 1 0 0 -5 5 0 +R 157 15 HIS A 15 96 LYS A 96 10.3010 1 1 1 1 191 193 0 +R 158 16 GLY A 16 12 MET A 12 6.5249 1 0 0 0 0 0 0 +R 159 16 GLY A 16 13 LYS A 13 5.3557 1 1 1 1 11 44 0 +R 160 16 GLY A 16 14 ARG A 14 5.5733 1 1 1 1 2 14 0 +R 161 16 GLY A 16 15 HIS A 15 3.8284 1 1 0 0 -32 379 0 +R 162 16 GLY A 16 17 LEU A 17 3.7882 1 1 1 1 23 340 0 +R 163 16 GLY A 16 18 ASP A 18 5.8126 1 1 1 0 -8 32 0 +R 164 16 GLY A 16 20 TYR A 20 6.7265 1 1 0 0 -129 130 0 +R 165 16 GLY A 16 96 LYS A 96 9.2491 1 1 0 0 0 24 0 +R 166 17 LEU A 17 12 MET A 12 5.4690 1 1 1 1 110 161 0 +R 167 17 LEU A 17 15 HIS A 15 5.8003 1 0 0 0 0 0 0 +R 168 17 LEU A 17 16 GLY A 16 3.7882 1 1 0 0 -18 366 0 +R 169 17 LEU A 17 18 ASP A 18 3.8027 1 1 1 1 12 357 0 +R 170 17 LEU A 17 19 ASN A 19 6.0755 1 1 1 1 30 30 0 +R 171 17 LEU A 17 20 TYR A 20 4.9158 1 1 1 1 43 43 0 +R 172 17 LEU A 17 28 TRP A 28 7.4830 1 1 1 1 217 217 0 +R 173 17 LEU A 17 92 VAL A 92 7.6268 1 1 1 1 89 89 0 +R 174 17 LEU A 17 96 LYS A 96 7.9140 1 1 1 1 155 155 0 +R 175 18 ASP A 18 13 LYS A 13 5.3900 1 1 1 1 2 165 0 +R 176 18 ASP A 18 16 GLY A 16 5.8126 1 1 0 0 -28 33 0 +R 177 18 ASP A 18 17 LEU A 17 3.8027 1 1 0 0 -35 354 0 +R 178 18 ASP A 18 19 ASN A 19 3.7747 1 1 1 1 115 510 0 +R 179 18 ASP A 18 20 TYR A 20 5.3255 1 1 1 1 5 6 0 +R 180 18 ASP A 18 24 SER A 24 5.1287 1 1 0 0 0 12 0 +R 181 18 ASP A 18 25 LEU A 25 4.4020 1 1 1 1 152 244 0 +R 182 19 ASN A 19 17 LEU A 17 6.0755 1 0 0 0 0 0 0 +R 183 19 ASN A 19 18 ASP A 18 3.7747 1 1 1 1 107 498 0 +R 184 19 ASN A 19 20 TYR A 20 3.7437 1 1 1 1 17 326 0 +R 185 19 ASN A 19 21 ARG A 21 5.8645 1 1 1 1 9 9 0 +R 186 19 ASN A 19 22 GLY A 22 4.5249 1 1 1 1 59 129 0 +R 187 19 ASN A 19 23 TYR A 23 4.4795 1 1 1 1 32 73 0 +R 188 19 ASN A 19 24 SER A 24 4.2956 1 1 1 1 9 109 0 +R 189 20 TYR A 20 16 GLY A 16 6.7265 1 1 0 0 -86 87 0 +R 190 20 TYR A 20 17 LEU A 17 4.9158 1 1 1 0 -66 84 0 +R 191 20 TYR A 20 18 ASP A 18 5.3255 1 1 0 0 0 9 0 +R 192 20 TYR A 20 19 ASN A 19 3.7437 1 1 0 0 -19 347 0 +R 193 20 TYR A 20 21 ARG A 21 3.8205 1 1 1 1 84 506 0 +R 194 20 TYR A 20 22 GLY A 22 5.3254 1 1 1 1 3 3 0 +R 195 20 TYR A 20 23 TYR A 23 5.5795 1 1 1 1 12 68 0 +R 196 20 TYR A 20 96 LYS A 96 7.7283 1 1 1 0 0 186 0 +R 197 20 TYR A 20 97 LYS A 97 10.9092 0 1 1 1 1 2 0 +R 198 20 TYR A 20 99 VAL A 99 8.7657 1 1 1 1 64 64 0 +R 199 20 TYR A 20 100 SER A 100 9.2326 1 1 1 1 87 87 0 +R 200 21 ARG A 21 19 ASN A 19 5.8645 1 1 1 1 10 10 0 +R 201 21 ARG A 21 20 TYR A 20 3.8205 1 1 1 1 40 461 0 +R 202 21 ARG A 21 22 GLY A 22 3.7772 1 1 1 1 13 344 0 +R 203 21 ARG A 21 23 TYR A 23 5.6467 1 1 1 0 -14 110 0 +R 204 21 ARG A 21 99 VAL A 99 7.5366 1 1 1 1 39 39 0 +R 205 21 ARG A 21 100 SER A 100 7.2028 1 1 1 1 180 220 0 +R 206 22 GLY A 22 19 ASN A 19 4.5249 1 1 1 1 6 85 0 +R 207 22 GLY A 22 20 TYR A 20 5.3254 1 0 0 0 0 0 0 +R 208 22 GLY A 22 21 ARG A 21 3.7772 1 1 0 0 -33 385 0 +R 209 22 GLY A 22 23 TYR A 23 3.8541 1 1 1 1 5 337 0 +R 210 22 GLY A 22 24 SER A 24 6.3302 1 1 1 1 23 31 0 +R 211 22 GLY A 22 27 ASN A 27 10.0766 0 1 1 1 5 5 0 +R 212 23 TYR A 23 19 ASN A 19 4.4795 1 1 1 1 110 110 0 +R 213 23 TYR A 23 20 TYR A 20 5.5795 1 1 0 0 -29 29 0 +R 214 23 TYR A 23 21 ARG A 21 5.6467 1 1 1 0 -120 126 0 +R 215 23 TYR A 23 22 GLY A 22 3.8541 1 1 0 0 -27 365 0 +R 216 23 TYR A 23 24 SER A 24 3.8095 1 1 1 1 20 358 0 +R 217 23 TYR A 23 25 LEU A 25 6.6706 1 0 0 0 0 0 0 +R 218 23 TYR A 23 27 ASN A 27 6.2528 1 1 0 0 -2 10 0 +R 219 23 TYR A 23 28 TRP A 28 7.5595 1 1 1 0 -54 94 0 +R 220 23 TYR A 23 99 VAL A 99 9.4052 1 1 1 1 96 96 0 +R 221 23 TYR A 23 103 ASN A 103 12.4992 0 1 1 1 16 16 0 +R 222 23 TYR A 23 104 GLY A 104 8.8920 1 1 0 0 0 47 0 +R 223 23 TYR A 23 105 MET A 105 8.1535 1 1 1 1 150 217 0 +R 224 23 TYR A 23 106 ASN A 106 11.3626 0 1 1 1 16 16 0 +R 225 23 TYR A 23 111 TRP A 111 11.4919 1 1 1 1 60 94 0 +R 226 24 SER A 24 18 ASP A 18 5.1287 1 1 0 0 0 35 0 +R 227 24 SER A 24 19 ASN A 19 4.2956 1 1 0 0 0 57 0 +R 228 24 SER A 24 22 GLY A 22 6.3302 1 1 1 1 7 14 0 +R 229 24 SER A 24 23 TYR A 23 3.8095 1 1 0 0 -10 366 0 +R 230 24 SER A 24 25 LEU A 25 3.8490 1 1 1 1 26 309 0 +R 231 24 SER A 24 26 GLY A 26 5.5205 1 1 1 1 31 37 0 +R 232 24 SER A 24 27 ASN A 27 5.6877 1 1 1 1 232 265 0 +R 233 24 SER A 24 28 TRP A 28 7.2581 1 1 0 0 -1 1 0 +R 234 24 SER A 24 120 VAL A 120 8.3132 1 1 0 0 -53 53 0 +R 235 24 SER A 24 121 GLN A 121 8.0270 0 1 0 0 -4 47 0 +R 236 25 LEU A 25 9 ALA A 9 6.8785 1 1 0 0 -75 75 0 +R 237 25 LEU A 25 12 MET A 12 7.5662 1 1 1 1 156 156 0 +R 238 25 LEU A 25 13 LYS A 13 6.9771 1 1 1 1 48 80 0 +R 239 25 LEU A 25 18 ASP A 18 4.4020 1 1 1 0 -33 86 0 +R 240 25 LEU A 25 23 TYR A 23 6.6706 1 1 1 1 3 3 0 +R 241 25 LEU A 25 24 SER A 24 3.8490 1 1 0 0 0 326 0 +R 242 25 LEU A 25 26 GLY A 26 3.8034 1 1 1 1 10 356 0 +R 243 25 LEU A 25 27 ASN A 27 5.4198 1 0 0 0 0 0 0 +R 244 25 LEU A 25 28 TRP A 28 5.3994 1 1 1 1 77 86 0 +R 245 25 LEU A 25 29 VAL A 29 6.4093 1 1 1 1 54 54 0 +R 246 25 LEU A 25 124 ILE A 124 7.3355 1 1 1 1 57 57 0 +R 247 25 LEU A 25 129 LEU A 129 10.5318 1 1 1 1 126 126 0 +R 248 26 GLY A 26 24 SER A 24 5.5205 1 1 1 1 12 16 0 +R 249 26 GLY A 26 25 LEU A 25 3.8034 1 1 0 0 -35 364 0 +R 250 26 GLY A 26 27 ASN A 27 3.8470 1 1 1 1 17 323 0 +R 251 26 GLY A 26 28 TRP A 28 5.5151 1 0 0 0 0 0 0 +R 252 26 GLY A 26 29 VAL A 29 5.1152 1 0 0 0 0 0 0 +R 253 26 GLY A 26 30 CYS A 30 5.9025 1 1 1 1 93 175 0 +R 254 26 GLY A 26 120 VAL A 120 4.8514 1 1 0 0 -1 120 0 +R 255 26 GLY A 26 123 TRP A 123 5.1305 1 0 0 0 0 0 0 +R 256 26 GLY A 26 124 ILE A 124 5.7057 1 1 0 0 -9 65 0 +R 257 27 ASN A 27 22 GLY A 22 10.0766 0 1 1 1 5 5 0 +R 258 27 ASN A 27 23 TYR A 23 6.2528 1 1 0 0 -6 33 0 +R 259 27 ASN A 27 24 SER A 24 5.6877 1 1 1 1 101 219 0 +R 260 27 ASN A 27 25 LEU A 25 5.4198 1 0 0 0 0 0 0 +R 261 27 ASN A 27 26 GLY A 26 3.8470 1 1 0 0 -20 351 0 +R 262 27 ASN A 27 28 TRP A 28 3.7858 1 1 1 1 4 333 0 +R 263 27 ASN A 27 29 VAL A 29 5.5161 1 0 0 0 0 0 0 +R 264 27 ASN A 27 30 CYS A 30 5.1016 1 0 0 0 0 0 0 +R 265 27 ASN A 27 31 ALA A 31 6.0825 1 1 1 1 119 171 0 +R 266 27 ASN A 27 105 MET A 105 8.5492 1 1 0 0 0 46 0 +R 267 27 ASN A 27 111 TRP A 111 7.6026 1 1 1 1 40 192 0 +R 268 27 ASN A 27 116 LYS A 116 7.7579 0 1 0 0 0 1 0 +R 269 27 ASN A 27 120 VAL A 120 5.7252 1 1 0 0 -82 87 0 +R 270 28 TRP A 28 12 MET A 12 7.8689 1 1 0 0 -32 95 0 +R 271 28 TRP A 28 17 LEU A 17 7.4830 1 1 1 1 81 218 0 +R 272 28 TRP A 28 20 TYR A 20 9.5686 0 1 0 0 -7 7 0 +R 273 28 TRP A 28 23 TYR A 23 7.5595 1 1 1 1 44 60 0 +R 274 28 TRP A 28 24 SER A 24 7.2581 1 1 0 0 -47 49 0 +R 275 28 TRP A 28 25 LEU A 25 5.3994 1 1 0 0 -18 19 0 +R 276 28 TRP A 28 26 GLY A 26 5.5151 1 0 0 0 0 0 0 +R 277 28 TRP A 28 27 ASN A 27 3.7858 1 1 0 0 -7 345 0 +R 278 28 TRP A 28 29 VAL A 29 3.8333 1 1 1 1 2 334 0 +R 279 28 TRP A 28 30 CYS A 30 5.4753 1 0 0 0 0 0 0 +R 280 28 TRP A 28 31 ALA A 31 5.1386 1 1 0 0 -1 1 0 +R 281 28 TRP A 28 32 ALA A 32 6.2956 1 1 1 1 132 132 0 +R 282 28 TRP A 28 56 LEU A 56 8.7724 0 1 1 1 25 25 0 +R 283 28 TRP A 28 95 ALA A 95 9.8227 1 1 1 1 35 35 0 +R 284 28 TRP A 28 99 VAL A 99 10.7709 1 1 1 1 240 240 0 +R 285 28 TRP A 28 105 MET A 105 8.7636 1 1 1 1 15 21 0 +R 286 28 TRP A 28 108 TRP A 108 10.2074 1 1 1 1 113 113 0 +R 287 29 VAL A 29 5 ARG A 5 7.3410 1 1 1 1 10 12 0 +R 288 29 VAL A 29 9 ALA A 9 6.2031 1 1 1 1 17 175 0 +R 289 29 VAL A 29 12 MET A 12 8.1611 1 1 0 0 0 34 0 +R 290 29 VAL A 29 25 LEU A 25 6.4093 1 1 0 0 -65 65 0 +R 291 29 VAL A 29 26 GLY A 26 5.1152 1 1 0 0 -10 10 0 +R 292 29 VAL A 29 27 ASN A 27 5.5161 1 0 0 0 0 0 0 +R 293 29 VAL A 29 28 TRP A 28 3.8333 1 1 0 0 -22 358 0 +R 294 29 VAL A 29 30 CYS A 30 3.7941 1 1 1 1 9 357 0 +R 295 29 VAL A 29 31 ALA A 31 5.3991 1 0 0 0 0 0 0 +R 296 29 VAL A 29 32 ALA A 32 5.1300 1 1 0 0 0 3 0 +R 297 29 VAL A 29 33 LYS A 33 6.2055 1 1 1 1 115 115 0 +R 298 29 VAL A 29 38 PHE A 38 8.4877 1 1 1 1 96 98 0 +R 299 29 VAL A 29 123 TRP A 123 6.3580 1 1 1 1 61 107 0 +R 300 29 VAL A 29 124 ILE A 124 7.6402 1 1 1 1 1 1 0 +R 301 30 CYS A 30 26 GLY A 26 5.9025 1 1 1 0 -65 79 0 +R 302 30 CYS A 30 27 ASN A 27 5.1016 1 1 0 0 -6 6 0 +R 303 30 CYS A 30 28 TRP A 28 5.4753 1 0 0 0 0 0 0 +R 304 30 CYS A 30 29 VAL A 29 3.7941 1 1 0 0 -11 343 0 +R 305 30 CYS A 30 31 ALA A 31 3.7849 1 1 1 1 12 355 0 +R 306 30 CYS A 30 32 ALA A 32 5.5042 1 0 0 0 0 0 0 +R 307 30 CYS A 30 33 LYS A 33 5.1917 1 0 0 0 0 0 0 +R 308 30 CYS A 30 34 PHE A 34 6.3992 1 1 1 1 96 170 0 +R 309 30 CYS A 30 115 CYS A 115 6.0621 1 1 1 1 10 238 0 +R 310 30 CYS A 30 120 VAL A 120 6.6406 1 0 0 0 0 0 0 +R 311 30 CYS A 30 123 TRP A 123 6.2969 1 1 1 1 34 144 0 +R 312 31 ALA A 31 27 ASN A 27 6.0825 1 1 1 0 -56 76 0 +R 313 31 ALA A 31 28 TRP A 28 5.1386 1 1 0 0 -10 10 0 +R 314 31 ALA A 31 29 VAL A 29 5.3991 1 0 0 0 0 0 0 +R 315 31 ALA A 31 30 CYS A 30 3.7849 1 1 0 0 -23 359 0 +R 316 31 ALA A 31 32 ALA A 32 3.8582 1 1 1 1 13 328 0 +R 317 31 ALA A 31 33 LYS A 33 5.4805 1 0 0 0 0 0 0 +R 318 31 ALA A 31 34 PHE A 34 5.3387 1 0 0 0 0 0 0 +R 319 31 ALA A 31 35 GLU A 35 5.8673 1 1 1 1 124 185 0 +R 320 31 ALA A 31 56 LEU A 56 7.1209 1 1 1 1 34 34 0 +R 321 31 ALA A 31 105 MET A 105 8.7729 1 1 1 1 112 112 0 +R 322 31 ALA A 31 111 TRP A 111 4.9166 1 1 1 1 50 56 0 +R 323 31 ALA A 31 115 CYS A 115 6.6938 1 1 0 0 0 26 0 +R 324 32 ALA A 32 8 LEU A 8 8.9719 1 1 1 1 134 134 0 +R 325 32 ALA A 32 12 MET A 12 10.4631 1 1 1 1 13 13 0 +R 326 32 ALA A 32 28 TRP A 28 6.2956 1 1 1 0 -46 72 0 +R 327 32 ALA A 32 29 VAL A 29 5.1300 1 0 0 0 0 0 0 +R 328 32 ALA A 32 30 CYS A 30 5.5042 1 0 0 0 0 0 0 +R 329 32 ALA A 32 31 ALA A 31 3.8582 1 1 0 0 -16 344 0 +R 330 32 ALA A 32 33 LYS A 33 3.7869 1 1 1 1 4 369 0 +R 331 32 ALA A 32 34 PHE A 34 5.4712 1 0 0 0 0 0 0 +R 332 32 ALA A 32 35 GLU A 35 5.0728 1 0 0 0 0 0 0 +R 333 32 ALA A 32 36 SER A 36 5.7631 1 1 1 1 146 146 0 +R 334 32 ALA A 32 37 ASN A 37 6.3799 1 0 0 0 0 0 0 +R 335 32 ALA A 32 38 PHE A 38 5.5773 1 0 0 0 0 0 0 +R 336 32 ALA A 32 55 ILE A 55 5.5963 1 1 1 0 -45 95 0 +R 337 32 ALA A 32 56 LEU A 56 5.4440 1 1 0 0 0 1 0 +R 338 33 LYS A 33 29 VAL A 29 6.2055 1 1 1 0 -25 53 0 +R 339 33 LYS A 33 30 CYS A 30 5.1917 1 1 0 0 -38 38 0 +R 340 33 LYS A 33 31 ALA A 31 5.4805 1 0 0 0 0 0 0 +R 341 33 LYS A 33 32 ALA A 32 3.7869 1 1 0 0 -19 351 0 +R 342 33 LYS A 33 34 PHE A 34 3.7560 1 1 1 1 23 393 0 +R 343 33 LYS A 33 35 GLU A 35 5.7170 1 0 0 0 0 0 0 +R 344 33 LYS A 33 37 ASN A 37 4.3141 1 1 1 1 179 307 0 +R 345 33 LYS A 33 38 PHE A 38 5.2101 1 1 1 1 29 126 0 +R 346 33 LYS A 33 123 TRP A 123 9.2780 1 1 1 1 84 121 0 +R 347 34 PHE A 34 30 CYS A 30 6.3992 1 1 1 0 -61 103 0 +R 348 34 PHE A 34 31 ALA A 31 5.3387 1 0 0 0 0 0 0 +R 349 34 PHE A 34 32 ALA A 32 5.4712 1 0 0 0 0 0 0 +R 350 34 PHE A 34 33 LYS A 33 3.7560 1 1 1 1 17 445 0 +R 351 34 PHE A 34 35 GLU A 35 3.8162 1 1 1 0 -2 355 0 +R 352 34 PHE A 34 36 SER A 36 5.8515 1 0 0 0 0 0 0 +R 353 34 PHE A 34 37 ASN A 37 5.6664 0 1 1 1 3 4 0 +R 354 34 PHE A 34 110 ALA A 110 5.8542 1 1 1 1 62 120 0 +R 355 34 PHE A 34 114 ARG A 114 7.4511 1 1 1 0 -10 291 0 +R 356 34 PHE A 34 115 CYS A 115 8.4896 1 0 0 0 0 0 0 +R 357 34 PHE A 34 123 TRP A 123 11.6342 1 1 1 1 156 156 0 +R 358 35 GLU A 35 31 ALA A 31 5.8673 1 1 1 0 -85 95 0 +R 359 35 GLU A 35 32 ALA A 32 5.0728 1 0 0 0 0 0 0 +R 360 35 GLU A 35 33 LYS A 33 5.7170 1 0 0 0 0 0 0 +R 361 35 GLU A 35 34 PHE A 34 3.8162 1 1 0 0 -42 384 0 +R 362 35 GLU A 35 36 SER A 36 3.7973 1 1 1 0 -1 326 0 +R 363 35 GLU A 35 37 ASN A 37 6.1632 1 0 0 0 0 0 0 +R 364 35 GLU A 35 44 ASN A 44 9.8723 0 1 1 1 31 31 0 +R 365 35 GLU A 35 55 ILE A 55 6.7296 1 1 0 0 -54 54 0 +R 366 35 GLU A 35 56 LEU A 56 5.8960 1 0 0 0 0 0 0 +R 367 35 GLU A 35 57 GLN A 57 6.0016 1 1 1 0 -184 219 0 +R 368 35 GLU A 35 108 TRP A 108 8.1006 1 1 1 0 -6 162 0 +R 369 35 GLU A 35 109 VAL A 109 8.4267 0 1 1 0 -31 49 0 +R 370 35 GLU A 35 110 ALA A 110 6.0785 1 1 1 1 137 176 0 +R 371 36 SER A 36 32 ALA A 32 5.7631 1 1 1 1 38 38 0 +R 372 36 SER A 36 34 PHE A 34 5.8515 1 0 0 0 0 0 0 +R 373 36 SER A 36 35 GLU A 35 3.7973 1 1 0 0 -2 362 0 +R 374 36 SER A 36 37 ASN A 37 3.8326 1 1 1 0 -26 382 0 +R 375 36 SER A 36 38 PHE A 38 5.1834 1 1 1 1 48 48 0 +R 376 36 SER A 36 39 ASN A 39 5.4539 1 1 1 1 3 162 0 +R 377 36 SER A 36 42 ALA A 42 5.5964 1 1 0 0 -9 33 0 +R 378 36 SER A 36 44 ASN A 44 9.2935 0 1 0 0 0 1 0 +R 379 36 SER A 36 54 GLY A 54 6.7929 1 1 0 0 0 40 0 +R 380 36 SER A 36 55 ILE A 55 5.1236 1 1 1 1 79 149 0 +R 381 36 SER A 36 57 GLN A 57 6.6652 1 0 0 0 0 0 0 +R 382 37 ASN A 37 2 VAL A 2 7.9443 0 1 0 0 -59 59 0 +R 383 37 ASN A 37 32 ALA A 32 6.3799 1 0 0 0 0 0 0 +R 384 37 ASN A 37 33 LYS A 33 4.3141 1 1 1 1 185 288 0 +R 385 37 ASN A 37 34 PHE A 34 5.6664 0 1 0 0 0 1 0 +R 386 37 ASN A 37 35 GLU A 35 6.1632 1 1 0 0 0 1 0 +R 387 37 ASN A 37 36 SER A 36 3.8326 1 1 0 0 -43 379 0 +R 388 37 ASN A 37 38 PHE A 38 3.8358 1 1 1 0 -29 388 0 +R 389 37 ASN A 37 39 ASN A 39 5.4975 1 1 1 1 8 18 0 +R 390 38 PHE A 38 1 LYS A 1 8.1596 1 1 0 0 -12 12 0 +R 391 38 PHE A 38 2 VAL A 2 5.5799 1 1 1 1 1 1 0 +R 392 38 PHE A 38 3 PHE A 3 5.3547 1 1 1 0 -5 210 0 +R 393 38 PHE A 38 5 ARG A 5 7.6636 1 1 1 1 21 94 0 +R 394 38 PHE A 38 8 LEU A 8 7.9077 1 1 1 1 78 78 0 +R 395 38 PHE A 38 29 VAL A 29 8.4877 1 1 1 1 43 117 0 +R 396 38 PHE A 38 32 ALA A 32 5.5773 1 0 0 0 0 0 0 +R 397 38 PHE A 38 33 LYS A 33 5.2101 1 1 1 1 22 242 0 +R 398 38 PHE A 38 36 SER A 36 5.1834 1 1 1 1 10 38 0 +R 399 38 PHE A 38 37 ASN A 37 3.8358 1 1 0 0 -67 379 0 +R 400 38 PHE A 38 39 ASN A 39 3.8122 1 1 1 1 24 317 0 +R 401 38 PHE A 38 40 THR A 40 6.4024 1 0 0 0 0 0 0 +R 402 38 PHE A 38 55 ILE A 55 5.7406 1 1 0 0 -18 31 0 +R 403 39 ASN A 39 1 LYS A 1 5.7421 1 1 0 0 -31 40 0 +R 404 39 ASN A 39 2 VAL A 2 4.2809 1 1 1 0 -29 96 0 +R 405 39 ASN A 39 36 SER A 36 5.4539 1 1 1 0 -49 115 0 +R 406 39 ASN A 39 37 ASN A 37 5.4975 1 1 1 0 -4 11 0 +R 407 39 ASN A 39 38 PHE A 38 3.8122 1 1 0 0 -14 363 0 +R 408 39 ASN A 39 40 THR A 40 3.8635 1 1 1 1 36 366 0 +R 409 39 ASN A 39 41 GLN A 41 5.4299 1 1 1 1 18 147 0 +R 410 39 ASN A 39 42 ALA A 42 5.7128 1 1 1 0 -23 110 0 +R 411 39 ASN A 39 55 ILE A 55 5.6995 1 0 0 0 0 0 0 +R 412 40 THR A 40 1 LYS A 1 5.4657 1 1 1 1 155 157 0 +R 413 40 THR A 40 3 PHE A 3 7.9444 1 1 1 1 154 154 0 +R 414 40 THR A 40 38 PHE A 38 6.4024 1 0 0 0 0 0 0 +R 415 40 THR A 40 39 ASN A 39 3.8635 1 1 0 0 0 339 0 +R 416 40 THR A 40 41 GLN A 41 3.8464 1 1 1 1 19 306 0 +R 417 40 THR A 40 42 ALA A 42 5.7069 1 0 0 0 0 0 0 +R 418 40 THR A 40 54 GLY A 54 4.5843 1 1 0 0 0 16 0 +R 419 40 THR A 40 55 ILE A 55 4.5521 1 1 1 1 34 54 0 +R 420 40 THR A 40 84 LEU A 84 5.0346 1 1 1 1 14 184 0 +R 421 40 THR A 40 85 SER A 85 6.2303 1 1 1 0 -71 109 0 +R 422 40 THR A 40 86 SER A 86 6.2290 1 1 0 0 0 2 0 +R 423 40 THR A 40 88 ILE A 88 7.7607 1 1 1 1 13 13 0 +R 424 41 GLN A 41 1 LYS A 1 6.8324 1 1 0 0 -73 76 0 +R 425 41 GLN A 41 39 ASN A 39 5.4299 1 1 1 0 -31 58 0 +R 426 41 GLN A 41 40 THR A 40 3.8464 1 1 0 0 -62 409 0 +R 427 41 GLN A 41 42 ALA A 42 3.8155 1 1 1 1 13 356 0 +R 428 41 GLN A 41 43 THR A 43 6.5152 1 1 1 0 -18 80 0 +R 429 41 GLN A 41 84 LEU A 84 4.8606 1 1 1 0 -79 95 0 +R 430 42 ALA A 42 36 SER A 36 5.5964 1 1 0 0 -19 94 0 +R 431 42 ALA A 42 39 ASN A 39 5.7128 1 1 1 0 -69 103 0 +R 432 42 ALA A 42 40 THR A 40 5.7069 1 0 0 0 0 0 0 +R 433 42 ALA A 42 41 GLN A 41 3.8155 1 1 0 0 -24 359 0 +R 434 42 ALA A 42 43 THR A 43 3.8859 1 1 1 1 5 326 0 +R 435 42 ALA A 42 44 ASN A 44 6.8831 0 1 0 0 -17 17 0 +R 436 42 ALA A 42 53 TYR A 53 6.0588 1 0 0 0 0 0 0 +R 437 42 ALA A 42 54 GLY A 54 5.0278 1 1 1 1 192 192 0 +R 438 42 ALA A 42 57 GLN A 57 7.3752 1 1 1 0 -61 69 0 +R 439 42 ALA A 42 84 LEU A 84 7.3563 1 0 0 0 0 0 0 +R 440 43 THR A 43 41 GLN A 41 6.5152 1 1 1 0 -27 55 0 +R 441 43 THR A 43 42 ALA A 42 3.8859 1 1 0 0 -37 391 0 +R 442 43 THR A 43 44 ASN A 44 3.7688 1 1 1 1 13 431 0 +R 443 43 THR A 43 51 THR A 51 6.7249 1 1 0 0 -1 34 0 +R 444 43 THR A 43 52 ASP A 52 5.4799 1 1 0 0 0 18 0 +R 445 43 THR A 43 53 TYR A 53 4.7167 1 1 1 1 138 138 0 +R 446 43 THR A 43 57 GLN A 57 7.1223 1 0 0 0 0 0 0 +R 447 43 THR A 43 84 LEU A 84 8.5599 1 1 1 1 36 36 0 +R 448 44 ASN A 44 35 GLU A 35 9.8723 0 1 1 1 45 45 0 +R 449 44 ASN A 44 42 ALA A 42 6.8831 0 1 0 0 -12 12 0 +R 450 44 ASN A 44 43 THR A 43 3.7688 1 1 1 0 -15 451 0 +R 451 44 ASN A 44 45 ARG A 45 3.7166 1 1 1 0 0 387 0 +R 452 44 ASN A 44 46 ASN A 46 6.5794 0 1 0 0 -6 6 0 +R 453 44 ASN A 44 51 THR A 51 5.5411 1 0 0 0 0 0 0 +R 454 44 ASN A 44 52 ASP A 52 5.2528 1 1 1 1 122 156 0 +R 455 44 ASN A 44 57 GLN A 57 7.9104 1 1 1 1 80 172 0 +R 456 45 ARG A 45 44 ASN A 44 3.7166 1 1 1 0 -12 381 0 +R 457 45 ARG A 45 46 ASN A 46 3.7641 1 1 1 0 -19 425 0 +R 458 45 ARG A 45 47 THR A 47 6.9141 0 1 1 1 3 4 0 +R 459 45 ARG A 45 49 GLY A 49 6.6305 1 1 1 1 15 60 0 +R 460 45 ARG A 45 50 SER A 50 6.1524 1 1 0 0 0 71 0 +R 461 45 ARG A 45 51 THR A 51 4.1733 1 1 0 0 0 23 0 +R 462 45 ARG A 45 68 ARG A 68 11.3353 1 1 0 0 -168 229 0 +R 463 46 ASN A 46 44 ASN A 44 6.5794 0 1 1 0 -9 12 0 +R 464 46 ASN A 46 45 ARG A 45 3.7641 1 1 1 0 -43 445 0 +R 465 46 ASN A 46 47 THR A 47 3.7875 1 1 1 0 -14 376 0 +R 466 46 ASN A 46 48 ASP A 48 5.4237 1 1 0 0 -52 57 0 +R 467 46 ASN A 46 49 GLY A 49 5.3347 1 1 1 1 86 87 0 +R 468 46 ASN A 46 50 SER A 50 5.3628 1 1 1 1 25 51 0 +R 469 46 ASN A 46 51 THR A 51 5.5953 1 0 0 0 0 0 0 +R 470 46 ASN A 46 52 ASP A 52 7.6137 1 1 1 1 75 130 0 +R 471 46 ASN A 46 59 ASN A 59 9.1269 1 1 1 1 182 188 0 +R 472 47 THR A 47 46 ASN A 46 3.7875 1 1 1 0 -15 361 0 +R 473 47 THR A 47 48 ASP A 48 3.7632 1 1 1 1 28 353 0 +R 474 47 THR A 47 49 GLY A 49 5.2181 1 1 1 1 35 47 0 +R 475 48 ASP A 48 46 ASN A 46 5.4237 1 1 0 0 -19 25 0 +R 476 48 ASP A 48 47 THR A 47 3.7632 1 1 0 0 -29 389 0 +R 477 48 ASP A 48 49 GLY A 49 3.7979 1 1 1 1 21 317 0 +R 478 48 ASP A 48 50 SER A 50 5.5073 1 1 1 1 235 235 0 +R 479 48 ASP A 48 59 ASN A 59 10.9299 0 1 1 0 -2 6 0 +R 480 48 ASP A 48 61 ARG A 61 8.7820 1 1 1 1 155 237 0 +R 481 48 ASP A 48 69 THR A 69 8.8838 0 1 0 0 -1 1 0 +R 482 49 GLY A 49 45 ARG A 45 6.6305 1 1 0 0 0 89 0 +R 483 49 GLY A 49 46 ASN A 46 5.3347 1 1 1 1 19 57 0 +R 484 49 GLY A 49 47 THR A 47 5.2181 1 1 0 0 0 17 0 +R 485 49 GLY A 49 48 ASP A 48 3.7979 1 1 0 0 -29 387 0 +R 486 49 GLY A 49 50 SER A 50 3.7017 1 1 1 1 14 349 0 +R 487 49 GLY A 49 51 THR A 51 6.5946 0 1 1 1 2 2 0 +R 488 49 GLY A 49 68 ARG A 68 8.1773 0 1 0 0 -40 53 0 +R 489 49 GLY A 49 69 THR A 69 6.4717 0 1 1 1 69 70 0 +R 490 49 GLY A 49 70 PRO A 70 8.6350 0 1 0 0 0 6 0 +R 491 50 SER A 50 45 ARG A 45 6.1524 1 0 0 0 0 0 0 +R 492 50 SER A 50 46 ASN A 46 5.3628 1 1 1 1 179 179 0 +R 493 50 SER A 50 48 ASP A 48 5.5073 1 1 1 1 91 116 0 +R 494 50 SER A 50 49 GLY A 49 3.7017 1 1 0 0 -24 393 0 +R 495 50 SER A 50 51 THR A 51 3.9416 1 1 1 1 36 307 0 +R 496 50 SER A 50 59 ASN A 59 6.7524 1 1 1 1 104 162 0 +R 497 50 SER A 50 60 SER A 60 5.4691 1 1 0 0 0 67 0 +R 498 50 SER A 50 61 ARG A 61 5.5177 1 1 0 0 0 6 0 +R 499 50 SER A 50 69 THR A 69 5.5332 1 1 0 0 0 50 0 +R 500 51 THR A 51 43 THR A 43 6.7249 1 1 0 0 0 19 0 +R 501 51 THR A 51 44 ASN A 44 5.5411 1 1 0 0 -64 88 0 +R 502 51 THR A 51 45 ARG A 45 4.1733 1 1 0 0 0 2 0 +R 503 51 THR A 51 46 ASN A 46 5.5953 1 0 0 0 0 0 0 +R 504 51 THR A 51 50 SER A 50 3.9416 1 1 1 1 10 379 0 +R 505 51 THR A 51 52 ASP A 52 3.8949 1 1 1 0 -40 355 0 +R 506 51 THR A 51 53 TYR A 53 6.5005 1 1 1 1 70 146 0 +R 507 51 THR A 51 59 ASN A 59 5.7402 1 0 0 0 0 0 0 +R 508 51 THR A 51 60 SER A 60 5.4996 1 1 1 1 168 168 0 +R 509 51 THR A 51 66 ASP A 66 8.3256 1 0 0 0 0 0 0 +R 510 51 THR A 51 68 ARG A 68 9.1481 1 1 1 1 115 157 0 +R 511 52 ASP A 52 43 THR A 43 5.4799 1 1 0 0 0 12 0 +R 512 52 ASP A 52 44 ASN A 44 5.2528 1 1 1 1 110 126 0 +R 513 52 ASP A 52 46 ASN A 46 7.6137 1 1 1 1 134 134 0 +R 514 52 ASP A 52 51 THR A 51 3.8949 1 1 0 0 -5 337 0 +R 515 52 ASP A 52 53 TYR A 53 3.7885 1 1 1 1 18 345 0 +R 516 52 ASP A 52 57 GLN A 57 4.5222 1 1 0 0 -155 164 0 +R 517 52 ASP A 52 58 ILE A 58 4.9171 1 1 0 0 0 5 0 +R 518 52 ASP A 52 59 ASN A 59 4.3832 1 1 1 1 120 202 0 +R 519 53 TYR A 53 42 ALA A 42 6.0588 1 1 0 0 0 1 0 +R 520 53 TYR A 53 43 THR A 43 4.7167 1 1 1 1 111 111 0 +R 521 53 TYR A 53 51 THR A 51 6.5005 1 1 1 0 -111 172 0 +R 522 53 TYR A 53 52 ASP A 52 3.7885 1 1 0 0 -1 354 0 +R 523 53 TYR A 53 54 GLY A 54 3.8089 1 1 1 1 16 350 0 +R 524 53 TYR A 53 57 GLN A 57 4.4524 1 1 1 1 4 4 0 +R 525 53 TYR A 53 58 ILE A 58 5.1266 1 1 1 1 72 153 0 +R 526 53 TYR A 53 60 SER A 60 7.7842 1 0 0 0 0 0 0 +R 527 53 TYR A 53 64 CYS A 64 9.1195 1 0 0 0 0 0 0 +R 528 53 TYR A 53 66 ASP A 66 9.7084 1 1 1 1 80 176 0 +R 529 53 TYR A 53 68 ARG A 68 13.3743 0 1 1 1 27 30 0 +R 530 53 TYR A 53 80 CYS A 80 6.5643 1 1 1 1 41 211 0 +R 531 53 TYR A 53 81 SER A 81 7.5160 0 1 0 0 -4 10 0 +R 532 53 TYR A 53 83 LEU A 83 6.1854 1 1 1 0 -3 11 0 +R 533 53 TYR A 53 84 LEU A 84 6.6054 1 1 1 1 22 22 0 +R 534 54 GLY A 54 36 SER A 36 6.7929 1 1 0 0 0 9 0 +R 535 54 GLY A 54 39 ASN A 39 7.0228 0 1 0 0 0 5 0 +R 536 54 GLY A 54 40 THR A 40 4.5843 1 1 0 0 0 102 0 +R 537 54 GLY A 54 42 ALA A 42 5.0278 1 1 1 1 49 51 0 +R 538 54 GLY A 54 53 TYR A 53 3.8089 1 1 0 0 -7 353 0 +R 539 54 GLY A 54 55 ILE A 55 3.7039 1 1 1 1 29 356 0 +R 540 54 GLY A 54 56 LEU A 56 5.3851 1 1 0 0 0 1 0 +R 541 54 GLY A 54 57 GLN A 57 4.9429 1 1 1 1 146 146 0 +R 542 54 GLY A 54 83 LEU A 83 5.3232 1 1 0 0 0 41 0 +R 543 54 GLY A 54 84 LEU A 84 4.8428 1 1 0 0 -4 4 0 +R 544 55 ILE A 55 3 PHE A 3 9.3473 1 1 1 1 98 98 0 +R 545 55 ILE A 55 8 LEU A 8 10.0426 1 1 1 1 62 62 0 +R 546 55 ILE A 55 12 MET A 12 11.3010 0 1 1 1 2 2 0 +R 547 55 ILE A 55 32 ALA A 32 5.5963 1 1 1 1 39 91 0 +R 548 55 ILE A 55 35 GLU A 35 6.7296 1 1 0 0 -1 1 0 +R 549 55 ILE A 55 36 SER A 36 5.1236 1 1 1 1 50 166 0 +R 550 55 ILE A 55 38 PHE A 38 5.7406 1 1 0 0 -109 112 0 +R 551 55 ILE A 55 39 ASN A 39 5.6995 1 1 1 1 2 2 0 +R 552 55 ILE A 55 40 THR A 40 4.5521 1 1 1 1 15 24 0 +R 553 55 ILE A 55 54 GLY A 54 3.7039 1 1 0 0 0 341 0 +R 554 55 ILE A 55 56 LEU A 56 3.7519 1 1 1 1 25 367 0 +R 555 55 ILE A 55 57 GLN A 57 5.6235 1 0 0 0 0 0 0 +R 556 55 ILE A 55 88 ILE A 88 8.0660 1 1 1 1 37 37 0 +R 557 55 ILE A 55 91 SER A 91 7.4339 1 1 0 0 -81 118 0 +R 558 56 LEU A 56 12 MET A 12 11.5983 1 1 1 1 79 79 0 +R 559 56 LEU A 56 28 TRP A 28 8.7724 0 1 1 0 -1 19 0 +R 560 56 LEU A 56 31 ALA A 31 7.1209 1 1 1 1 70 70 0 +R 561 56 LEU A 56 32 ALA A 32 5.4440 1 1 1 0 -98 114 0 +R 562 56 LEU A 56 35 GLU A 35 5.8960 1 1 0 0 0 1 0 +R 563 56 LEU A 56 54 GLY A 54 5.3851 1 1 0 0 0 3 0 +R 564 56 LEU A 56 55 ILE A 55 3.7519 1 1 1 0 -20 429 0 +R 565 56 LEU A 56 57 GLN A 57 3.7252 1 1 1 1 12 337 0 +R 566 56 LEU A 56 58 ILE A 58 5.6664 1 1 1 1 37 37 0 +R 567 56 LEU A 56 91 SER A 91 6.9590 0 1 0 0 -29 32 0 +R 568 56 LEU A 56 92 VAL A 92 8.3697 0 1 0 0 0 1 0 +R 569 56 LEU A 56 95 ALA A 95 7.7189 1 1 1 1 140 140 0 +R 570 56 LEU A 56 108 TRP A 108 8.2153 1 1 1 1 131 203 0 +R 571 57 GLN A 57 35 GLU A 35 6.0016 1 1 0 0 -170 175 0 +R 572 57 GLN A 57 36 SER A 36 6.6652 1 0 0 0 0 0 0 +R 573 57 GLN A 57 42 ALA A 42 7.3752 1 1 1 1 118 142 0 +R 574 57 GLN A 57 43 THR A 43 7.1223 1 0 0 0 0 0 0 +R 575 57 GLN A 57 44 ASN A 44 7.9104 1 1 1 1 150 163 0 +R 576 57 GLN A 57 52 ASP A 52 4.5222 1 1 1 0 -86 120 0 +R 577 57 GLN A 57 53 TYR A 53 4.4524 1 1 0 0 0 5 0 +R 578 57 GLN A 57 54 GLY A 54 4.9429 1 1 1 1 108 124 0 +R 579 57 GLN A 57 55 ILE A 55 5.6235 1 0 0 0 0 0 0 +R 580 57 GLN A 57 56 LEU A 56 3.7252 1 1 0 0 -62 391 0 +R 581 57 GLN A 57 58 ILE A 58 3.8369 1 1 1 1 20 351 0 +R 582 57 GLN A 57 59 ASN A 59 6.4000 1 1 1 1 9 19 0 +R 583 57 GLN A 57 108 TRP A 108 8.2910 0 1 1 1 13 33 0 +R 584 58 ILE A 58 52 ASP A 52 4.9171 1 1 0 0 0 1 0 +R 585 58 ILE A 58 53 TYR A 53 5.1266 1 1 1 1 85 125 0 +R 586 58 ILE A 58 56 LEU A 56 5.6664 1 1 1 0 -21 50 0 +R 587 58 ILE A 58 57 GLN A 57 3.8369 1 1 0 0 -1 340 0 +R 588 58 ILE A 58 59 ASN A 59 3.7920 1 1 1 1 8 375 0 +R 589 58 ILE A 58 63 TRP A 63 6.7289 1 1 1 1 142 142 0 +R 590 58 ILE A 58 83 LEU A 83 7.8716 1 1 1 1 62 62 0 +R 591 58 ILE A 58 91 SER A 91 7.7587 1 1 0 0 -148 183 0 +R 592 58 ILE A 58 94 CYS A 94 8.1513 1 1 1 1 27 28 0 +R 593 58 ILE A 58 95 ALA A 95 7.7436 1 1 0 0 -3 9 0 +R 594 58 ILE A 58 98 ILE A 98 8.9872 1 1 1 1 91 96 0 +R 595 59 ASN A 59 46 ASN A 46 9.1269 1 1 1 1 18 18 0 +R 596 59 ASN A 59 48 ASP A 48 10.9299 0 1 1 1 4 7 0 +R 597 59 ASN A 59 50 SER A 50 6.7524 1 1 1 1 128 134 0 +R 598 59 ASN A 59 51 THR A 51 5.7402 1 0 0 0 0 0 0 +R 599 59 ASN A 59 52 ASP A 52 4.3832 1 1 1 1 78 125 0 +R 600 59 ASN A 59 57 GLN A 57 6.4000 1 1 0 0 -7 7 0 +R 601 59 ASN A 59 58 ILE A 58 3.7920 1 1 0 0 -9 353 0 +R 602 59 ASN A 59 60 SER A 60 3.8442 1 1 1 1 25 327 0 +R 603 59 ASN A 59 61 ARG A 61 5.5522 1 1 1 1 50 218 0 +R 604 59 ASN A 59 62 TRP A 62 6.1912 1 1 1 1 1 30 0 +R 605 59 ASN A 59 63 TRP A 63 5.8889 1 1 1 1 162 200 0 +R 606 60 SER A 60 50 SER A 50 5.4691 1 0 0 0 0 0 0 +R 607 60 SER A 60 51 THR A 51 5.4996 1 1 1 1 101 120 0 +R 608 60 SER A 60 53 TYR A 53 7.7842 1 0 0 0 0 0 0 +R 609 60 SER A 60 59 ASN A 59 3.8442 1 1 0 0 0 339 0 +R 610 60 SER A 60 61 ARG A 61 3.8908 1 1 1 1 17 283 0 +R 611 60 SER A 60 62 TRP A 62 5.5049 1 0 0 0 0 0 0 +R 612 60 SER A 60 64 CYS A 64 5.0013 1 1 0 0 -1 31 0 +R 613 60 SER A 60 66 ASP A 66 6.3315 1 1 0 0 0 125 0 +R 614 60 SER A 60 69 THR A 69 6.5717 1 1 1 1 101 105 0 +R 615 60 SER A 60 72 SER A 72 6.4249 1 1 1 1 199 206 0 +R 616 60 SER A 60 80 CYS A 80 6.8143 1 1 0 0 0 32 0 +R 617 61 ARG A 61 48 ASP A 48 8.7820 1 1 1 1 204 281 0 +R 618 61 ARG A 61 50 SER A 50 5.5177 1 1 0 0 0 4 0 +R 619 61 ARG A 61 59 ASN A 59 5.5522 1 1 1 0 -68 70 0 +R 620 61 ARG A 61 60 SER A 60 3.8908 1 1 1 0 -12 362 0 +R 621 61 ARG A 61 62 TRP A 62 3.8101 1 1 1 1 110 481 0 +R 622 61 ARG A 61 69 THR A 69 6.2823 1 1 0 0 -70 92 0 +R 623 61 ARG A 61 70 PRO A 70 8.0292 1 1 1 1 167 167 0 +R 624 61 ARG A 61 71 GLY A 71 7.0231 0 1 0 0 -2 17 0 +R 625 61 ARG A 61 72 SER A 72 4.5693 1 1 0 0 0 14 0 +R 626 61 ARG A 61 73 ARG A 73 6.4875 1 1 1 1 130 130 0 +R 627 62 TRP A 62 59 ASN A 59 6.1912 1 1 1 0 -15 51 0 +R 628 62 TRP A 62 60 SER A 60 5.5049 1 0 0 0 0 0 0 +R 629 62 TRP A 62 61 ARG A 61 3.8101 1 1 1 1 9 531 0 +R 630 62 TRP A 62 63 TRP A 63 3.7646 1 1 1 0 -14 426 0 +R 631 62 TRP A 62 64 CYS A 64 6.3048 1 1 0 0 0 3 0 +R 632 62 TRP A 62 73 ARG A 73 4.7823 1 1 1 0 -49 187 0 +R 633 62 TRP A 62 74 ASN A 74 5.5079 1 1 1 1 11 11 0 +R 634 62 TRP A 62 75 LEU A 75 5.9402 1 1 1 1 178 204 0 +R 635 63 TRP A 63 58 ILE A 58 6.7289 1 1 1 1 89 89 0 +R 636 63 TRP A 63 59 ASN A 59 5.8889 1 1 0 0 -69 69 0 +R 637 63 TRP A 63 62 TRP A 62 3.7646 1 1 1 0 -6 481 0 +R 638 63 TRP A 63 64 CYS A 64 3.7610 1 1 1 0 -5 343 0 +R 639 63 TRP A 63 74 ASN A 74 4.6495 1 0 0 0 0 0 0 +R 640 63 TRP A 63 75 LEU A 75 4.5592 1 1 1 1 117 117 0 +R 641 63 TRP A 63 76 CYS A 76 5.1313 1 1 1 1 103 169 0 +R 642 63 TRP A 63 78 ILE A 78 7.9100 1 0 0 0 0 0 0 +R 643 63 TRP A 63 94 CYS A 94 7.4243 1 1 0 0 0 1 0 +R 644 63 TRP A 63 97 LYS A 97 9.0609 1 1 1 1 22 24 0 +R 645 63 TRP A 63 98 ILE A 98 8.1327 1 1 1 1 99 261 0 +R 646 63 TRP A 63 101 ASP A 101 11.5849 1 1 0 0 -76 144 0 +R 647 63 TRP A 63 107 ALA A 107 11.8922 0 1 1 1 4 4 0 +R 648 64 CYS A 64 53 TYR A 53 9.1195 1 1 0 0 0 10 0 +R 649 64 CYS A 64 59 ASN A 59 6.9688 0 1 0 0 0 4 0 +R 650 64 CYS A 64 60 SER A 60 5.0013 1 1 0 0 -120 167 0 +R 651 64 CYS A 64 62 TRP A 62 6.3048 1 1 0 0 0 3 0 +R 652 64 CYS A 64 63 TRP A 63 3.7610 1 1 0 0 -18 385 0 +R 653 64 CYS A 64 65 ASN A 65 3.7533 1 1 1 1 19 339 0 +R 654 64 CYS A 64 72 SER A 72 7.6034 1 1 1 1 5 5 0 +R 655 64 CYS A 64 74 ASN A 74 4.3585 1 1 0 0 0 24 0 +R 656 64 CYS A 64 78 ILE A 78 5.2721 1 1 1 0 -50 52 0 +R 657 64 CYS A 64 79 PRO A 79 5.5062 1 0 0 0 0 0 0 +R 658 64 CYS A 64 80 CYS A 80 4.9610 1 1 0 0 0 244 0 +R 659 64 CYS A 64 83 LEU A 83 8.6424 1 1 1 1 39 94 0 +R 660 65 ASN A 65 64 CYS A 64 3.7533 1 1 0 0 0 356 0 +R 661 65 ASN A 65 66 ASP A 66 3.8054 1 1 1 1 25 333 0 +R 662 65 ASN A 65 67 GLY A 67 5.7673 1 1 1 1 35 159 0 +R 663 65 ASN A 65 72 SER A 72 6.7196 0 1 1 1 39 61 0 +R 664 65 ASN A 65 74 ASN A 74 5.3596 1 1 1 0 -106 121 0 +R 665 65 ASN A 65 78 ILE A 78 6.2178 1 1 1 1 4 14 0 +R 666 65 ASN A 65 79 PRO A 79 4.7112 1 1 1 0 -55 57 0 +R 667 65 ASN A 65 80 CYS A 80 5.3811 1 1 1 1 88 88 0 +R 668 66 ASP A 66 51 THR A 51 8.3256 1 1 0 0 0 7 0 +R 669 66 ASP A 66 53 TYR A 53 9.7084 1 1 1 1 36 176 0 +R 670 66 ASP A 66 60 SER A 60 6.3315 1 1 1 1 32 36 0 +R 671 66 ASP A 66 65 ASN A 65 3.8054 1 1 0 0 0 362 0 +R 672 66 ASP A 66 67 GLY A 67 3.8249 1 1 1 1 10 319 0 +R 673 66 ASP A 66 68 ARG A 68 5.5275 1 1 1 0 -7 127 0 +R 674 66 ASP A 66 69 THR A 69 6.6481 1 1 1 1 191 194 0 +R 675 66 ASP A 66 79 PRO A 79 5.9021 0 1 0 0 0 3 0 +R 676 66 ASP A 66 80 CYS A 80 5.2749 1 1 1 1 7 42 0 +R 677 66 ASP A 66 81 SER A 81 7.3090 0 1 0 0 -1 5 0 +R 678 67 GLY A 67 65 ASN A 65 5.7673 1 1 1 1 14 97 0 +R 679 67 GLY A 67 66 ASP A 66 3.8249 1 1 1 0 -35 376 0 +R 680 67 GLY A 67 68 ARG A 68 3.7098 1 1 1 1 4 349 0 +R 681 67 GLY A 67 69 THR A 69 6.0387 1 1 0 0 0 3 0 +R 682 68 ARG A 68 45 ARG A 45 11.3353 1 1 0 0 -233 270 0 +R 683 68 ARG A 68 49 GLY A 49 8.1773 0 1 0 0 -21 24 0 +R 684 68 ARG A 68 51 THR A 51 9.1481 1 1 1 1 73 136 0 +R 685 68 ARG A 68 53 TYR A 53 13.3743 0 1 1 1 8 18 0 +R 686 68 ARG A 68 66 ASP A 66 5.5275 1 1 1 0 -50 78 0 +R 687 68 ARG A 68 67 GLY A 67 3.7098 1 1 0 0 -29 397 0 +R 688 68 ARG A 68 69 THR A 69 3.8098 1 1 1 1 2 345 0 +R 689 68 ARG A 68 70 PRO A 70 6.1627 1 1 0 0 -60 79 0 +R 690 69 THR A 69 49 GLY A 49 6.4717 0 1 1 1 9 9 0 +R 691 69 THR A 69 50 SER A 50 5.5332 1 1 0 0 0 60 0 +R 692 69 THR A 69 60 SER A 60 6.5717 1 1 1 0 -24 149 0 +R 693 69 THR A 69 61 ARG A 61 6.2823 1 1 0 0 -127 127 0 +R 694 69 THR A 69 66 ASP A 66 6.6481 1 1 1 1 128 149 0 +R 695 69 THR A 69 67 GLY A 67 6.0387 1 0 0 0 0 0 0 +R 696 69 THR A 69 68 ARG A 68 3.8098 1 1 1 0 -11 357 0 +R 697 69 THR A 69 70 PRO A 70 3.8378 1 1 0 0 -10 323 0 +R 698 69 THR A 69 71 GLY A 71 6.1353 1 1 1 1 1 1 0 +R 699 69 THR A 69 72 SER A 72 5.4835 1 1 1 1 166 196 0 +R 700 70 PRO A 70 49 GLY A 49 8.6350 0 1 0 0 -12 17 0 +R 701 70 PRO A 70 61 ARG A 61 8.0292 1 1 1 1 74 96 0 +R 702 70 PRO A 70 68 ARG A 68 6.1627 1 1 0 0 -40 50 0 +R 703 70 PRO A 70 69 THR A 69 3.8378 1 1 1 0 -8 416 0 +R 704 70 PRO A 70 71 GLY A 71 3.7037 1 1 1 0 -7 364 0 +R 705 70 PRO A 70 72 SER A 72 5.5397 1 0 0 0 0 0 0 +R 706 71 GLY A 71 61 ARG A 61 7.0231 0 1 1 0 -8 65 0 +R 707 71 GLY A 71 69 THR A 69 6.1353 1 1 1 1 1 1 0 +R 708 71 GLY A 71 70 PRO A 70 3.7037 1 1 0 0 -62 367 0 +R 709 71 GLY A 71 72 SER A 72 3.7913 1 1 1 1 16 371 0 +R 710 71 GLY A 71 73 ARG A 73 6.3954 1 1 1 0 -31 70 0 +R 711 72 SER A 72 60 SER A 60 6.4249 1 1 1 1 96 125 0 +R 712 72 SER A 72 61 ARG A 61 4.5693 1 1 0 0 0 31 0 +R 713 72 SER A 72 64 CYS A 64 7.6034 1 1 1 1 90 93 0 +R 714 72 SER A 72 65 ASN A 65 6.7196 0 1 0 0 0 44 0 +R 715 72 SER A 72 69 THR A 69 5.4835 1 1 1 1 6 95 0 +R 716 72 SER A 72 70 PRO A 70 5.5397 1 0 0 0 0 0 0 +R 717 72 SER A 72 71 GLY A 71 3.7913 1 1 1 0 -18 376 0 +R 718 72 SER A 72 73 ARG A 73 3.8449 1 1 1 1 35 355 0 +R 719 72 SER A 72 74 ASN A 74 5.9277 1 1 1 1 7 24 0 +R 720 73 ARG A 73 61 ARG A 61 6.4875 1 1 1 1 13 13 0 +R 721 73 ARG A 73 62 TRP A 62 4.7823 1 1 1 0 -114 187 0 +R 722 73 ARG A 73 71 GLY A 71 6.3954 1 1 0 0 -41 43 0 +R 723 73 ARG A 73 72 SER A 72 3.8449 1 1 0 0 -4 357 0 +R 724 73 ARG A 73 74 ASN A 74 3.8190 1 1 1 0 -20 388 0 +R 725 73 ARG A 73 75 LEU A 75 5.6080 1 1 1 0 -44 102 0 +R 726 74 ASN A 74 62 TRP A 62 5.5079 1 1 1 1 13 21 0 +R 727 74 ASN A 74 63 TRP A 63 4.6495 1 1 0 0 0 12 0 +R 728 74 ASN A 74 64 CYS A 64 4.3585 1 1 0 0 0 15 0 +R 729 74 ASN A 74 65 ASN A 65 5.3596 1 1 1 0 -112 159 0 +R 730 74 ASN A 74 72 SER A 72 5.9277 1 1 1 0 -2 24 0 +R 731 74 ASN A 74 73 ARG A 73 3.8190 1 1 0 0 -48 374 0 +R 732 74 ASN A 74 75 LEU A 75 3.7831 1 1 1 1 15 371 0 +R 733 74 ASN A 74 76 CYS A 76 5.6175 1 0 0 0 0 0 0 +R 734 74 ASN A 74 77 ASN A 77 5.1976 1 1 1 1 25 156 0 +R 735 74 ASN A 74 78 ILE A 78 6.8599 1 1 1 1 14 235 0 +R 736 74 ASN A 74 79 PRO A 79 8.2352 0 1 0 0 -2 3 0 +R 737 75 LEU A 75 62 TRP A 62 5.9402 1 1 1 0 0 128 0 +R 738 75 LEU A 75 63 TRP A 63 4.5592 1 1 1 1 134 134 0 +R 739 75 LEU A 75 73 ARG A 73 5.6080 1 1 1 0 -23 144 0 +R 740 75 LEU A 75 74 ASN A 74 3.7831 1 1 0 0 -13 349 0 +R 741 75 LEU A 75 76 CYS A 76 3.8164 1 1 1 1 18 338 0 +R 742 75 LEU A 75 77 ASN A 77 5.4213 1 1 1 0 -15 21 0 +R 743 75 LEU A 75 97 LYS A 97 8.3701 0 1 1 0 -39 65 0 +R 744 75 LEU A 75 101 ASP A 101 10.9431 0 1 0 0 -36 36 0 +R 745 76 CYS A 76 63 TRP A 63 5.1313 1 1 1 0 -12 99 0 +R 746 76 CYS A 76 74 ASN A 74 5.6175 1 0 0 0 0 0 0 +R 747 76 CYS A 76 75 LEU A 75 3.8164 1 1 0 0 -15 369 0 +R 748 76 CYS A 76 77 ASN A 77 3.7920 1 1 1 0 -31 391 0 +R 749 76 CYS A 76 78 ILE A 78 5.6591 1 1 1 0 -13 45 0 +R 750 76 CYS A 76 94 CYS A 94 5.4641 1 1 1 1 31 297 0 +R 751 76 CYS A 76 97 LYS A 97 7.3462 1 1 1 1 1 27 0 +R 752 77 ASN A 77 74 ASN A 74 5.1976 1 1 1 0 -37 102 0 +R 753 77 ASN A 77 75 LEU A 75 5.4213 1 1 0 0 -13 13 0 +R 754 77 ASN A 77 76 CYS A 76 3.7920 1 1 0 0 -63 407 0 +R 755 77 ASN A 77 78 ILE A 78 3.7096 1 1 1 0 -12 368 0 +R 756 77 ASN A 77 79 PRO A 79 7.0593 0 1 0 0 -8 8 0 +R 757 78 ILE A 78 63 TRP A 63 7.9100 1 0 0 0 0 0 0 +R 758 78 ILE A 78 64 CYS A 64 5.2721 1 1 1 1 22 22 0 +R 759 78 ILE A 78 65 ASN A 65 6.2178 1 1 1 1 125 126 0 +R 760 78 ILE A 78 74 ASN A 74 6.8599 1 1 1 0 0 12 0 +R 761 78 ILE A 78 76 CYS A 76 5.6591 1 1 1 1 40 132 0 +R 762 78 ILE A 78 77 ASN A 77 3.7096 1 1 0 0 -33 394 0 +R 763 78 ILE A 78 79 PRO A 79 3.7780 1 1 1 0 -15 412 0 +R 764 78 ILE A 78 80 CYS A 80 6.2029 1 0 0 0 0 0 0 +R 765 78 ILE A 78 82 ALA A 82 6.8387 1 1 1 1 55 55 0 +R 766 78 ILE A 78 83 LEU A 83 8.3786 1 1 1 1 191 191 0 +R 767 78 ILE A 78 90 ALA A 90 8.2888 0 1 1 1 46 47 0 +R 768 78 ILE A 78 94 CYS A 94 8.8596 1 1 1 1 5 5 0 +R 769 79 PRO A 79 64 CYS A 64 5.5062 1 0 0 0 0 0 0 +R 770 79 PRO A 79 65 ASN A 65 4.7112 1 1 1 0 -57 79 0 +R 771 79 PRO A 79 66 ASP A 66 5.9021 0 1 0 0 0 2 0 +R 772 79 PRO A 79 74 ASN A 74 8.2352 0 1 0 0 -5 5 0 +R 773 79 PRO A 79 77 ASN A 77 7.0593 0 1 0 0 -8 8 0 +R 774 79 PRO A 79 78 ILE A 78 3.7780 1 1 1 1 24 426 0 +R 775 79 PRO A 79 80 CYS A 80 3.8413 1 1 1 0 -13 376 0 +R 776 79 PRO A 79 81 SER A 81 5.4310 1 1 0 0 -74 74 0 +R 777 79 PRO A 79 82 ALA A 82 5.6534 1 1 1 1 81 143 0 +R 778 80 CYS A 80 53 TYR A 53 6.5643 1 1 1 1 74 104 0 +R 779 80 CYS A 80 60 SER A 60 6.8143 1 1 0 0 0 16 0 +R 780 80 CYS A 80 64 CYS A 64 4.9610 1 1 0 0 0 284 0 +R 781 80 CYS A 80 65 ASN A 65 5.3811 1 1 1 1 23 52 0 +R 782 80 CYS A 80 66 ASP A 66 5.2749 1 1 1 1 11 49 0 +R 783 80 CYS A 80 78 ILE A 78 6.2029 1 0 0 0 0 0 0 +R 784 80 CYS A 80 79 PRO A 79 3.8413 1 1 0 0 -57 340 0 +R 785 80 CYS A 80 81 SER A 81 3.8305 1 1 1 1 7 326 0 +R 786 80 CYS A 80 82 ALA A 82 5.3155 1 0 0 0 0 0 0 +R 787 80 CYS A 80 83 LEU A 83 5.4505 1 1 1 1 57 153 0 +R 788 81 SER A 81 53 TYR A 53 7.5160 0 1 0 0 0 9 0 +R 789 81 SER A 81 79 PRO A 79 5.4310 1 1 0 0 -86 87 0 +R 790 81 SER A 81 80 CYS A 80 3.8305 1 1 0 0 -25 371 0 +R 791 81 SER A 81 82 ALA A 82 3.8111 1 1 1 1 44 373 0 +R 792 81 SER A 81 83 LEU A 83 5.1899 1 0 0 0 0 0 0 +R 793 81 SER A 81 84 LEU A 84 5.4183 1 1 1 1 42 165 0 +R 794 81 SER A 81 85 SER A 85 7.5229 0 1 1 1 10 14 0 +R 795 82 ALA A 82 78 ILE A 78 6.8387 1 1 1 1 107 107 0 +R 796 82 ALA A 82 79 PRO A 79 5.6534 1 1 1 0 -24 101 0 +R 797 82 ALA A 82 80 CYS A 80 5.3155 1 0 0 0 0 0 0 +R 798 82 ALA A 82 81 SER A 81 3.8111 1 1 1 0 -1 378 0 +R 799 82 ALA A 82 83 LEU A 83 3.7944 1 1 1 1 8 341 0 +R 800 82 ALA A 82 84 LEU A 84 5.4609 1 1 1 1 13 13 0 +R 801 82 ALA A 82 85 SER A 85 5.9325 1 1 0 0 0 115 0 +R 802 82 ALA A 82 90 ALA A 90 6.7558 1 1 1 0 -10 50 0 +R 803 83 LEU A 83 40 THR A 40 7.4963 0 1 0 0 -2 3 0 +R 804 83 LEU A 83 53 TYR A 53 6.1854 1 1 1 1 30 30 0 +R 805 83 LEU A 83 54 GLY A 54 5.3232 1 1 0 0 0 93 0 +R 806 83 LEU A 83 55 ILE A 55 7.8149 0 1 1 1 1 1 0 +R 807 83 LEU A 83 58 ILE A 58 7.8716 1 1 1 1 103 103 0 +R 808 83 LEU A 83 64 CYS A 64 8.6424 1 1 1 1 7 170 0 +R 809 83 LEU A 83 78 ILE A 78 8.3786 1 1 1 1 102 102 0 +R 810 83 LEU A 83 80 CYS A 80 5.4505 1 1 0 0 -36 36 0 +R 811 83 LEU A 83 81 SER A 81 5.1899 1 0 0 0 0 0 0 +R 812 83 LEU A 83 82 ALA A 82 3.7944 1 1 0 0 -15 371 0 +R 813 83 LEU A 83 84 LEU A 84 3.8682 1 1 1 1 25 309 0 +R 814 83 LEU A 83 85 SER A 85 5.7541 1 1 1 1 2 4 0 +R 815 83 LEU A 83 90 ALA A 90 6.0317 1 1 0 0 -1 2 0 +R 816 83 LEU A 83 91 SER A 91 5.2891 1 1 1 0 -36 193 0 +R 817 83 LEU A 83 94 CYS A 94 8.8633 1 1 1 1 3 3 0 +R 818 84 LEU A 84 40 THR A 40 5.0346 1 1 1 1 15 152 0 +R 819 84 LEU A 84 41 GLN A 41 4.8606 1 1 1 0 -53 101 0 +R 820 84 LEU A 84 42 ALA A 42 7.3563 1 1 0 0 -30 30 0 +R 821 84 LEU A 84 43 THR A 43 8.5599 1 1 1 1 95 95 0 +R 822 84 LEU A 84 53 TYR A 53 6.6054 1 1 1 1 40 40 0 +R 823 84 LEU A 84 54 GLY A 54 4.8428 1 1 0 0 -115 115 0 +R 824 84 LEU A 84 80 CYS A 80 7.5698 0 1 0 0 -15 15 0 +R 825 84 LEU A 84 81 SER A 81 5.4183 1 1 0 0 -39 91 0 +R 826 84 LEU A 84 82 ALA A 82 5.4609 1 0 0 0 0 0 0 +R 827 84 LEU A 84 83 LEU A 83 3.8682 1 1 0 0 -13 366 0 +R 828 84 LEU A 84 85 SER A 85 3.7737 1 1 1 1 10 356 0 +R 829 84 LEU A 84 86 SER A 86 6.7769 0 1 1 1 3 3 0 +R 830 85 SER A 85 40 THR A 40 6.2303 1 1 0 0 -14 75 0 +R 831 85 SER A 85 81 SER A 81 7.5229 0 1 1 1 2 13 0 +R 832 85 SER A 85 82 ALA A 82 5.9325 1 1 0 0 0 73 0 +R 833 85 SER A 85 83 LEU A 83 5.7541 1 1 0 0 -1 1 0 +R 834 85 SER A 85 84 LEU A 84 3.7737 1 1 0 0 -16 376 0 +R 835 85 SER A 85 86 SER A 86 3.8390 1 1 1 1 59 381 0 +R 836 85 SER A 85 87 ASP A 87 5.2323 1 1 1 1 8 169 0 +R 837 86 SER A 86 1 LYS A 1 5.1894 1 1 1 0 -65 208 0 +R 838 86 SER A 86 3 PHE A 3 8.8941 1 1 0 0 -115 115 0 +R 839 86 SER A 86 40 THR A 40 6.2290 1 0 0 0 0 0 0 +R 840 86 SER A 86 84 LEU A 84 6.7769 0 1 1 1 2 2 0 +R 841 86 SER A 86 85 SER A 85 3.8390 1 1 1 1 5 348 0 +R 842 86 SER A 86 87 ASP A 87 3.8507 1 1 1 1 20 342 0 +R 843 86 SER A 86 88 ILE A 88 6.0595 1 1 1 1 25 25 0 +R 844 87 ASP A 87 3 PHE A 3 10.7648 0 1 0 0 0 1 0 +R 845 87 ASP A 87 15 HIS A 15 10.7991 0 1 1 1 6 22 0 +R 846 87 ASP A 87 85 SER A 85 5.2323 1 1 0 0 -45 134 0 +R 847 87 ASP A 87 86 SER A 86 3.8507 1 1 0 0 -16 361 0 +R 848 87 ASP A 87 88 ILE A 88 3.8129 1 1 1 1 35 371 0 +R 849 87 ASP A 87 89 THR A 89 5.6671 1 1 1 1 207 234 0 +R 850 87 ASP A 87 90 ALA A 90 7.7602 0 1 1 1 9 9 0 +R 851 88 ILE A 88 3 PHE A 3 10.4372 1 1 1 1 143 143 0 +R 852 88 ILE A 88 8 LEU A 8 9.1166 1 0 0 0 0 0 0 +R 853 88 ILE A 88 11 ALA A 11 7.9512 1 1 1 1 135 162 0 +R 854 88 ILE A 88 12 MET A 12 8.1191 1 1 1 1 11 35 0 +R 855 88 ILE A 88 15 HIS A 15 8.6713 1 1 1 0 -29 35 0 +R 856 88 ILE A 88 40 THR A 40 7.7607 1 1 1 1 47 47 0 +R 857 88 ILE A 88 55 ILE A 55 8.0660 1 1 1 1 35 35 0 +R 858 88 ILE A 88 86 SER A 86 6.0595 1 1 0 0 -4 4 0 +R 859 88 ILE A 88 87 ASP A 87 3.8129 1 1 1 1 1 353 0 +R 860 88 ILE A 88 89 THR A 89 3.7790 1 1 1 1 2 372 0 +R 861 88 ILE A 88 90 ALA A 90 5.7738 1 1 0 0 0 1 0 +R 862 88 ILE A 88 91 SER A 91 5.4216 1 1 1 1 4 23 0 +R 863 88 ILE A 88 92 VAL A 92 6.1853 1 1 1 1 212 212 0 +R 864 89 THR A 89 14 ARG A 14 10.0339 0 1 1 1 3 3 0 +R 865 89 THR A 89 15 HIS A 15 7.1554 1 1 1 1 55 149 0 +R 866 89 THR A 89 87 ASP A 87 5.6671 1 1 1 1 106 158 0 +R 867 89 THR A 89 88 ILE A 88 3.7790 1 1 0 0 -8 335 0 +R 868 89 THR A 89 90 ALA A 90 3.8512 1 1 1 1 13 372 0 +R 869 89 THR A 89 91 SER A 91 5.5409 1 0 0 0 0 0 0 +R 870 89 THR A 89 92 VAL A 92 5.2314 1 0 0 0 0 0 0 +R 871 89 THR A 89 93 ASN A 93 6.2336 1 1 1 1 47 199 0 +R 872 90 ALA A 90 78 ILE A 78 8.2888 0 1 1 1 45 45 0 +R 873 90 ALA A 90 82 ALA A 82 6.7558 1 1 1 0 -58 158 0 +R 874 90 ALA A 90 83 LEU A 83 6.0317 1 1 1 1 27 27 0 +R 875 90 ALA A 90 87 ASP A 87 7.7602 0 1 1 0 -2 4 0 +R 876 90 ALA A 90 88 ILE A 88 5.7738 1 0 0 0 0 0 0 +R 877 90 ALA A 90 89 THR A 89 3.8512 1 1 1 0 -8 373 0 +R 878 90 ALA A 90 91 SER A 91 3.8404 1 1 1 1 8 356 0 +R 879 90 ALA A 90 92 VAL A 92 5.4287 1 0 0 0 0 0 0 +R 880 90 ALA A 90 93 ASN A 93 5.1567 1 1 0 0 -1 28 0 +R 881 90 ALA A 90 94 CYS A 94 6.0715 1 1 1 1 85 133 0 +R 882 91 SER A 91 55 ILE A 55 7.4339 1 1 1 0 -16 119 0 +R 883 91 SER A 91 58 ILE A 58 7.7587 1 1 0 0 -3 14 0 +R 884 91 SER A 91 83 LEU A 83 5.2891 1 1 1 1 145 220 0 +R 885 91 SER A 91 88 ILE A 88 5.4216 1 1 0 0 0 37 0 +R 886 91 SER A 91 89 THR A 89 5.5409 1 0 0 0 0 0 0 +R 887 91 SER A 91 90 ALA A 90 3.8404 1 1 0 0 -14 349 0 +R 888 91 SER A 91 92 VAL A 92 3.7489 1 1 1 1 20 342 0 +R 889 91 SER A 91 93 ASN A 93 5.6148 1 0 0 0 0 0 0 +R 890 91 SER A 91 94 CYS A 94 5.2309 1 0 0 0 0 0 0 +R 891 91 SER A 91 95 ALA A 95 5.9715 1 1 1 1 115 161 0 +R 892 92 VAL A 92 12 MET A 12 7.4759 0 1 1 1 3 3 0 +R 893 92 VAL A 92 15 HIS A 15 7.1674 1 1 1 1 73 167 0 +R 894 92 VAL A 92 17 LEU A 17 7.6268 1 1 1 1 98 98 0 +R 895 92 VAL A 92 56 LEU A 56 8.3697 0 1 1 1 3 3 0 +R 896 92 VAL A 92 88 ILE A 88 6.1853 1 1 1 1 57 201 0 +R 897 92 VAL A 92 89 THR A 89 5.2314 1 1 0 0 -8 9 0 +R 898 92 VAL A 92 90 ALA A 90 5.4287 1 0 0 0 0 0 0 +R 899 92 VAL A 92 91 SER A 91 3.7489 1 1 0 0 -15 368 0 +R 900 92 VAL A 92 93 ASN A 93 3.8908 1 1 1 0 0 322 0 +R 901 92 VAL A 92 94 CYS A 94 5.4376 1 0 0 0 0 0 0 +R 902 92 VAL A 92 95 ALA A 95 4.9484 1 1 0 0 0 11 0 +R 903 92 VAL A 92 96 LYS A 96 6.2030 1 1 1 1 105 187 0 +R 904 93 ASN A 93 15 HIS A 15 8.5240 0 1 1 0 -2 4 0 +R 905 93 ASN A 93 89 THR A 89 6.2336 1 1 1 0 -125 178 0 +R 906 93 ASN A 93 90 ALA A 90 5.1567 1 1 1 0 -12 29 0 +R 907 93 ASN A 93 91 SER A 91 5.6148 1 0 0 0 0 0 0 +R 908 93 ASN A 93 92 VAL A 92 3.8908 1 1 0 0 -18 349 0 +R 909 93 ASN A 93 94 CYS A 94 3.7884 1 1 1 0 -4 357 0 +R 910 93 ASN A 93 95 ALA A 95 5.4444 1 0 0 0 0 0 0 +R 911 93 ASN A 93 96 LYS A 96 5.2091 1 1 1 0 -70 183 0 +R 912 93 ASN A 93 97 LYS A 97 6.7656 1 1 1 1 21 82 0 +R 913 94 CYS A 94 58 ILE A 58 8.1513 1 1 1 1 12 144 0 +R 914 94 CYS A 94 63 TRP A 63 7.4243 1 1 0 0 0 1 0 +R 915 94 CYS A 94 76 CYS A 76 5.4641 1 1 1 1 17 234 0 +R 916 94 CYS A 94 78 ILE A 78 8.8596 1 1 1 1 8 9 0 +R 917 94 CYS A 94 83 LEU A 83 8.8633 1 0 0 0 0 0 0 +R 918 94 CYS A 94 90 ALA A 90 6.0715 1 1 1 0 -62 76 0 +R 919 94 CYS A 94 91 SER A 91 5.2309 1 1 0 0 -11 11 0 +R 920 94 CYS A 94 92 VAL A 92 5.4376 1 0 0 0 0 0 0 +R 921 94 CYS A 94 93 ASN A 93 3.7884 1 1 0 0 -18 346 0 +R 922 94 CYS A 94 95 ALA A 95 3.8019 1 1 1 1 14 349 0 +R 923 94 CYS A 94 96 LYS A 96 5.3813 1 0 0 0 0 0 0 +R 924 94 CYS A 94 97 LYS A 97 5.2610 1 1 1 1 58 70 0 +R 925 94 CYS A 94 98 ILE A 98 6.4204 1 1 1 1 41 63 0 +R 926 95 ALA A 95 28 TRP A 28 9.8227 1 1 1 1 23 23 0 +R 927 95 ALA A 95 56 LEU A 56 7.7189 1 1 1 1 73 73 0 +R 928 95 ALA A 95 58 ILE A 58 7.7436 1 0 0 0 0 0 0 +R 929 95 ALA A 95 91 SER A 91 5.9715 1 1 1 0 -55 81 0 +R 930 95 ALA A 95 92 VAL A 92 4.9484 1 1 0 0 -18 18 0 +R 931 95 ALA A 95 93 ASN A 93 5.4444 1 0 0 0 0 0 0 +R 932 95 ALA A 95 94 CYS A 94 3.8019 1 1 0 0 -25 362 0 +R 933 95 ALA A 95 96 LYS A 96 3.7722 1 1 1 1 15 324 0 +R 934 95 ALA A 95 97 LYS A 97 5.3622 1 0 0 0 0 0 0 +R 935 95 ALA A 95 98 ILE A 98 4.9201 1 1 0 0 0 11 0 +R 936 95 ALA A 95 99 VAL A 99 6.0948 1 1 1 1 142 164 0 +R 937 95 ALA A 95 108 TRP A 108 10.0572 1 1 1 1 87 115 0 +R 938 96 LYS A 96 15 HIS A 15 10.3010 1 1 1 1 121 172 0 +R 939 96 LYS A 96 16 GLY A 16 9.2491 1 1 0 0 0 33 0 +R 940 96 LYS A 96 17 LEU A 17 7.9140 1 1 1 1 21 25 0 +R 941 96 LYS A 96 20 TYR A 20 7.7283 1 1 1 1 24 198 0 +R 942 96 LYS A 96 92 VAL A 92 6.2030 1 1 1 0 -37 54 0 +R 943 96 LYS A 96 93 ASN A 93 5.2091 1 1 0 0 -108 108 0 +R 944 96 LYS A 96 94 CYS A 94 5.3813 1 0 0 0 0 0 0 +R 945 96 LYS A 96 95 ALA A 95 3.7722 1 1 0 0 -8 346 0 +R 946 96 LYS A 96 97 LYS A 97 3.8989 1 1 1 1 13 346 0 +R 947 96 LYS A 96 98 ILE A 98 5.4629 1 0 0 0 0 0 0 +R 948 96 LYS A 96 99 VAL A 99 5.3592 1 1 0 0 0 2 0 +R 949 96 LYS A 96 100 SER A 100 6.2176 1 1 1 1 160 160 0 +R 950 97 LYS A 97 63 TRP A 63 9.0609 1 1 1 1 19 21 0 +R 951 97 LYS A 97 75 LEU A 75 8.3701 0 1 0 0 -14 51 0 +R 952 97 LYS A 97 76 CYS A 76 7.3462 1 1 1 1 4 83 0 +R 953 97 LYS A 97 93 ASN A 93 6.7656 1 1 0 0 -41 44 0 +R 954 97 LYS A 97 94 CYS A 94 5.2610 1 1 0 0 -30 31 0 +R 955 97 LYS A 97 95 ALA A 95 5.3622 1 0 0 0 0 0 0 +R 956 97 LYS A 97 96 LYS A 96 3.8989 1 1 0 0 -9 339 0 +R 957 97 LYS A 97 98 ILE A 98 3.7983 1 1 1 0 -7 374 0 +R 958 97 LYS A 97 99 VAL A 99 5.7111 1 0 0 0 0 0 0 +R 959 97 LYS A 97 100 SER A 100 5.2541 1 1 1 1 55 84 0 +R 960 97 LYS A 97 101 ASP A 101 6.4431 1 1 1 1 20 69 0 +R 961 98 ILE A 98 58 ILE A 58 8.9872 1 1 1 1 183 184 0 +R 962 98 ILE A 98 63 TRP A 63 8.1327 1 1 1 1 140 169 0 +R 963 98 ILE A 98 94 CYS A 94 6.4204 1 1 0 0 -44 44 0 +R 964 98 ILE A 98 95 ALA A 95 4.9201 1 1 0 0 -12 12 0 +R 965 98 ILE A 98 96 LYS A 96 5.4629 1 0 0 0 0 0 0 +R 966 98 ILE A 98 97 LYS A 97 3.7983 1 1 0 0 -16 354 0 +R 967 98 ILE A 98 99 VAL A 99 3.8242 1 1 1 1 2 332 0 +R 968 98 ILE A 98 100 SER A 100 5.4112 1 0 0 0 0 0 0 +R 969 98 ILE A 98 101 ASP A 101 5.2299 1 1 0 0 -140 143 0 +R 970 98 ILE A 98 104 GLY A 104 7.3510 0 1 0 0 -10 10 0 +R 971 98 ILE A 98 107 ALA A 107 7.4522 1 1 1 1 145 145 0 +R 972 98 ILE A 98 108 TRP A 108 9.5294 1 1 1 1 25 25 0 +R 973 99 VAL A 99 20 TYR A 20 8.7657 1 1 1 1 115 115 0 +R 974 99 VAL A 99 21 ARG A 21 7.5366 1 1 1 0 -13 25 0 +R 975 99 VAL A 99 23 TYR A 23 9.4052 1 1 1 1 105 105 0 +R 976 99 VAL A 99 28 TRP A 28 10.7709 1 1 1 1 28 28 0 +R 977 99 VAL A 99 95 ALA A 95 6.0948 1 1 1 0 -50 86 0 +R 978 99 VAL A 99 96 LYS A 96 5.3592 1 1 0 0 -29 29 0 +R 979 99 VAL A 99 97 LYS A 97 5.7111 1 0 0 0 0 0 0 +R 980 99 VAL A 99 98 ILE A 98 3.8242 1 1 0 0 -4 345 0 +R 981 99 VAL A 99 100 SER A 100 3.8421 1 1 1 0 -7 356 0 +R 982 99 VAL A 99 101 ASP A 101 5.3917 1 0 0 0 0 0 0 +R 983 99 VAL A 99 102 GLY A 102 7.0039 0 1 1 1 1 1 0 +R 984 99 VAL A 99 104 GLY A 104 4.3408 1 1 0 0 0 177 0 +R 985 99 VAL A 99 105 MET A 105 5.6156 1 1 1 1 46 46 0 +R 986 99 VAL A 99 108 TRP A 108 9.1731 1 1 1 1 5 5 0 +R 987 100 SER A 100 20 TYR A 20 9.2326 1 1 1 1 32 33 0 +R 988 100 SER A 100 21 ARG A 21 7.2028 1 1 1 1 183 249 0 +R 989 100 SER A 100 96 LYS A 96 6.2176 1 1 1 1 89 119 0 +R 990 100 SER A 100 97 LYS A 97 5.2541 1 1 0 0 0 48 0 +R 991 100 SER A 100 98 ILE A 98 5.4112 1 0 0 0 0 0 0 +R 992 100 SER A 100 99 VAL A 99 3.8421 1 1 0 0 -13 357 0 +R 993 100 SER A 100 101 ASP A 101 3.8203 1 1 1 1 13 316 0 +R 994 100 SER A 100 102 GLY A 102 5.9600 1 1 1 1 44 50 0 +R 995 101 ASP A 101 63 TRP A 63 11.5849 1 1 0 0 -131 140 0 +R 996 101 ASP A 101 75 LEU A 75 10.9431 0 1 0 0 -44 44 0 +R 997 101 ASP A 101 97 LYS A 97 6.4431 1 1 0 0 -35 37 0 +R 998 101 ASP A 101 98 ILE A 98 5.2299 1 1 0 0 -86 92 0 +R 999 101 ASP A 101 99 VAL A 99 5.3917 1 0 0 0 0 0 0 +R 1000 101 ASP A 101 100 SER A 100 3.8203 1 1 0 0 -8 347 0 +R 1001 101 ASP A 101 102 GLY A 102 3.7587 1 1 1 1 27 326 0 +R 1002 101 ASP A 101 103 ASN A 103 6.3794 1 1 1 1 17 20 0 +R 1003 102 GLY A 102 99 VAL A 99 7.0039 0 1 0 0 0 1 0 +R 1004 102 GLY A 102 100 SER A 100 5.9600 1 1 1 1 29 43 0 +R 1005 102 GLY A 102 101 ASP A 101 3.7587 1 1 0 0 -28 409 0 +R 1006 102 GLY A 102 103 ASN A 103 3.8452 1 1 1 1 49 380 0 +R 1007 102 GLY A 102 104 GLY A 104 5.4960 1 1 1 1 2 18 0 +R 1008 103 ASN A 103 23 TYR A 23 12.4992 0 1 0 0 0 1 0 +R 1009 103 ASN A 103 101 ASP A 101 6.3794 1 1 1 0 -1 11 0 +R 1010 103 ASN A 103 102 GLY A 102 3.8452 1 1 1 1 10 398 0 +R 1011 103 ASN A 103 104 GLY A 104 3.8263 1 1 1 1 18 340 0 +R 1012 103 ASN A 103 105 MET A 105 6.4440 1 0 0 0 0 0 0 +R 1013 103 ASN A 103 106 ASN A 106 5.4867 1 1 1 1 228 242 0 +R 1014 103 ASN A 103 107 ALA A 107 6.1089 0 1 1 0 -27 32 0 +R 1015 104 GLY A 104 23 TYR A 23 8.8920 1 1 0 0 0 56 0 +R 1016 104 GLY A 104 99 VAL A 99 4.3408 1 1 1 1 6 132 0 +R 1017 104 GLY A 104 102 GLY A 102 5.4960 1 1 1 1 2 26 0 +R 1018 104 GLY A 104 103 ASN A 103 3.8263 1 1 0 0 -32 376 0 +R 1019 104 GLY A 104 105 MET A 105 3.8395 1 1 1 1 27 367 0 +R 1020 104 GLY A 104 106 ASN A 106 5.3817 1 1 1 1 5 5 0 +R 1021 104 GLY A 104 107 ALA A 107 6.2555 1 1 1 0 -10 94 0 +R 1022 105 MET A 105 23 TYR A 23 8.1535 1 1 1 1 72 178 0 +R 1023 105 MET A 105 27 ASN A 27 8.5492 1 1 0 0 -13 66 0 +R 1024 105 MET A 105 28 TRP A 28 8.7636 1 1 1 1 53 65 0 +R 1025 105 MET A 105 31 ALA A 31 8.7729 1 1 1 1 99 99 0 +R 1026 105 MET A 105 99 VAL A 99 5.6156 1 1 1 1 57 57 0 +R 1027 105 MET A 105 103 ASN A 103 6.4440 1 0 0 0 0 0 0 +R 1028 105 MET A 105 104 GLY A 104 3.8395 1 1 0 0 0 343 0 +R 1029 105 MET A 105 106 ASN A 106 3.7700 1 1 1 1 18 321 0 +R 1030 105 MET A 105 107 ALA A 107 5.0282 1 1 0 0 0 4 0 +R 1031 105 MET A 105 108 TRP A 108 5.6343 1 1 1 1 127 148 0 +R 1032 105 MET A 105 111 TRP A 111 6.7413 1 1 1 1 127 195 0 +R 1033 106 ASN A 106 23 TYR A 23 11.3626 0 1 1 1 22 22 0 +R 1034 106 ASN A 106 103 ASN A 103 5.4867 1 1 1 1 84 175 0 +R 1035 106 ASN A 106 104 GLY A 104 5.3817 1 0 0 0 0 0 0 +R 1036 106 ASN A 106 105 MET A 105 3.7700 1 1 0 0 -17 357 0 +R 1037 106 ASN A 106 107 ALA A 107 3.8144 1 1 1 1 11 348 0 +R 1038 106 ASN A 106 108 TRP A 108 5.0992 1 1 1 1 12 12 0 +R 1039 106 ASN A 106 111 TRP A 111 6.6687 1 1 0 0 -47 56 0 +R 1040 106 ASN A 106 112 ARG A 112 5.3634 1 1 1 1 52 179 0 +R 1041 106 ASN A 106 116 LYS A 116 8.4376 1 1 1 1 81 209 0 +R 1042 107 ALA A 107 63 TRP A 63 11.8922 0 1 1 1 15 15 0 +R 1043 107 ALA A 107 98 ILE A 98 7.4522 1 1 1 1 134 144 0 +R 1044 107 ALA A 107 103 ASN A 103 6.1089 0 1 1 1 17 34 0 +R 1045 107 ALA A 107 104 GLY A 104 6.2555 1 1 1 0 -68 78 0 +R 1046 107 ALA A 107 105 MET A 105 5.0282 1 0 0 0 0 0 0 +R 1047 107 ALA A 107 106 ASN A 106 3.8144 1 1 0 0 -31 366 0 +R 1048 107 ALA A 107 108 TRP A 108 3.8323 1 1 1 1 1 344 0 +R 1049 107 ALA A 107 109 VAL A 109 6.1899 1 1 1 1 11 40 0 +R 1050 107 ALA A 107 112 ARG A 112 7.9613 0 1 1 1 4 4 0 +R 1051 108 TRP A 108 28 TRP A 28 10.2074 1 1 1 1 79 79 0 +R 1052 108 TRP A 108 31 ALA A 31 7.3841 0 1 1 1 1 1 0 +R 1053 108 TRP A 108 35 GLU A 35 8.1006 1 1 1 0 -56 82 0 +R 1054 108 TRP A 108 56 LEU A 56 8.2153 1 1 1 1 43 175 0 +R 1055 108 TRP A 108 57 GLN A 57 8.2910 0 1 1 1 8 22 0 +R 1056 108 TRP A 108 58 ILE A 58 8.7782 0 1 0 0 -2 2 0 +R 1057 108 TRP A 108 95 ALA A 95 10.0572 1 1 1 1 155 217 0 +R 1058 108 TRP A 108 98 ILE A 98 9.5294 1 1 1 1 106 112 0 +R 1059 108 TRP A 108 99 VAL A 99 9.1731 1 1 1 1 4 4 0 +R 1060 108 TRP A 108 105 MET A 105 5.6343 1 1 1 0 -53 139 0 +R 1061 108 TRP A 108 106 ASN A 106 5.0992 1 0 0 0 0 0 0 +R 1062 108 TRP A 108 107 ALA A 107 3.8323 1 1 0 0 -33 366 0 +R 1063 108 TRP A 108 109 VAL A 109 3.7513 1 1 1 1 24 373 0 +R 1064 108 TRP A 108 110 ALA A 110 5.5900 1 0 0 0 0 0 0 +R 1065 108 TRP A 108 111 TRP A 111 5.1466 1 1 1 1 47 47 0 +R 1066 108 TRP A 108 112 ARG A 112 6.3103 1 1 1 1 120 126 0 +R 1067 109 VAL A 109 35 GLU A 35 8.4267 0 1 0 0 -59 59 0 +R 1068 109 VAL A 109 107 ALA A 107 6.1899 1 1 1 0 -7 19 0 +R 1069 109 VAL A 109 108 TRP A 108 3.7513 1 1 0 0 -3 339 0 +R 1070 109 VAL A 109 110 ALA A 110 3.8699 1 1 1 0 -4 348 0 +R 1071 109 VAL A 109 111 TRP A 111 5.3384 1 0 0 0 0 0 0 +R 1072 109 VAL A 109 112 ARG A 112 5.1089 1 1 0 0 -73 99 0 +R 1073 109 VAL A 109 113 ASN A 113 6.1028 1 1 1 1 44 250 0 +R 1074 110 ALA A 110 34 PHE A 34 5.8542 1 1 1 1 122 157 0 +R 1075 110 ALA A 110 35 GLU A 35 6.0785 1 1 0 0 -66 82 0 +R 1076 110 ALA A 110 108 TRP A 108 5.5900 1 0 0 0 0 0 0 +R 1077 110 ALA A 110 109 VAL A 109 3.8699 1 1 1 0 -23 376 0 +R 1078 110 ALA A 110 111 TRP A 111 3.7781 1 1 1 1 1 300 0 +R 1079 110 ALA A 110 112 ARG A 112 5.4225 1 0 0 0 0 0 0 +R 1080 110 ALA A 110 113 ASN A 113 5.0166 1 1 0 0 0 2 0 +R 1081 110 ALA A 110 114 ARG A 114 5.4505 1 1 1 1 153 261 0 +R 1082 110 ALA A 110 115 CYS A 115 7.0432 1 0 0 0 0 0 0 +R 1083 111 TRP A 111 23 TYR A 23 11.4919 1 1 1 1 99 99 0 +R 1084 111 TRP A 111 27 ASN A 27 7.6026 1 1 1 1 11 193 0 +R 1085 111 TRP A 111 31 ALA A 31 4.9166 1 1 1 1 14 14 0 +R 1086 111 TRP A 111 105 MET A 105 6.7413 1 1 1 1 2 178 0 +R 1087 111 TRP A 111 106 ASN A 106 6.6687 1 1 0 0 -113 113 0 +R 1088 111 TRP A 111 108 TRP A 108 5.1466 1 1 1 1 38 95 0 +R 1089 111 TRP A 111 109 VAL A 109 5.3384 1 0 0 0 0 0 0 +R 1090 111 TRP A 111 110 ALA A 110 3.7781 1 1 0 0 -34 370 0 +R 1091 111 TRP A 111 112 ARG A 112 3.7781 1 1 1 0 -31 326 0 +R 1092 111 TRP A 111 113 ASN A 113 5.5291 1 0 0 0 0 0 0 +R 1093 111 TRP A 111 114 ARG A 114 5.3790 1 0 0 0 0 0 0 +R 1094 111 TRP A 111 115 CYS A 115 4.7065 1 1 1 1 79 128 0 +R 1095 111 TRP A 111 116 LYS A 116 5.8402 1 1 1 1 317 340 0 +R 1096 111 TRP A 111 117 GLY A 117 9.5925 0 1 0 0 -2 2 0 +R 1097 112 ARG A 112 106 ASN A 106 5.3634 1 1 1 1 43 215 0 +R 1098 112 ARG A 112 107 ALA A 107 7.9613 0 1 1 1 6 6 0 +R 1099 112 ARG A 112 108 TRP A 108 6.3103 1 1 1 0 -6 24 0 +R 1100 112 ARG A 112 109 VAL A 109 5.1089 1 1 0 0 -58 149 0 +R 1101 112 ARG A 112 110 ALA A 110 5.4225 1 0 0 0 0 0 0 +R 1102 112 ARG A 112 111 TRP A 111 3.7781 1 1 0 0 -46 402 0 +R 1103 112 ARG A 112 113 ASN A 113 3.8018 1 1 1 1 50 413 0 +R 1104 112 ARG A 112 114 ARG A 114 5.8854 1 0 0 0 0 0 0 +R 1105 112 ARG A 112 116 LYS A 116 5.0012 1 1 1 0 -56 117 0 +R 1106 113 ASN A 113 109 VAL A 109 6.1028 1 1 0 0 -184 184 0 +R 1107 113 ASN A 113 110 ALA A 110 5.0166 1 1 0 0 0 1 0 +R 1108 113 ASN A 113 111 TRP A 111 5.5291 1 0 0 0 0 0 0 +R 1109 113 ASN A 113 112 ARG A 112 3.8018 1 1 1 1 12 483 0 +R 1110 113 ASN A 113 114 ARG A 114 3.7971 1 1 1 1 50 378 0 +R 1111 113 ASN A 113 115 CYS A 115 6.1707 1 0 0 0 0 0 0 +R 1112 114 ARG A 114 30 CYS A 30 8.0485 0 1 0 0 0 14 0 +R 1113 114 ARG A 114 34 PHE A 34 7.4511 1 1 1 0 -135 302 0 +R 1114 114 ARG A 114 110 ALA A 110 5.4505 1 1 1 0 -36 105 0 +R 1115 114 ARG A 114 111 TRP A 111 5.3790 1 0 0 0 0 0 0 +R 1116 114 ARG A 114 112 ARG A 112 5.8854 1 0 0 0 0 0 0 +R 1117 114 ARG A 114 113 ASN A 113 3.7971 1 1 1 1 11 420 0 +R 1118 114 ARG A 114 115 CYS A 115 3.7433 1 1 1 1 15 327 0 +R 1119 114 ARG A 114 116 LYS A 116 6.0770 1 0 0 0 0 0 0 +R 1120 114 ARG A 114 118 THR A 118 7.6414 1 1 1 0 -71 93 0 +R 1121 115 CYS A 115 30 CYS A 30 6.0621 1 1 1 1 1 281 0 +R 1122 115 CYS A 115 31 ALA A 31 6.6938 1 1 0 0 0 11 0 +R 1123 115 CYS A 115 34 PHE A 34 8.4896 1 1 0 0 0 16 0 +R 1124 115 CYS A 115 110 ALA A 110 7.0432 1 0 0 0 0 0 0 +R 1125 115 CYS A 115 111 TRP A 111 4.7065 1 1 1 1 89 123 0 +R 1126 115 CYS A 115 113 ASN A 113 6.1707 1 0 0 0 0 0 0 +R 1127 115 CYS A 115 114 ARG A 114 3.7433 1 1 0 0 -25 384 0 +R 1128 115 CYS A 115 116 LYS A 116 3.7040 1 1 1 0 -10 351 0 +R 1129 115 CYS A 115 117 GLY A 117 6.2355 1 1 1 1 2 2 0 +R 1130 115 CYS A 115 118 THR A 118 5.5424 1 1 1 1 145 145 0 +R 1131 115 CYS A 115 120 VAL A 120 6.5881 1 1 0 0 -19 19 0 +R 1132 116 LYS A 116 106 ASN A 106 8.4376 1 1 1 1 80 167 0 +R 1133 116 LYS A 116 111 TRP A 111 5.8402 1 1 1 1 35 186 0 +R 1134 116 LYS A 116 112 ARG A 112 5.0012 1 1 1 0 -34 104 0 +R 1135 116 LYS A 116 113 ASN A 113 6.5212 0 1 0 0 0 1 0 +R 1136 116 LYS A 116 114 ARG A 114 6.0770 1 1 1 1 1 1 0 +R 1137 116 LYS A 116 115 CYS A 115 3.7040 1 1 0 0 -6 350 0 +R 1138 116 LYS A 116 117 GLY A 117 3.8305 1 1 1 0 -5 378 0 +R 1139 116 LYS A 116 118 THR A 118 5.6274 1 1 1 0 -36 42 0 +R 1140 117 GLY A 117 111 TRP A 111 9.5925 0 1 0 0 -11 11 0 +R 1141 117 GLY A 117 115 CYS A 115 6.2355 1 1 1 1 2 2 0 +R 1142 117 GLY A 117 116 LYS A 116 3.8305 1 1 0 0 -24 389 0 +R 1143 117 GLY A 117 118 THR A 118 3.8121 1 1 1 1 5 362 0 +R 1144 117 GLY A 117 119 ASP A 119 6.8454 0 1 1 1 3 3 0 +R 1145 117 GLY A 117 120 VAL A 120 7.8645 0 1 0 0 -1 1 0 +R 1146 118 THR A 118 30 CYS A 30 9.7068 0 1 0 0 0 8 0 +R 1147 118 THR A 118 114 ARG A 114 7.6414 1 1 1 0 -66 98 0 +R 1148 118 THR A 118 115 CYS A 115 5.5424 1 1 1 1 38 121 0 +R 1149 118 THR A 118 116 LYS A 116 5.6274 1 1 0 0 -51 51 0 +R 1150 118 THR A 118 117 GLY A 117 3.8121 1 1 0 0 -20 397 0 +R 1151 118 THR A 118 119 ASP A 119 3.8550 1 1 1 1 39 360 0 +R 1152 118 THR A 118 120 VAL A 120 5.5102 1 1 1 0 -26 145 0 +R 1153 118 THR A 118 123 TRP A 123 10.4382 0 1 1 1 4 4 0 +R 1154 119 ASP A 119 117 GLY A 117 6.8454 0 1 1 1 2 2 0 +R 1155 119 ASP A 119 118 THR A 118 3.8550 1 1 1 1 2 342 0 +R 1156 119 ASP A 119 120 VAL A 120 3.7995 1 1 1 1 24 333 0 +R 1157 119 ASP A 119 121 GLN A 121 5.3570 1 1 1 0 -131 165 0 +R 1158 119 ASP A 119 122 ALA A 122 5.9464 1 1 1 0 -52 178 0 +R 1159 119 ASP A 119 123 TRP A 123 8.2961 0 1 1 0 -5 7 0 +R 1160 120 VAL A 120 24 SER A 24 8.3132 1 1 0 0 -27 27 0 +R 1161 120 VAL A 120 26 GLY A 26 4.8514 1 1 0 0 -2 84 0 +R 1162 120 VAL A 120 27 ASN A 27 5.7252 1 1 0 0 -182 182 0 +R 1163 120 VAL A 120 30 CYS A 30 6.6406 1 1 1 1 5 5 0 +R 1164 120 VAL A 120 115 CYS A 115 6.5881 1 1 1 0 -114 184 0 +R 1165 120 VAL A 120 118 THR A 118 5.5102 1 1 1 0 -21 53 0 +R 1166 120 VAL A 120 119 ASP A 119 3.7995 1 1 0 0 0 339 0 +R 1167 120 VAL A 120 121 GLN A 121 3.7722 1 1 1 1 5 364 0 +R 1168 120 VAL A 120 122 ALA A 122 5.1321 1 1 0 0 0 4 0 +R 1169 120 VAL A 120 123 TRP A 123 5.6692 1 1 1 1 75 93 0 +R 1170 121 GLN A 121 24 SER A 24 8.0270 0 1 0 0 -27 39 0 +R 1171 121 GLN A 121 119 ASP A 119 5.3570 1 1 1 0 -40 78 0 +R 1172 121 GLN A 121 120 VAL A 120 3.7722 1 1 1 1 14 385 0 +R 1173 121 GLN A 121 122 ALA A 122 3.7981 1 1 1 1 20 347 0 +R 1174 121 GLN A 121 123 TRP A 123 5.2614 1 0 0 0 0 0 0 +R 1175 121 GLN A 121 124 ILE A 124 5.7666 1 1 1 0 -5 212 0 +R 1176 121 GLN A 121 125 ARG A 125 6.5900 1 1 1 1 15 31 0 +R 1177 122 ALA A 122 5 ARG A 5 10.7979 1 1 1 1 28 33 0 +R 1178 122 ALA A 122 119 ASP A 119 5.9464 1 1 1 0 -111 132 0 +R 1179 122 ALA A 122 120 VAL A 120 5.1321 1 0 0 0 0 0 0 +R 1180 122 ALA A 122 121 GLN A 121 3.7981 1 1 0 0 -25 367 0 +R 1181 122 ALA A 122 123 TRP A 123 3.8012 1 1 1 1 22 381 0 +R 1182 122 ALA A 122 124 ILE A 124 5.5575 1 1 1 1 12 12 0 +R 1183 122 ALA A 122 125 ARG A 125 5.1332 1 1 1 0 -27 197 0 +R 1184 123 TRP A 123 5 ARG A 5 7.4230 1 1 1 1 60 235 0 +R 1185 123 TRP A 123 26 GLY A 26 5.1305 1 1 0 0 -12 12 0 +R 1186 123 TRP A 123 29 VAL A 29 6.3580 1 1 1 1 87 87 0 +R 1187 123 TRP A 123 30 CYS A 30 6.2969 1 1 1 1 63 137 0 +R 1188 123 TRP A 123 33 LYS A 33 9.2780 1 1 1 1 169 181 0 +R 1189 123 TRP A 123 34 PHE A 34 11.6342 1 1 1 1 115 121 0 +R 1190 123 TRP A 123 118 THR A 118 10.4382 0 1 1 1 12 12 0 +R 1191 123 TRP A 123 119 ASP A 119 8.2961 0 1 1 1 14 14 0 +R 1192 123 TRP A 123 120 VAL A 120 5.6692 1 1 0 0 -65 95 0 +R 1193 123 TRP A 123 121 GLN A 121 5.2614 1 0 0 0 0 0 0 +R 1194 123 TRP A 123 122 ALA A 122 3.8012 1 1 0 0 -32 379 0 +R 1195 123 TRP A 123 124 ILE A 124 3.7623 1 1 1 1 15 327 0 +R 1196 123 TRP A 123 125 ARG A 125 5.6814 1 0 0 0 0 0 0 +R 1197 124 ILE A 124 5 ARG A 5 7.5648 1 1 0 0 0 6 0 +R 1198 124 ILE A 124 9 ALA A 9 6.6308 1 1 1 1 111 111 0 +R 1199 124 ILE A 124 25 LEU A 25 7.3355 1 1 1 1 109 113 0 +R 1200 124 ILE A 124 26 GLY A 26 5.7057 1 1 0 0 -36 41 0 +R 1201 124 ILE A 124 29 VAL A 29 7.6402 1 1 1 1 2 2 0 +R 1202 124 ILE A 124 121 GLN A 121 5.7666 1 1 1 0 -135 159 0 +R 1203 124 ILE A 124 122 ALA A 122 5.5575 1 0 0 0 0 0 0 +R 1204 124 ILE A 124 123 TRP A 123 3.7623 1 1 0 0 -12 388 0 +R 1205 124 ILE A 124 125 ARG A 125 3.8072 1 1 1 1 13 344 0 +R 1206 124 ILE A 124 126 GLY A 126 6.3927 1 1 1 1 1 1 0 +R 1207 124 ILE A 124 127 CYS A 127 5.6869 1 1 1 1 82 107 0 +R 1208 124 ILE A 124 129 LEU A 129 8.6327 1 1 1 1 73 73 0 +R 1209 125 ARG A 125 5 ARG A 5 9.6347 1 1 1 1 174 208 0 +R 1210 125 ARG A 125 121 GLN A 121 6.5900 1 1 1 0 -20 38 0 +R 1211 125 ARG A 125 122 ALA A 122 5.1332 1 1 1 1 2 181 0 +R 1212 125 ARG A 125 123 TRP A 123 5.6814 1 0 0 0 0 0 0 +R 1213 125 ARG A 125 124 ILE A 124 3.8072 1 1 0 0 -21 350 0 +R 1214 125 ARG A 125 126 GLY A 126 3.8134 1 1 1 0 -8 370 0 +R 1215 125 ARG A 125 127 CYS A 127 5.5076 1 0 0 0 0 0 0 +R 1216 126 GLY A 126 5 ARG A 5 10.0418 0 1 1 1 2 13 0 +R 1217 126 GLY A 126 6 CYS A 6 7.9731 0 1 0 0 0 25 0 +R 1218 126 GLY A 126 124 ILE A 124 6.3927 1 1 1 1 1 1 0 +R 1219 126 GLY A 126 125 ARG A 125 3.8134 1 1 0 0 -21 405 0 +R 1220 126 GLY A 126 127 CYS A 127 3.7148 1 1 1 1 21 351 0 +R 1221 126 GLY A 126 128 ARG A 128 6.5352 1 1 1 1 10 24 0 +R 1222 127 CYS A 127 5 ARG A 5 8.4264 1 1 0 0 0 42 0 +R 1223 127 CYS A 127 6 CYS A 6 5.3179 1 1 1 1 22 251 0 +R 1224 127 CYS A 127 124 ILE A 124 5.6869 1 1 1 0 -32 103 0 +R 1225 127 CYS A 127 125 ARG A 125 5.5076 1 0 0 0 0 0 0 +R 1226 127 CYS A 127 126 GLY A 126 3.7148 1 1 1 0 -24 391 0 +R 1227 127 CYS A 127 128 ARG A 128 3.7185 1 1 1 1 10 344 0 +R 1228 127 CYS A 127 129 LEU A 129 5.8167 1 1 1 1 102 126 0 +R 1229 128 ARG A 128 6 CYS A 6 7.4354 0 1 0 0 -5 11 0 +R 1230 128 ARG A 128 10 ALA A 10 7.8262 0 1 0 0 -52 52 0 +R 1231 128 ARG A 128 126 GLY A 126 6.5352 1 1 1 0 -1 17 0 +R 1232 128 ARG A 128 127 CYS A 127 3.7185 1 1 0 0 -5 354 0 +R 1233 128 ARG A 128 129 LEU A 129 3.7614 1 1 1 0 -47 416 0 +R 1234 129 LEU A 129 9 ALA A 9 7.9700 1 1 1 0 -1 20 0 +R 1235 129 LEU A 129 10 ALA A 10 6.1221 1 1 1 0 -12 221 0 +R 1236 129 LEU A 129 13 LYS A 13 8.0834 1 1 1 0 -26 153 0 +R 1237 129 LEU A 129 25 LEU A 25 10.5318 1 1 1 1 101 101 0 +R 1238 129 LEU A 129 124 ILE A 124 8.6327 1 1 1 1 138 138 0 +R 1239 129 LEU A 129 127 CYS A 127 5.8167 1 1 1 1 31 53 0 +R 1240 129 LEU A 129 128 ARG A 128 3.7614 1 1 0 0 -27 412 0 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb new file mode 100644 index 00000000..745c7e5c --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/cg.pdb @@ -0,0 +1,616 @@ +ATOM 1 BB LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 2 SC1 LYS A 1 -0.175 10.268 8.951 1.00 0.00 +ATOM 3 SC2 LYS A 1 -3.127 10.593 7.836 1.00 0.00 +ATOM 4 CA LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 5 BB VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 6 SC1 VAL A 2 3.923 14.682 6.344 1.00 0.00 +ATOM 7 CA VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 8 BB PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 9 SC1 PHE A 3 -2.271 14.922 9.060 1.00 0.00 +ATOM 10 SC2 PHE A 3 -2.225 13.320 10.859 1.00 0.00 +ATOM 11 SC3 PHE A 3 -3.911 13.493 10.120 1.00 0.00 +ATOM 12 CA PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 13 BB GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 14 CA GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 15 BB ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 16 SC1 ARG A 5 -4.291 23.082 5.095 1.00 0.00 +ATOM 17 SC2 ARG A 5 -6.292 24.514 3.025 1.00 0.00 +ATOM 18 CA ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 19 BB CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 20 SC1 CYS A 6 -8.652 20.827 3.310 1.00 0.00 +ATOM 21 CA CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 22 BB GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 23 SC1 GLU A 7 -5.177 13.208 6.001 1.00 0.00 +ATOM 24 CA GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 25 BB LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 26 SC1 LEU A 8 -4.062 18.230 11.133 1.00 0.00 +ATOM 27 CA LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 28 BB ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 29 SC1 ALA A 9 -9.039 21.012 8.954 1.00 0.00 +ATOM 30 CA ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 31 BB ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 32 SC1 ALA A 10 -11.457 16.297 8.313 1.00 0.00 +ATOM 33 CA ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 34 BB ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 35 SC1 ALA A 11 -8.153 14.250 12.041 1.00 0.00 +ATOM 36 CA ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 37 BB MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 38 SC1 MET A 12 -6.277 19.726 14.570 1.00 0.00 +ATOM 39 CA MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 40 BB LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 41 SC1 LYS A 13 -14.633 19.476 12.605 1.00 0.00 +ATOM 42 SC2 LYS A 13 -17.419 20.478 11.394 1.00 0.00 +ATOM 43 CA LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 44 BB ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 45 SC1 ARG A 14 -13.808 12.618 13.693 1.00 0.00 +ATOM 46 SC2 ARG A 14 -12.388 9.675 14.151 1.00 0.00 +ATOM 47 CA ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 48 BB HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 49 SC1 HIS A 15 -10.087 14.082 17.707 1.00 0.00 +ATOM 50 SC2 HIS A 15 -9.556 11.718 17.990 1.00 0.00 +ATOM 51 SC3 HIS A 15 -9.583 12.289 16.299 1.00 0.00 +ATOM 52 CA HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 53 BB GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 54 CA GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 55 BB LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 56 SC1 LEU A 17 -8.675 20.110 19.004 1.00 0.00 +ATOM 57 CA LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 58 BB ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 59 SC1 ASP A 18 -14.750 24.262 14.952 1.00 0.00 +ATOM 60 CA ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 61 BB ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 62 SC1 ASN A 19 -15.703 27.056 17.780 1.00 0.00 +ATOM 63 CA ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 64 BB TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 65 SC1 TYR A 20 -11.624 22.480 22.680 1.00 0.00 +ATOM 66 SC2 TYR A 20 -12.378 20.931 24.472 1.00 0.00 +ATOM 67 SC3 TYR A 20 -10.403 22.290 24.823 1.00 0.00 +ATOM 68 SC4 TYR A 20 -11.170 20.782 26.643 1.00 0.00 +ATOM 69 CA TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 70 BB ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 71 SC1 ARG A 21 -11.039 25.993 26.476 1.00 0.00 +ATOM 72 SC2 ARG A 21 -11.248 25.333 29.887 1.00 0.00 +ATOM 73 CA ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 74 BB GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 75 CA GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 76 BB TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 77 SC1 TYR A 23 -8.709 28.306 20.758 1.00 0.00 +ATOM 78 SC2 TYR A 23 -7.220 30.161 21.378 1.00 0.00 +ATOM 79 SC3 TYR A 23 -8.220 28.823 23.132 1.00 0.00 +ATOM 80 SC4 TYR A 23 -6.690 30.729 23.724 1.00 0.00 +ATOM 81 CA TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 82 BB SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 83 SC1 SER A 24 -11.357 29.505 15.047 1.00 0.00 +ATOM 84 CA SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 85 BB LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 86 SC1 LEU A 25 -11.124 23.037 12.733 1.00 0.00 +ATOM 87 CA LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 88 BB GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 89 CA GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 90 BB ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 91 SC1 ASN A 27 -7.130 30.091 16.604 1.00 0.00 +ATOM 92 CA ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 93 BB TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 94 SC1 TRP A 28 -6.816 23.669 16.888 1.00 0.00 +ATOM 95 SC2 TRP A 28 -8.472 24.497 18.485 1.00 0.00 +ATOM 96 SC3 TRP A 28 -7.007 23.915 19.324 1.00 0.00 +ATOM 97 SC4 TRP A 28 -5.190 23.090 19.929 1.00 0.00 +ATOM 98 SC5 TRP A 28 -6.586 23.809 21.385 1.00 0.00 +ATOM 99 CA TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 100 BB VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 101 SC1 VAL A 29 -5.534 23.426 10.637 1.00 0.00 +ATOM 102 CA VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 103 BB CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 104 SC1 CYS A 30 -1.819 29.329 12.180 1.00 0.00 +ATOM 105 CA CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 106 BB ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 107 SC1 ALA A 31 -1.089 25.781 16.704 1.00 0.00 +ATOM 108 CA ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 109 BB ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 110 SC1 ALA A 32 -0.823 21.268 13.540 1.00 0.00 +ATOM 111 CA ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 112 BB LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 113 SC1 LYS A 33 1.528 24.936 8.648 1.00 0.00 +ATOM 114 SC2 LYS A 33 3.181 24.241 6.023 1.00 0.00 +ATOM 115 CA LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 116 BB PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 117 SC1 PHE A 34 3.533 28.017 11.764 1.00 0.00 +ATOM 118 SC2 PHE A 34 3.676 28.811 9.478 1.00 0.00 +ATOM 119 SC3 PHE A 34 2.119 29.392 10.320 1.00 0.00 +ATOM 120 CA PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 121 BB GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 122 SC1 GLU A 35 4.384 24.445 17.868 1.00 0.00 +ATOM 123 CA GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 124 BB SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 125 SC1 SER A 36 3.910 19.302 13.526 1.00 0.00 +ATOM 126 CA SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 127 BB ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 128 SC1 ASN A 37 5.825 21.444 7.332 1.00 0.00 +ATOM 129 CA ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 130 BB PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 131 SC1 PHE A 38 0.483 19.631 8.557 1.00 0.00 +ATOM 132 SC2 PHE A 38 -0.946 21.473 9.190 1.00 0.00 +ATOM 133 SC3 PHE A 38 -0.576 21.466 7.384 1.00 0.00 +ATOM 134 CA PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 135 BB ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 136 SC1 ASN A 39 6.545 14.631 10.411 1.00 0.00 +ATOM 137 CA ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 138 BB THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 139 SC1 THR A 40 2.081 11.990 13.217 1.00 0.00 +ATOM 140 CA THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 141 BB GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 142 SC1 GLN A 41 7.443 9.446 12.260 1.00 0.00 +ATOM 143 CA GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 144 BB ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 145 SC1 ALA A 42 7.744 17.108 14.349 1.00 0.00 +ATOM 146 CA ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 147 BB THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 148 SC1 THR A 43 11.479 14.266 18.039 1.00 0.00 +ATOM 149 CA THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 150 BB ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 151 SC1 ASN A 44 11.937 20.259 16.961 1.00 0.00 +ATOM 152 CA ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 153 BB ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 154 SC1 ARG A 45 16.691 18.207 23.144 1.00 0.00 +ATOM 155 SC2 ARG A 45 18.247 15.570 23.629 1.00 0.00 +ATOM 156 CA ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 157 BB ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 158 SC1 ASN A 46 12.650 22.425 24.012 1.00 0.00 +ATOM 159 CA ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 160 BB THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 161 SC1 THR A 47 18.237 25.668 25.594 1.00 0.00 +ATOM 162 CA THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 163 BB ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 164 SC1 ASP A 48 14.075 22.841 29.287 1.00 0.00 +ATOM 165 CA ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 166 BB GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 167 CA GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 168 BB SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 169 SC1 SER A 50 12.091 20.191 27.770 1.00 0.00 +ATOM 170 CA SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 171 BB THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 172 SC1 THR A 51 12.864 16.026 23.443 1.00 0.00 +ATOM 173 CA THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 174 BB ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 175 SC1 ASP A 52 9.031 21.088 22.419 1.00 0.00 +ATOM 176 CA ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 177 BB TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 178 SC1 TYR A 53 7.247 14.330 21.880 1.00 0.00 +ATOM 179 SC2 TYR A 53 8.942 14.562 23.703 1.00 0.00 +ATOM 180 SC3 TYR A 53 9.232 12.836 22.050 1.00 0.00 +ATOM 181 SC4 TYR A 53 10.883 13.050 23.887 1.00 0.00 +ATOM 182 CA TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 183 BB GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 184 CA GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 185 BB ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 186 SC1 ILE A 55 0.153 16.813 14.439 1.00 0.00 +ATOM 187 CA ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 188 BB LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 189 SC1 LEU A 56 -1.026 20.379 18.593 1.00 0.00 +ATOM 190 CA LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 191 BB GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 192 SC1 GLN A 57 7.224 19.970 18.175 1.00 0.00 +ATOM 193 CA GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 194 BB ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 195 SC1 ILE A 58 1.868 17.963 23.794 1.00 0.00 +ATOM 196 CA ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 197 BB ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 198 SC1 ASN A 59 8.436 20.830 27.190 1.00 0.00 +ATOM 199 CA ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 200 BB SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 201 SC1 SER A 60 10.130 16.060 27.751 1.00 0.00 +ATOM 202 CA SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 203 BB ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 204 SC1 ARG A 61 9.759 21.040 32.156 1.00 0.00 +ATOM 205 SC2 ARG A 61 12.735 20.588 32.524 1.00 0.00 +ATOM 206 CA ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 207 BB TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 208 SC1 TRP A 62 4.900 20.805 31.898 1.00 0.00 +ATOM 209 SC2 TRP A 62 6.376 22.506 31.097 1.00 0.00 +ATOM 210 SC3 TRP A 62 6.294 22.487 32.881 1.00 0.00 +ATOM 211 SC4 TRP A 62 5.936 22.198 34.895 1.00 0.00 +ATOM 212 SC5 TRP A 62 7.247 23.716 34.252 1.00 0.00 +ATOM 213 CA TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 214 BB TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 215 SC1 TRP A 63 2.540 18.368 28.720 1.00 0.00 +ATOM 216 SC2 TRP A 63 2.928 20.769 28.863 1.00 0.00 +ATOM 217 SC3 TRP A 63 1.466 20.330 29.738 1.00 0.00 +ATOM 218 SC4 TRP A 63 -0.224 19.473 30.655 1.00 0.00 +ATOM 219 SC5 TRP A 63 0.131 21.566 30.772 1.00 0.00 +ATOM 220 CA TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 221 BB CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 222 SC1 CYS A 64 5.333 13.856 26.701 1.00 0.00 +ATOM 223 CA CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 224 BB ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 225 SC1 ASN A 65 8.140 9.329 31.687 1.00 0.00 +ATOM 226 CA ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 227 BB ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 228 SC1 ASP A 66 11.494 12.585 27.497 1.00 0.00 +ATOM 229 CA ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 230 BB GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 231 CA GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 232 BB ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 233 SC1 ARG A 68 15.780 11.749 27.753 1.00 0.00 +ATOM 234 SC2 ARG A 68 16.274 12.982 24.249 1.00 0.00 +ATOM 235 CA ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 236 BB THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 237 SC1 THR A 69 12.492 15.745 30.301 1.00 0.00 +ATOM 238 CA THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 239 BB PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 240 SC1 PRO A 70 16.140 15.248 34.269 1.00 0.00 +ATOM 241 CA PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 242 BB GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 243 CA GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 244 BB SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 245 SC1 SER A 72 8.557 14.615 32.981 1.00 0.00 +ATOM 246 CA SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 247 BB ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 248 SC1 ARG A 73 5.100 18.319 36.883 1.00 0.00 +ATOM 249 SC2 ARG A 73 4.230 20.855 39.417 1.00 0.00 +ATOM 250 CA ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 251 BB ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 252 SC1 ASN A 74 3.473 11.411 32.304 1.00 0.00 +ATOM 253 CA ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 254 BB LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 255 SC1 LEU A 75 0.573 17.947 34.719 1.00 0.00 +ATOM 256 CA LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 257 BB CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 258 SC1 CYS A 76 -1.265 15.571 28.787 1.00 0.00 +ATOM 259 CA CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 260 BB ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 261 SC1 ASN A 77 -1.365 8.776 33.204 1.00 0.00 +ATOM 262 CA ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 263 BB ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 264 SC1 ILE A 78 0.451 10.630 27.183 1.00 0.00 +ATOM 265 CA ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 266 BB PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 267 SC1 PRO A 79 3.738 6.626 27.089 1.00 0.00 +ATOM 268 CA PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 269 BB CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 270 SC1 CYS A 80 7.217 12.587 26.174 1.00 0.00 +ATOM 271 CA CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 272 BB SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 273 SC1 SER A 81 6.595 6.616 22.740 1.00 0.00 +ATOM 274 CA SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 275 BB ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 276 SC1 ALA A 82 1.481 8.009 23.384 1.00 0.00 +ATOM 277 CA ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 278 BB LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 279 SC1 LEU A 83 2.319 13.242 22.880 1.00 0.00 +ATOM 280 CA LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 281 BB LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 282 SC1 LEU A 84 6.667 10.906 18.168 1.00 0.00 +ATOM 283 CA LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 284 BB SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 285 SC1 SER A 85 -0.052 7.196 16.978 1.00 0.00 +ATOM 286 CA SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 287 BB SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 288 SC1 SER A 86 0.142 7.237 11.707 1.00 0.00 +ATOM 289 CA SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 290 BB ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 291 SC1 ASP A 87 -5.391 7.382 16.677 1.00 0.00 +ATOM 292 CA ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 293 BB ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 294 SC1 ILE A 88 -4.687 13.702 15.370 1.00 0.00 +ATOM 295 CA ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 296 BB THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 297 SC1 THR A 89 -7.305 9.653 19.626 1.00 0.00 +ATOM 298 CA THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 299 BB ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 300 SC1 ALA A 90 -2.331 10.290 22.751 1.00 0.00 +ATOM 301 CA ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 302 BB SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 303 SC1 SER A 91 -0.683 14.603 19.718 1.00 0.00 +ATOM 304 CA SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 305 BB VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 306 SC1 VAL A 92 -6.856 15.900 19.617 1.00 0.00 +ATOM 307 CA VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 308 BB ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 309 SC1 ASN A 93 -7.766 12.659 24.393 1.00 0.00 +ATOM 310 CA ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 311 BB CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 312 SC1 CYS A 94 -0.957 16.123 26.475 1.00 0.00 +ATOM 313 CA CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 314 BB ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 315 SC1 ALA A 95 -3.774 19.698 22.627 1.00 0.00 +ATOM 316 CA ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 317 BB LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 318 SC1 LYS A 96 -9.033 18.462 24.585 1.00 0.00 +ATOM 319 SC2 LYS A 96 -11.333 17.085 22.831 1.00 0.00 +ATOM 320 CA LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 321 BB LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 322 SC1 LYS A 97 -5.546 17.841 30.375 1.00 0.00 +ATOM 323 SC2 LYS A 97 -7.854 16.295 31.743 1.00 0.00 +ATOM 324 CA LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 325 BB ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 326 SC1 ILE A 98 -0.911 21.639 26.782 1.00 0.00 +ATOM 327 CA ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 328 BB VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 329 SC1 VAL A 99 -6.389 24.959 25.034 1.00 0.00 +ATOM 330 CA VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 331 BB SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 332 SC1 SER A 100 -8.629 23.014 29.561 1.00 0.00 +ATOM 333 CA SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 334 BB ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 335 SC1 ASP A 101 -2.145 24.522 32.746 1.00 0.00 +ATOM 336 CA ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 337 BB GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 338 CA GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 339 BB ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 340 SC1 ASN A 103 -0.657 31.446 30.604 1.00 0.00 +ATOM 341 CA ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 342 BB GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 343 CA GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 344 BB MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 345 SC1 MET A 105 -4.583 27.642 20.426 1.00 0.00 +ATOM 346 CA MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 347 BB ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 348 SC1 ASN A 106 -1.234 33.304 24.677 1.00 0.00 +ATOM 349 CA ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 350 BB ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 351 SC1 ALA A 107 0.585 26.599 26.143 1.00 0.00 +ATOM 352 CA ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 353 BB TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 354 SC1 TRP A 108 1.201 25.872 21.084 1.00 0.00 +ATOM 355 SC2 TRP A 108 1.421 23.478 21.263 1.00 0.00 +ATOM 356 SC3 TRP A 108 -0.097 24.022 21.986 1.00 0.00 +ATOM 357 SC4 TRP A 108 -1.738 24.948 22.755 1.00 0.00 +ATOM 358 SC5 TRP A 108 -1.597 22.821 22.864 1.00 0.00 +ATOM 359 CA TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 360 BB VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 361 SC1 VAL A 109 6.981 29.495 20.948 1.00 0.00 +ATOM 362 CA VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 363 BB ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 364 SC1 ALA A 110 4.783 28.117 16.262 1.00 0.00 +ATOM 365 CA ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 366 BB TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 367 SC1 TRP A 111 -0.914 29.450 18.540 1.00 0.00 +ATOM 368 SC2 TRP A 111 -3.120 29.950 17.528 1.00 0.00 +ATOM 369 SC3 TRP A 111 -2.831 30.936 19.012 1.00 0.00 +ATOM 370 SC4 TRP A 111 -2.231 31.907 20.786 1.00 0.00 +ATOM 371 SC5 TRP A 111 -4.106 32.361 19.902 1.00 0.00 +ATOM 372 CA TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 373 BB ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 374 SC1 ARG A 112 2.360 34.094 21.939 1.00 0.00 +ATOM 375 SC2 ARG A 112 4.788 33.235 23.642 1.00 0.00 +ATOM 376 CA ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 377 BB ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 378 SC1 ASN A 113 6.187 34.311 18.635 1.00 0.00 +ATOM 379 CA ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 380 BB ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 381 SC1 ARG A 114 4.636 31.613 13.473 1.00 0.00 +ATOM 382 SC2 ARG A 114 6.636 30.401 10.985 1.00 0.00 +ATOM 383 CA ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 384 BB CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 385 SC1 CYS A 115 -0.808 30.194 14.254 1.00 0.00 +ATOM 386 CA CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 387 BB LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 388 SC1 LYS A 116 -2.027 35.559 19.418 1.00 0.00 +ATOM 389 SC2 LYS A 116 -2.220 36.558 22.473 1.00 0.00 +ATOM 390 CA LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 391 BB GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 392 CA GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 393 BB THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 394 SC1 THR A 118 -2.485 35.254 11.745 1.00 0.00 +ATOM 395 CA THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 396 BB ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 397 SC1 ASP A 119 -8.345 35.153 7.571 1.00 0.00 +ATOM 398 CA ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 399 BB VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 400 SC1 VAL A 120 -6.503 31.706 12.841 1.00 0.00 +ATOM 401 CA VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 402 BB GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 403 SC1 GLN A 121 -12.840 31.907 8.761 1.00 0.00 +ATOM 404 CA GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 405 BB ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 406 SC1 ALA A 122 -6.378 31.657 5.724 1.00 0.00 +ATOM 407 CA ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 408 BB TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 409 SC1 TRP A 123 -4.923 27.686 8.656 1.00 0.00 +ATOM 410 SC2 TRP A 123 -3.421 29.540 9.108 1.00 0.00 +ATOM 411 SC3 TRP A 123 -2.625 28.266 8.146 1.00 0.00 +ATOM 412 SC4 TRP A 123 -2.046 26.596 7.064 1.00 0.00 +ATOM 413 SC5 TRP A 123 -0.697 28.183 7.392 1.00 0.00 +ATOM 414 CA TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 415 BB ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 416 SC1 ILE A 124 -10.902 25.947 8.637 1.00 0.00 +ATOM 417 CA ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 418 BB ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 419 SC1 ARG A 125 -10.343 29.456 2.036 1.00 0.00 +ATOM 420 SC2 ARG A 125 -7.917 30.428 0.891 1.00 0.00 +ATOM 421 CA ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 422 BB GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 423 CA GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 424 BB CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 425 SC1 CYS A 127 -10.025 22.210 4.507 1.00 0.00 +ATOM 426 CA CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 427 BB ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 428 SC1 ARG A 128 -16.241 17.914 2.040 1.00 0.00 +ATOM 429 SC2 ARG A 128 -15.487 16.199 -0.582 1.00 0.00 +ATOM 430 CA ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 431 BB LEU A 129 -17.104 19.979 6.793 1.00 0.00 +ATOM 432 SC1 LEU A 129 -13.806 20.960 8.017 1.00 0.00 +ATOM 433 CA LEU A 129 -17.104 19.979 6.793 1.00 0.00 +TER 434 LEU A 129 +CONECT 1 2 5 +CONECT 2 3 +CONECT 5 6 8 +CONECT 8 9 13 +CONECT 9 10 11 +CONECT 10 11 +CONECT 13 15 +CONECT 15 16 19 +CONECT 16 17 +CONECT 19 20 22 +CONECT 22 23 25 +CONECT 25 26 28 +CONECT 28 29 31 +CONECT 31 32 34 +CONECT 34 35 37 +CONECT 37 38 40 +CONECT 40 41 44 +CONECT 41 42 +CONECT 44 45 48 +CONECT 45 46 +CONECT 48 49 53 +CONECT 49 50 51 +CONECT 50 51 +CONECT 53 55 +CONECT 55 56 58 +CONECT 58 59 61 +CONECT 61 62 64 +CONECT 64 65 70 +CONECT 65 66 67 +CONECT 66 67 68 +CONECT 67 68 +CONECT 70 71 74 +CONECT 71 72 +CONECT 74 76 +CONECT 76 77 82 +CONECT 77 78 79 +CONECT 78 79 80 +CONECT 79 80 +CONECT 82 83 85 +CONECT 85 86 88 +CONECT 88 90 +CONECT 90 91 93 +CONECT 93 94 100 +CONECT 94 95 97 +CONECT 95 97 98 +CONECT 97 98 +CONECT 100 101 103 +CONECT 103 104 106 +CONECT 106 107 109 +CONECT 109 110 112 +CONECT 112 113 116 +CONECT 113 114 +CONECT 116 117 121 +CONECT 117 118 119 +CONECT 118 119 +CONECT 121 122 124 +CONECT 124 125 127 +CONECT 127 128 130 +CONECT 130 131 135 +CONECT 131 132 133 +CONECT 132 133 +CONECT 135 136 138 +CONECT 138 139 141 +CONECT 141 142 144 +CONECT 144 145 147 +CONECT 147 148 150 +CONECT 150 151 153 +CONECT 153 154 157 +CONECT 154 155 +CONECT 157 158 160 +CONECT 160 161 163 +CONECT 163 164 166 +CONECT 166 168 +CONECT 168 169 171 +CONECT 171 172 174 +CONECT 174 175 177 +CONECT 177 178 183 +CONECT 178 179 180 +CONECT 179 180 181 +CONECT 180 181 +CONECT 183 185 +CONECT 185 186 188 +CONECT 188 189 191 +CONECT 191 192 194 +CONECT 194 195 197 +CONECT 197 198 200 +CONECT 200 201 203 +CONECT 203 204 207 +CONECT 204 205 +CONECT 207 208 214 +CONECT 208 209 211 +CONECT 209 211 212 +CONECT 211 212 +CONECT 214 215 221 +CONECT 215 216 218 +CONECT 216 218 219 +CONECT 218 219 +CONECT 221 222 224 +CONECT 224 225 227 +CONECT 227 228 230 +CONECT 230 232 +CONECT 232 233 236 +CONECT 233 234 +CONECT 236 237 239 +CONECT 239 240 242 +CONECT 242 244 +CONECT 244 245 247 +CONECT 247 248 251 +CONECT 248 249 +CONECT 251 252 254 +CONECT 254 255 257 +CONECT 257 258 260 +CONECT 260 261 263 +CONECT 263 264 266 +CONECT 266 267 269 +CONECT 269 270 272 +CONECT 272 273 275 +CONECT 275 276 278 +CONECT 278 279 281 +CONECT 281 282 284 +CONECT 284 285 287 +CONECT 287 288 290 +CONECT 290 291 293 +CONECT 293 294 296 +CONECT 296 297 299 +CONECT 299 300 302 +CONECT 302 303 305 +CONECT 305 306 308 +CONECT 308 309 311 +CONECT 311 312 314 +CONECT 314 315 317 +CONECT 317 318 321 +CONECT 318 319 +CONECT 321 322 325 +CONECT 322 323 +CONECT 325 326 328 +CONECT 328 329 331 +CONECT 331 332 334 +CONECT 334 335 337 +CONECT 337 339 +CONECT 339 340 342 +CONECT 342 344 +CONECT 344 345 347 +CONECT 347 348 350 +CONECT 350 351 353 +CONECT 353 354 360 +CONECT 354 355 357 +CONECT 355 357 358 +CONECT 357 358 +CONECT 360 361 363 +CONECT 363 364 366 +CONECT 366 367 373 +CONECT 367 368 370 +CONECT 368 370 371 +CONECT 370 371 +CONECT 373 374 377 +CONECT 374 375 +CONECT 377 378 380 +CONECT 380 381 384 +CONECT 381 382 +CONECT 384 385 387 +CONECT 387 388 391 +CONECT 388 389 +CONECT 391 393 +CONECT 393 394 396 +CONECT 396 397 399 +CONECT 399 400 402 +CONECT 402 403 405 +CONECT 405 406 408 +CONECT 408 409 415 +CONECT 409 410 412 +CONECT 410 412 413 +CONECT 412 413 +CONECT 415 416 418 +CONECT 418 419 422 +CONECT 419 420 +CONECT 422 424 +CONECT 424 425 427 +CONECT 427 428 431 +CONECT 428 429 +CONECT 431 432 +END \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation new file mode 100644 index 00000000..6209c13b --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation @@ -0,0 +1 @@ +Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command new file mode 100755 index 00000000..40e34be2 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command @@ -0,0 +1,12 @@ +martinize2 +-f ../aa.pdb +-ff martini3001 +-x cg.pdb +-o topol.top +-ignore HOH +-ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC +-elastic +-ef 700 +-eu 0.85 +-water-bias +-water-bias-eps E:-.5 C:1.0 H:-1.0 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp new file mode 100644 index 00000000..87a5e995 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/molecule_0.itp @@ -0,0 +1,1901 @@ +; This file was generated using the following command: +; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -elastic -ef 700 -eu 0.85 -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 +; martinize with vermouth 0.9.7.dev79 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Pleas cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 molecule_0_1 1 LYS CA 305 0 0.0 + 5 SP2 2 VAL BB 4 0.0 + 6 SC3 2 VAL SC1 5 0.0 + 7 molecule_0_2 2 VAL CA 306 0 0.0 + 8 P2 3 PHE BB 6 0.0 + 9 SC4 3 PHE SC1 7 0.0 + 10 TC5 3 PHE SC2 8 0.0 + 11 TC5 3 PHE SC3 9 0.0 + 12 molecule_0_3 3 PHE CA 307 0 0.0 + 13 SP1 4 GLY BB 10 0.0 + 14 molecule_0_4 4 GLY CA 308 0 0.0 + 15 P2 5 ARG BB 11 0.0 + 16 SC3 5 ARG SC1 12 0.0 + 17 SQ3p 5 ARG SC2 13 1.0 + 18 molecule_0_5 5 ARG CA 309 0 0.0 + 19 P2 6 CYS BB 14 0.0 + 20 TC6 6 CYS SC1 15 0.0 + 21 molecule_0_6 6 CYS CA 310 0 0.0 + 22 P2 7 GLU BB 16 0.0 + 23 Q5n 7 GLU SC1 17 -1.0 + 24 molecule_0_7 7 GLU CA 311 0 0.0 + 25 P2 8 LEU BB 18 0.0 + 26 SC2 8 LEU SC1 19 0.0 + 27 molecule_0_8 8 LEU CA 312 0 0.0 + 28 SP2 9 ALA BB 20 0.0 + 29 TC3 9 ALA SC1 21 0.0 + 30 molecule_0_9 9 ALA CA 313 0 0.0 + 31 SP2 10 ALA BB 22 0.0 + 32 TC3 10 ALA SC1 23 0.0 + 33 molecule_0_10 10 ALA CA 314 0 0.0 + 34 SP2 11 ALA BB 24 0.0 + 35 TC3 11 ALA SC1 25 0.0 + 36 molecule_0_11 11 ALA CA 315 0 0.0 + 37 P2 12 MET BB 26 0.0 + 38 C6 12 MET SC1 27 0.0 + 39 molecule_0_12 12 MET CA 316 0 0.0 + 40 P2 13 LYS BB 28 0.0 + 41 SC3 13 LYS SC1 29 0.0 + 42 SQ4p 13 LYS SC2 30 1.0 + 43 molecule_0_13 13 LYS CA 317 0 0.0 + 44 P2 14 ARG BB 31 0.0 + 45 SC3 14 ARG SC1 32 0.0 + 46 SQ3p 14 ARG SC2 33 1.0 + 47 molecule_0_14 14 ARG CA 318 0 0.0 + 48 P2 15 HIS BB 34 0.0 + 49 TC4 15 HIS SC1 35 0.0 + 50 TN6d 15 HIS SC2 36 0.0 + 51 TN5a 15 HIS SC3 37 0.0 + 52 molecule_0_15 15 HIS CA 319 0 0.0 + 53 SP1 16 GLY BB 38 0.0 + 54 molecule_0_16 16 GLY CA 320 0 0.0 + 55 P2 17 LEU BB 39 0.0 + 56 SC2 17 LEU SC1 40 0.0 + 57 molecule_0_17 17 LEU CA 321 0 0.0 + 58 P2 18 ASP BB 41 0.0 + 59 SQ5n 18 ASP SC1 42 -1.0 + 60 molecule_0_18 18 ASP CA 322 0 0.0 + 61 P2 19 ASN BB 43 0.0 + 62 SP5 19 ASN SC1 44 0.0 + 63 molecule_0_19 19 ASN CA 323 0 0.0 + 64 P2 20 TYR BB 45 0.0 + 65 TC4 20 TYR SC1 46 0.0 + 66 TC5 20 TYR SC2 47 0.0 + 67 TC5 20 TYR SC3 48 0.0 + 68 TN6 20 TYR SC4 49 0.0 + 69 molecule_0_20 20 TYR CA 324 0 0.0 + 70 P2 21 ARG BB 50 0.0 + 71 SC3 21 ARG SC1 51 0.0 + 72 SQ3p 21 ARG SC2 52 1.0 + 73 molecule_0_21 21 ARG CA 325 0 0.0 + 74 SP1 22 GLY BB 53 0.0 + 75 molecule_0_22 22 GLY CA 326 0 0.0 + 76 P2 23 TYR BB 54 0.0 + 77 TC4 23 TYR SC1 55 0.0 + 78 TC5 23 TYR SC2 56 0.0 + 79 TC5 23 TYR SC3 57 0.0 + 80 TN6 23 TYR SC4 58 0.0 + 81 molecule_0_23 23 TYR CA 327 0 0.0 + 82 P2 24 SER BB 59 0.0 + 83 TP1 24 SER SC1 60 0.0 + 84 molecule_0_24 24 SER CA 328 0 0.0 + 85 P2 25 LEU BB 61 0.0 + 86 SC2 25 LEU SC1 62 0.0 + 87 molecule_0_25 25 LEU CA 329 0 0.0 + 88 SP1 26 GLY BB 63 0.0 + 89 molecule_0_26 26 GLY CA 330 0 0.0 + 90 P2 27 ASN BB 64 0.0 + 91 SP5 27 ASN SC1 65 0.0 + 92 molecule_0_27 27 ASN CA 331 0 0.0 + 93 P2 28 TRP BB 66 0.0 + 94 TC4 28 TRP SC1 67 0.0 36.0 + 95 TN6d 28 TRP SC2 68 0.0 36.0 + 96 TC5 28 TRP SC3 69 0.0 0.0 + 97 TC5 28 TRP SC4 70 0.0 36.0 + 98 TC5 28 TRP SC5 71 0.0 36.0 + 99 molecule_0_28 28 TRP CA 332 0 0.0 +100 SP2 29 VAL BB 72 0.0 +101 SC3 29 VAL SC1 73 0.0 +102 molecule_0_29 29 VAL CA 333 0 0.0 +103 P2 30 CYS BB 74 0.0 +104 TC6 30 CYS SC1 75 0.0 +105 molecule_0_30 30 CYS CA 334 0 0.0 +106 SP2 31 ALA BB 76 0.0 +107 TC3 31 ALA SC1 77 0.0 +108 molecule_0_31 31 ALA CA 335 0 0.0 +109 SP2 32 ALA BB 78 0.0 +110 TC3 32 ALA SC1 79 0.0 +111 molecule_0_32 32 ALA CA 336 0 0.0 +112 P2 33 LYS BB 80 0.0 +113 SC3 33 LYS SC1 81 0.0 +114 SQ4p 33 LYS SC2 82 1.0 +115 molecule_0_33 33 LYS CA 337 0 0.0 +116 P2 34 PHE BB 83 0.0 +117 SC4 34 PHE SC1 84 0.0 +118 TC5 34 PHE SC2 85 0.0 +119 TC5 34 PHE SC3 86 0.0 +120 molecule_0_34 34 PHE CA 338 0 0.0 +121 P2 35 GLU BB 87 0.0 +122 Q5n 35 GLU SC1 88 -1.0 +123 molecule_0_35 35 GLU CA 339 0 0.0 +124 P2 36 SER BB 89 0.0 +125 TP1 36 SER SC1 90 0.0 +126 molecule_0_36 36 SER CA 340 0 0.0 +127 P2 37 ASN BB 91 0.0 +128 SP5 37 ASN SC1 92 0.0 +129 molecule_0_37 37 ASN CA 341 0 0.0 +130 P2 38 PHE BB 93 0.0 +131 SC4 38 PHE SC1 94 0.0 +132 TC5 38 PHE SC2 95 0.0 +133 TC5 38 PHE SC3 96 0.0 +134 molecule_0_38 38 PHE CA 342 0 0.0 +135 P2 39 ASN BB 97 0.0 +136 SP5 39 ASN SC1 98 0.0 +137 molecule_0_39 39 ASN CA 343 0 0.0 +138 P2 40 THR BB 99 0.0 +139 SP1 40 THR SC1 100 0.0 +140 molecule_0_40 40 THR CA 344 0 0.0 +141 P2 41 GLN BB 101 0.0 +142 P5 41 GLN SC1 102 0.0 +143 molecule_0_41 41 GLN CA 345 0 0.0 +144 SP2 42 ALA BB 103 0.0 +145 TC3 42 ALA SC1 104 0.0 +146 molecule_0_42 42 ALA CA 346 0 0.0 +147 P2 43 THR BB 105 0.0 +148 SP1 43 THR SC1 106 0.0 +149 molecule_0_43 43 THR CA 347 0 0.0 +150 P2 44 ASN BB 107 0.0 +151 SP5 44 ASN SC1 108 0.0 +152 molecule_0_44 44 ASN CA 348 0 0.0 +153 P2 45 ARG BB 109 0.0 +154 SC3 45 ARG SC1 110 0.0 +155 SQ3p 45 ARG SC2 111 1.0 +156 molecule_0_45 45 ARG CA 349 0 0.0 +157 P2 46 ASN BB 112 0.0 +158 SP5 46 ASN SC1 113 0.0 +159 molecule_0_46 46 ASN CA 350 0 0.0 +160 P2 47 THR BB 114 0.0 +161 SP1 47 THR SC1 115 0.0 +162 molecule_0_47 47 THR CA 351 0 0.0 +163 P2 48 ASP BB 116 0.0 +164 SQ5n 48 ASP SC1 117 -1.0 +165 molecule_0_48 48 ASP CA 352 0 0.0 +166 SP1 49 GLY BB 118 0.0 +167 molecule_0_49 49 GLY CA 353 0 0.0 +168 P2 50 SER BB 119 0.0 +169 TP1 50 SER SC1 120 0.0 +170 molecule_0_50 50 SER CA 354 0 0.0 +171 P2 51 THR BB 121 0.0 +172 SP1 51 THR SC1 122 0.0 +173 molecule_0_51 51 THR CA 355 0 0.0 +174 P2 52 ASP BB 123 0.0 +175 SQ5n 52 ASP SC1 124 -1.0 +176 molecule_0_52 52 ASP CA 356 0 0.0 +177 P2 53 TYR BB 125 0.0 +178 TC4 53 TYR SC1 126 0.0 +179 TC5 53 TYR SC2 127 0.0 +180 TC5 53 TYR SC3 128 0.0 +181 TN6 53 TYR SC4 129 0.0 +182 molecule_0_53 53 TYR CA 357 0 0.0 +183 SP1 54 GLY BB 130 0.0 +184 molecule_0_54 54 GLY CA 358 0 0.0 +185 P2 55 ILE BB 131 0.0 +186 SC2 55 ILE SC1 132 0.0 +187 molecule_0_55 55 ILE CA 359 0 0.0 +188 P2 56 LEU BB 133 0.0 +189 SC2 56 LEU SC1 134 0.0 +190 molecule_0_56 56 LEU CA 360 0 0.0 +191 P2 57 GLN BB 135 0.0 +192 P5 57 GLN SC1 136 0.0 +193 molecule_0_57 57 GLN CA 361 0 0.0 +194 P2 58 ILE BB 137 0.0 +195 SC2 58 ILE SC1 138 0.0 +196 molecule_0_58 58 ILE CA 362 0 0.0 +197 P2 59 ASN BB 139 0.0 +198 SP5 59 ASN SC1 140 0.0 +199 molecule_0_59 59 ASN CA 363 0 0.0 +200 P2 60 SER BB 141 0.0 +201 TP1 60 SER SC1 142 0.0 +202 molecule_0_60 60 SER CA 364 0 0.0 +203 P2 61 ARG BB 143 0.0 +204 SC3 61 ARG SC1 144 0.0 +205 SQ3p 61 ARG SC2 145 1.0 +206 molecule_0_61 61 ARG CA 365 0 0.0 +207 P2 62 TRP BB 146 0.0 +208 TC4 62 TRP SC1 147 0.0 36.0 +209 TN6d 62 TRP SC2 148 0.0 36.0 +210 TC5 62 TRP SC3 149 0.0 0.0 +211 TC5 62 TRP SC4 150 0.0 36.0 +212 TC5 62 TRP SC5 151 0.0 36.0 +213 molecule_0_62 62 TRP CA 366 0 0.0 +214 P2 63 TRP BB 152 0.0 +215 TC4 63 TRP SC1 153 0.0 36.0 +216 TN6d 63 TRP SC2 154 0.0 36.0 +217 TC5 63 TRP SC3 155 0.0 0.0 +218 TC5 63 TRP SC4 156 0.0 36.0 +219 TC5 63 TRP SC5 157 0.0 36.0 +220 molecule_0_63 63 TRP CA 367 0 0.0 +221 P2 64 CYS BB 158 0.0 +222 TC6 64 CYS SC1 159 0.0 +223 molecule_0_64 64 CYS CA 368 0 0.0 +224 P2 65 ASN BB 160 0.0 +225 SP5 65 ASN SC1 161 0.0 +226 molecule_0_65 65 ASN CA 369 0 0.0 +227 P2 66 ASP BB 162 0.0 +228 SQ5n 66 ASP SC1 163 -1.0 +229 molecule_0_66 66 ASP CA 370 0 0.0 +230 SP1 67 GLY BB 164 0.0 +231 molecule_0_67 67 GLY CA 371 0 0.0 +232 P2 68 ARG BB 165 0.0 +233 SC3 68 ARG SC1 166 0.0 +234 SQ3p 68 ARG SC2 167 1.0 +235 molecule_0_68 68 ARG CA 372 0 0.0 +236 P2 69 THR BB 168 0.0 +237 SP1 69 THR SC1 169 0.0 +238 molecule_0_69 69 THR CA 373 0 0.0 +239 SP2a 70 PRO BB 170 0.0 +240 SC3 70 PRO SC1 171 0.0 +241 molecule_0_70 70 PRO CA 374 0 0.0 +242 SP1 71 GLY BB 172 0.0 +243 molecule_0_71 71 GLY CA 375 0 0.0 +244 P2 72 SER BB 173 0.0 +245 TP1 72 SER SC1 174 0.0 +246 molecule_0_72 72 SER CA 376 0 0.0 +247 P2 73 ARG BB 175 0.0 +248 SC3 73 ARG SC1 176 0.0 +249 SQ3p 73 ARG SC2 177 1.0 +250 molecule_0_73 73 ARG CA 377 0 0.0 +251 P2 74 ASN BB 178 0.0 +252 SP5 74 ASN SC1 179 0.0 +253 molecule_0_74 74 ASN CA 378 0 0.0 +254 P2 75 LEU BB 180 0.0 +255 SC2 75 LEU SC1 181 0.0 +256 molecule_0_75 75 LEU CA 379 0 0.0 +257 P2 76 CYS BB 182 0.0 +258 TC6 76 CYS SC1 183 0.0 +259 molecule_0_76 76 CYS CA 380 0 0.0 +260 P2 77 ASN BB 184 0.0 +261 SP5 77 ASN SC1 185 0.0 +262 molecule_0_77 77 ASN CA 381 0 0.0 +263 P2 78 ILE BB 186 0.0 +264 SC2 78 ILE SC1 187 0.0 +265 molecule_0_78 78 ILE CA 382 0 0.0 +266 SP2a 79 PRO BB 188 0.0 +267 SC3 79 PRO SC1 189 0.0 +268 molecule_0_79 79 PRO CA 383 0 0.0 +269 P2 80 CYS BB 190 0.0 +270 TC6 80 CYS SC1 191 0.0 +271 molecule_0_80 80 CYS CA 384 0 0.0 +272 P2 81 SER BB 192 0.0 +273 TP1 81 SER SC1 193 0.0 +274 molecule_0_81 81 SER CA 385 0 0.0 +275 SP2 82 ALA BB 194 0.0 +276 TC3 82 ALA SC1 195 0.0 +277 molecule_0_82 82 ALA CA 386 0 0.0 +278 P2 83 LEU BB 196 0.0 +279 SC2 83 LEU SC1 197 0.0 +280 molecule_0_83 83 LEU CA 387 0 0.0 +281 P2 84 LEU BB 198 0.0 +282 SC2 84 LEU SC1 199 0.0 +283 molecule_0_84 84 LEU CA 388 0 0.0 +284 P2 85 SER BB 200 0.0 +285 TP1 85 SER SC1 201 0.0 +286 molecule_0_85 85 SER CA 389 0 0.0 +287 P2 86 SER BB 202 0.0 +288 TP1 86 SER SC1 203 0.0 +289 molecule_0_86 86 SER CA 390 0 0.0 +290 P2 87 ASP BB 204 0.0 +291 SQ5n 87 ASP SC1 205 -1.0 +292 molecule_0_87 87 ASP CA 391 0 0.0 +293 P2 88 ILE BB 206 0.0 +294 SC2 88 ILE SC1 207 0.0 +295 molecule_0_88 88 ILE CA 392 0 0.0 +296 P2 89 THR BB 208 0.0 +297 SP1 89 THR SC1 209 0.0 +298 molecule_0_89 89 THR CA 393 0 0.0 +299 SP2 90 ALA BB 210 0.0 +300 TC3 90 ALA SC1 211 0.0 +301 molecule_0_90 90 ALA CA 394 0 0.0 +302 P2 91 SER BB 212 0.0 +303 TP1 91 SER SC1 213 0.0 +304 molecule_0_91 91 SER CA 395 0 0.0 +305 SP2 92 VAL BB 214 0.0 +306 SC3 92 VAL SC1 215 0.0 +307 molecule_0_92 92 VAL CA 396 0 0.0 +308 P2 93 ASN BB 216 0.0 +309 SP5 93 ASN SC1 217 0.0 +310 molecule_0_93 93 ASN CA 397 0 0.0 +311 P2 94 CYS BB 218 0.0 +312 TC6 94 CYS SC1 219 0.0 +313 molecule_0_94 94 CYS CA 398 0 0.0 +314 SP2 95 ALA BB 220 0.0 +315 TC3 95 ALA SC1 221 0.0 +316 molecule_0_95 95 ALA CA 399 0 0.0 +317 P2 96 LYS BB 222 0.0 +318 SC3 96 LYS SC1 223 0.0 +319 SQ4p 96 LYS SC2 224 1.0 +320 molecule_0_96 96 LYS CA 400 0 0.0 +321 P2 97 LYS BB 225 0.0 +322 SC3 97 LYS SC1 226 0.0 +323 SQ4p 97 LYS SC2 227 1.0 +324 molecule_0_97 97 LYS CA 401 0 0.0 +325 P2 98 ILE BB 228 0.0 +326 SC2 98 ILE SC1 229 0.0 +327 molecule_0_98 98 ILE CA 402 0 0.0 +328 SP2 99 VAL BB 230 0.0 +329 SC3 99 VAL SC1 231 0.0 +330 molecule_0_99 99 VAL CA 403 0 0.0 +331 P2 100 SER BB 232 0.0 +332 TP1 100 SER SC1 233 0.0 +333 molecule_0_100 100 SER CA 404 0 0.0 +334 P2 101 ASP BB 234 0.0 +335 SQ5n 101 ASP SC1 235 -1.0 +336 molecule_0_101 101 ASP CA 405 0 0.0 +337 SP1 102 GLY BB 236 0.0 +338 molecule_0_102 102 GLY CA 406 0 0.0 +339 P2 103 ASN BB 237 0.0 +340 SP5 103 ASN SC1 238 0.0 +341 molecule_0_103 103 ASN CA 407 0 0.0 +342 SP1 104 GLY BB 239 0.0 +343 molecule_0_104 104 GLY CA 408 0 0.0 +344 P2 105 MET BB 240 0.0 +345 C6 105 MET SC1 241 0.0 +346 molecule_0_105 105 MET CA 409 0 0.0 +347 P2 106 ASN BB 242 0.0 +348 SP5 106 ASN SC1 243 0.0 +349 molecule_0_106 106 ASN CA 410 0 0.0 +350 SP2 107 ALA BB 244 0.0 +351 TC3 107 ALA SC1 245 0.0 +352 molecule_0_107 107 ALA CA 411 0 0.0 +353 P2 108 TRP BB 246 0.0 +354 TC4 108 TRP SC1 247 0.0 36.0 +355 TN6d 108 TRP SC2 248 0.0 36.0 +356 TC5 108 TRP SC3 249 0.0 0.0 +357 TC5 108 TRP SC4 250 0.0 36.0 +358 TC5 108 TRP SC5 251 0.0 36.0 +359 molecule_0_108 108 TRP CA 412 0 0.0 +360 SP2 109 VAL BB 252 0.0 +361 SC3 109 VAL SC1 253 0.0 +362 molecule_0_109 109 VAL CA 413 0 0.0 +363 SP2 110 ALA BB 254 0.0 +364 TC3 110 ALA SC1 255 0.0 +365 molecule_0_110 110 ALA CA 414 0 0.0 +366 P2 111 TRP BB 256 0.0 +367 TC4 111 TRP SC1 257 0.0 36.0 +368 TN6d 111 TRP SC2 258 0.0 36.0 +369 TC5 111 TRP SC3 259 0.0 0.0 +370 TC5 111 TRP SC4 260 0.0 36.0 +371 TC5 111 TRP SC5 261 0.0 36.0 +372 molecule_0_111 111 TRP CA 415 0 0.0 +373 P2 112 ARG BB 262 0.0 +374 SC3 112 ARG SC1 263 0.0 +375 SQ3p 112 ARG SC2 264 1.0 +376 molecule_0_112 112 ARG CA 416 0 0.0 +377 P2 113 ASN BB 265 0.0 +378 SP5 113 ASN SC1 266 0.0 +379 molecule_0_113 113 ASN CA 417 0 0.0 +380 P2 114 ARG BB 267 0.0 +381 SC3 114 ARG SC1 268 0.0 +382 SQ3p 114 ARG SC2 269 1.0 +383 molecule_0_114 114 ARG CA 418 0 0.0 +384 P2 115 CYS BB 270 0.0 +385 TC6 115 CYS SC1 271 0.0 +386 molecule_0_115 115 CYS CA 419 0 0.0 +387 P2 116 LYS BB 272 0.0 +388 SC3 116 LYS SC1 273 0.0 +389 SQ4p 116 LYS SC2 274 1.0 +390 molecule_0_116 116 LYS CA 420 0 0.0 +391 SP1 117 GLY BB 275 0.0 +392 molecule_0_117 117 GLY CA 421 0 0.0 +393 P2 118 THR BB 276 0.0 +394 SP1 118 THR SC1 277 0.0 +395 molecule_0_118 118 THR CA 422 0 0.0 +396 P2 119 ASP BB 278 0.0 +397 SQ5n 119 ASP SC1 279 -1.0 +398 molecule_0_119 119 ASP CA 423 0 0.0 +399 SP2 120 VAL BB 280 0.0 +400 SC3 120 VAL SC1 281 0.0 +401 molecule_0_120 120 VAL CA 424 0 0.0 +402 P2 121 GLN BB 282 0.0 +403 P5 121 GLN SC1 283 0.0 +404 molecule_0_121 121 GLN CA 425 0 0.0 +405 SP2 122 ALA BB 284 0.0 +406 TC3 122 ALA SC1 285 0.0 +407 molecule_0_122 122 ALA CA 426 0 0.0 +408 P2 123 TRP BB 286 0.0 +409 TC4 123 TRP SC1 287 0.0 36.0 +410 TN6d 123 TRP SC2 288 0.0 36.0 +411 TC5 123 TRP SC3 289 0.0 0.0 +412 TC5 123 TRP SC4 290 0.0 36.0 +413 TC5 123 TRP SC5 291 0.0 36.0 +414 molecule_0_123 123 TRP CA 427 0 0.0 +415 P2 124 ILE BB 292 0.0 +416 SC2 124 ILE SC1 293 0.0 +417 molecule_0_124 124 ILE CA 428 0 0.0 +418 P2 125 ARG BB 294 0.0 +419 SC3 125 ARG SC1 295 0.0 +420 SQ3p 125 ARG SC2 296 1.0 +421 molecule_0_125 125 ARG CA 429 0 0.0 +422 SP1 126 GLY BB 297 0.0 +423 molecule_0_126 126 GLY CA 430 0 0.0 +424 P2 127 CYS BB 298 0.0 +425 TC6 127 CYS SC1 299 0.0 +426 molecule_0_127 127 CYS CA 431 0 0.0 +427 P2 128 ARG BB 300 0.0 +428 SC3 128 ARG SC1 301 0.0 +429 SQ3p 128 ARG SC2 302 1.0 +430 molecule_0_128 128 ARG CA 432 0 0.0 +431 Q5 129 LEU BB 303 -1 +432 SC2 129 LEU SC1 304 0.0 +433 molecule_0_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 5 1 0.350 4000 + 5 8 1 0.350 4000 + 8 13 1 0.350 4000 + 48 53 1 0.350 4000 + 53 55 1 0.350 4000 + 55 58 1 0.350 4000 + 58 61 1 0.350 4000 + 61 64 1 0.350 4000 + 64 70 1 0.350 4000 + 70 74 1 0.350 4000 + 74 76 1 0.350 4000 + 76 82 1 0.350 4000 +127 130 1 0.350 4000 +130 135 1 0.350 4000 +135 138 1 0.350 4000 +138 141 1 0.350 4000 +141 144 1 0.350 4000 +144 147 1 0.350 4000 +147 150 1 0.350 4000 +150 153 1 0.350 4000 +153 157 1 0.350 4000 +157 160 1 0.350 4000 +160 163 1 0.350 4000 +163 166 1 0.350 4000 +166 168 1 0.350 4000 +168 171 1 0.350 4000 +171 174 1 0.350 4000 +174 177 1 0.350 4000 +177 183 1 0.350 4000 +183 185 1 0.350 4000 +185 188 1 0.350 4000 +188 191 1 0.350 4000 +191 194 1 0.350 4000 +194 197 1 0.350 4000 +197 200 1 0.350 4000 +200 203 1 0.350 4000 +203 207 1 0.350 4000 +207 214 1 0.350 4000 +214 221 1 0.350 4000 +221 224 1 0.350 4000 +224 227 1 0.350 4000 +227 230 1 0.350 4000 +230 232 1 0.350 4000 +232 236 1 0.350 4000 +236 239 1 0.350 4000 +239 242 1 0.350 4000 +242 244 1 0.350 4000 +244 247 1 0.350 4000 +247 251 1 0.350 4000 +251 254 1 0.350 4000 +254 257 1 0.350 4000 +257 260 1 0.350 4000 +260 263 1 0.350 4000 +263 266 1 0.350 4000 +284 287 1 0.350 4000 +287 290 1 0.350 4000 +290 293 1 0.350 4000 +334 337 1 0.350 4000 +337 339 1 0.350 4000 +384 387 1 0.350 4000 +387 391 1 0.350 4000 +391 393 1 0.350 4000 +393 396 1 0.350 4000 +418 422 1 0.350 4000 +422 424 1 0.350 4000 +424 427 1 0.350 4000 +427 431 1 0.350 4000 + +; Rubber band + 1 130 1 0.64484 700.0 + 1 135 1 0.52375 700.0 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409 + +; Virtual go site + 4 1 1 + 7 1 5 + 12 1 8 + 14 1 13 + 18 1 15 + 21 1 19 + 24 1 22 + 27 1 25 + 30 1 28 + 33 1 31 + 36 1 34 + 39 1 37 + 43 1 40 + 47 1 44 + 52 1 48 + 54 1 53 + 57 1 55 + 60 1 58 + 63 1 61 + 69 1 64 + 73 1 70 + 75 1 74 + 81 1 76 + 84 1 82 + 87 1 85 + 89 1 88 + 92 1 90 + 99 1 93 +102 1 100 +105 1 103 +108 1 106 +111 1 109 +115 1 112 +120 1 116 +123 1 121 +126 1 124 +129 1 127 +134 1 130 +137 1 135 +140 1 138 +143 1 141 +146 1 144 +149 1 147 +152 1 150 +156 1 153 +159 1 157 +162 1 160 +165 1 163 +167 1 166 +170 1 168 +173 1 171 +176 1 174 +182 1 177 +184 1 183 +187 1 185 +190 1 188 +193 1 191 +196 1 194 +199 1 197 +202 1 200 +206 1 203 +213 1 207 +220 1 214 +223 1 221 +226 1 224 +229 1 227 +231 1 230 +235 1 232 +238 1 236 +241 1 239 +243 1 242 +246 1 244 +250 1 247 +253 1 251 +256 1 254 +259 1 257 +262 1 260 +265 1 263 +268 1 266 +271 1 269 +274 1 272 +277 1 275 +280 1 278 +283 1 281 +286 1 284 +289 1 287 +292 1 290 +295 1 293 +298 1 296 +301 1 299 +304 1 302 +307 1 305 +310 1 308 +313 1 311 +316 1 314 +320 1 317 +324 1 321 +327 1 325 +330 1 328 +333 1 331 +336 1 334 +338 1 337 +341 1 339 +343 1 342 +346 1 344 +349 1 347 +352 1 350 +359 1 353 +362 1 360 +365 1 363 +372 1 366 +376 1 373 +379 1 377 +383 1 380 +386 1 384 +390 1 387 +392 1 391 +395 1 393 +398 1 396 +401 1 399 +404 1 402 +407 1 405 +414 1 408 +417 1 415 +421 1 418 +423 1 422 +426 1 424 +430 1 427 +433 1 431 + diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top new file mode 100644 index 00000000..21d9bb95 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top @@ -0,0 +1,12 @@ + +#include "martini.itp" + + #include "virtual_sites_atomtypes.itp" + #include "virtual_sites_nonbond_params.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp new file mode 100644 index 00000000..bcbcf614 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_atomtypes.itp @@ -0,0 +1,130 @@ +[ atomtypes ] +molecule_0_1 0.0 0 A 0.00000000 0.00000000 +molecule_0_2 0.0 0 A 0.00000000 0.00000000 +molecule_0_3 0.0 0 A 0.00000000 0.00000000 +molecule_0_4 0.0 0 A 0.00000000 0.00000000 +molecule_0_5 0.0 0 A 0.00000000 0.00000000 +molecule_0_6 0.0 0 A 0.00000000 0.00000000 +molecule_0_7 0.0 0 A 0.00000000 0.00000000 +molecule_0_8 0.0 0 A 0.00000000 0.00000000 +molecule_0_9 0.0 0 A 0.00000000 0.00000000 +molecule_0_10 0.0 0 A 0.00000000 0.00000000 +molecule_0_11 0.0 0 A 0.00000000 0.00000000 +molecule_0_12 0.0 0 A 0.00000000 0.00000000 +molecule_0_13 0.0 0 A 0.00000000 0.00000000 +molecule_0_14 0.0 0 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+molecule_0_81 0.0 0 A 0.00000000 0.00000000 +molecule_0_82 0.0 0 A 0.00000000 0.00000000 +molecule_0_83 0.0 0 A 0.00000000 0.00000000 +molecule_0_84 0.0 0 A 0.00000000 0.00000000 +molecule_0_85 0.0 0 A 0.00000000 0.00000000 +molecule_0_86 0.0 0 A 0.00000000 0.00000000 +molecule_0_87 0.0 0 A 0.00000000 0.00000000 +molecule_0_88 0.0 0 A 0.00000000 0.00000000 +molecule_0_89 0.0 0 A 0.00000000 0.00000000 +molecule_0_90 0.0 0 A 0.00000000 0.00000000 +molecule_0_91 0.0 0 A 0.00000000 0.00000000 +molecule_0_92 0.0 0 A 0.00000000 0.00000000 +molecule_0_93 0.0 0 A 0.00000000 0.00000000 +molecule_0_94 0.0 0 A 0.00000000 0.00000000 +molecule_0_95 0.0 0 A 0.00000000 0.00000000 +molecule_0_96 0.0 0 A 0.00000000 0.00000000 +molecule_0_97 0.0 0 A 0.00000000 0.00000000 +molecule_0_98 0.0 0 A 0.00000000 0.00000000 +molecule_0_99 0.0 0 A 0.00000000 0.00000000 +molecule_0_100 0.0 0 A 0.00000000 0.00000000 +molecule_0_101 0.0 0 A 0.00000000 0.00000000 +molecule_0_102 0.0 0 A 0.00000000 0.00000000 +molecule_0_103 0.0 0 A 0.00000000 0.00000000 +molecule_0_104 0.0 0 A 0.00000000 0.00000000 +molecule_0_105 0.0 0 A 0.00000000 0.00000000 +molecule_0_106 0.0 0 A 0.00000000 0.00000000 +molecule_0_107 0.0 0 A 0.00000000 0.00000000 +molecule_0_108 0.0 0 A 0.00000000 0.00000000 +molecule_0_109 0.0 0 A 0.00000000 0.00000000 +molecule_0_110 0.0 0 A 0.00000000 0.00000000 +molecule_0_111 0.0 0 A 0.00000000 0.00000000 +molecule_0_112 0.0 0 A 0.00000000 0.00000000 +molecule_0_113 0.0 0 A 0.00000000 0.00000000 +molecule_0_114 0.0 0 A 0.00000000 0.00000000 +molecule_0_115 0.0 0 A 0.00000000 0.00000000 +molecule_0_116 0.0 0 A 0.00000000 0.00000000 +molecule_0_117 0.0 0 A 0.00000000 0.00000000 +molecule_0_118 0.0 0 A 0.00000000 0.00000000 +molecule_0_119 0.0 0 A 0.00000000 0.00000000 +molecule_0_120 0.0 0 A 0.00000000 0.00000000 +molecule_0_121 0.0 0 A 0.00000000 0.00000000 +molecule_0_122 0.0 0 A 0.00000000 0.00000000 +molecule_0_123 0.0 0 A 0.00000000 0.00000000 +molecule_0_124 0.0 0 A 0.00000000 0.00000000 +molecule_0_125 0.0 0 A 0.00000000 0.00000000 +molecule_0_126 0.0 0 A 0.00000000 0.00000000 +molecule_0_127 0.0 0 A 0.00000000 0.00000000 +molecule_0_128 0.0 0 A 0.00000000 0.00000000 +molecule_0_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp new file mode 100644 index 00000000..a76a4568 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/virtual_sites_nonbond_params.itp @@ -0,0 +1,46 @@ +[ nonbond_params ] +W molecule_0_1 1 0.47000000 1.00000000 ;water bias C +W molecule_0_2 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_3 1 0.47000000 1.00000000 ;water bias C +W molecule_0_4 1 0.41000000 1.00000000 ;water bias C +W molecule_0_9 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_10 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_17 1 0.47000000 1.00000000 ;water bias C +W molecule_0_20 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_23 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_24 1 0.47000000 1.00000000 ;water bias C +W molecule_0_29 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_30 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_31 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_32 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_39 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_42 1 0.41000000 1.00000000 ;water bias C +W molecule_0_43 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_44 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_45 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_46 1 0.47000000 1.00000000 ;water bias C +W molecule_0_50 1 0.47000000 1.00000000 ;water bias C +W molecule_0_51 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_52 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_53 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_58 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_59 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_64 1 0.47000000 1.00000000 ;water bias C +W molecule_0_65 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_66 1 0.47000000 1.00000000 ;water bias C +W molecule_0_68 1 0.47000000 1.00000000 ;water bias C +W molecule_0_69 1 0.47000000 1.00000000 ;water bias C +W molecule_0_72 1 0.47000000 1.00000000 ;water bias C +W molecule_0_73 1 0.47000000 1.00000000 ;water bias C +W molecule_0_74 1 0.47000000 1.00000000 ;water bias C +W molecule_0_77 1 0.47000000 1.00000000 ;water bias C +W molecule_0_79 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_88 1 0.47000000 1.00000000 ;water bias C +W molecule_0_93 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_94 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_95 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_96 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_119 1 0.47000000 1.00000000 ;water bias C +W molecule_0_127 1 0.47000000 1.00000000 ;water bias C +W molecule_0_128 1 0.47000000 1.00000000 ;water bias C +W molecule_0_129 1 0.47000000 1.00000000 ;water bias C diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README index dc9a10d5..2b233d39 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README @@ -6,6 +6,6 @@ ### TEST: -# -ff martini 30 open beta +# -ff martini 3001 # -scfix and GO # adding specific cys bridge as CONECT records diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README new file mode 100644 index 00000000..e7bae9df --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README @@ -0,0 +1,11 @@ +### DETAILS: + +# Original PDB CODE: 3LZT +# Structure from X-ray crystallography experiment. +# Select atoms with occupancy higuer than 0.5 + +### TEST: + +# -ff martini 3001 +# -scfix, GO and BB-W bias +# adding specific cys bridge as CONECT records diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb new file mode 100644 index 00000000..39371e9a --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/aa.pdb @@ -0,0 +1,1549 @@ +HEADER HYDROLASE(O-GLYCOSYL) 10-JAN-92 1HEL +TITLE STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING MUTATIONS WITHIN +TITLE 2 THE CORE OF CHICKEN EGG WHITE LYSOZYME +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: HEN EGG WHITE LYSOZYME; +COMPND 3 CHAIN: A; +COMPND 4 EC: 3.2.1.17; +COMPND 5 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; +SOURCE 3 ORGANISM_COMMON: CHICKEN; +SOURCE 4 ORGANISM_TAXID: 9031; +SOURCE 5 ORGAN: EGG +KEYWDS HYDROLASE(O-GLYCOSYL) +EXPDTA X-RAY DIFFRACTION +AUTHOR K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +REVDAT 3 16-NOV-11 1HEL 1 VERSN HETATM +REVDAT 2 24-FEB-09 1HEL 1 VERSN +REVDAT 1 31-OCT-93 1HEL 0 +JRNL AUTH K.P.WILSON,B.A.MALCOLM,B.W.MATTHEWS +JRNL TITL STRUCTURAL AND THERMODYNAMIC ANALYSIS OF COMPENSATING +JRNL TITL 2 MUTATIONS WITHIN THE CORE OF CHICKEN EGG WHITE LYSOZYME. +JRNL REF J.BIOL.CHEM. V. 267 10842 1992 +JRNL REFN ISSN 0021-9258 +JRNL PMID 1587860 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH B.A.MALCOLM,K.P.WILSON,B.W.MATTHEWS,J.F.KIRSCH,A.C.WILSON +REMARK 1 TITL ANCESTRAL LYSOZYMES RECONSTRUCTED, NEUTRALITY TESTED, AND +REMARK 1 TITL 2 THERMOSTABILITY LINKED TO HYDROCARBON PACKING +REMARK 1 REF NATURE V. 344 86 1990 +REMARK 1 REFN ISSN 0028-0836 +REMARK 2 +REMARK 2 RESOLUTION. 1.70 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : TNT +REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL +REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL +REMARK 3 COMPLETENESS FOR RANGE (%) : NULL +REMARK 3 NUMBER OF REFLECTIONS : NULL +REMARK 3 +REMARK 3 USING DATA ABOVE SIGMA CUTOFF. +REMARK 3 CROSS-VALIDATION METHOD : NULL +REMARK 3 FREE R VALUE TEST SET SELECTION : NULL +REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 +REMARK 3 R VALUE (WORKING SET) : NULL +REMARK 3 FREE R VALUE : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT : NULL +REMARK 3 +REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. +REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL +REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE (NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL +REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL +REMARK 3 +REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. +REMARK 3 PROTEIN ATOMS : 1001 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 185 +REMARK 3 +REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL +REMARK 3 +REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT +REMARK 3 BOND LENGTHS (A) : 0.019 ; NULL ; NULL +REMARK 3 BOND ANGLES (DEGREES) : 2.400 ; NULL ; NULL +REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL +REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL +REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL +REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL +REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL +REMARK 3 +REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL +REMARK 3 +REMARK 3 BULK SOLVENT MODELING. +REMARK 3 METHOD USED : NULL +REMARK 3 KSOL : NULL +REMARK 3 BSOL : NULL +REMARK 3 +REMARK 3 RESTRAINT LIBRARIES. +REMARK 3 STEREOCHEMISTRY : NULL +REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 1HEL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : NULL +REMARK 200 TEMPERATURE (KELVIN) : NULL +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : NULL +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : NULL +REMARK 200 RADIATION SOURCE : NULL +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : NULL +REMARK 200 DETECTOR MANUFACTURER : NULL +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL +REMARK 200 RESOLUTION RANGE HIGH (A) : NULL +REMARK 200 RESOLUTION RANGE LOW (A) : NULL +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: NULL +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 40.52 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X,-Y,Z+1/2 +REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 +REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 +REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 +REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 +REMARK 290 7555 Y,X,-Z +REMARK 290 8555 -Y,-X,-Z+1/2 +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.95000 +REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.42500 +REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.47500 +REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.42500 +REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.55000 +REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.55000 +REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.47500 +REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.95000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 375 +REMARK 375 SPECIAL POSITION +REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS +REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL +REMARK 375 POSITIONS. +REMARK 375 +REMARK 375 ATOM RES CSSEQI +REMARK 375 HOH A 318 LIES ON A SPECIAL POSITION. +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC +REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 +REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A +REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 +REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE +REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. +REMARK 500 +REMARK 500 DISTANCE CUTOFF: +REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS +REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE +REMARK 500 O HOH A 275 O HOH A 275 8555 0.35 +REMARK 500 O HOH A 203 O HOH A 203 7556 1.38 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: COVALENT BOND ANGLES +REMARK 500 +REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES +REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE +REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) +REMARK 500 +REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 +REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 +REMARK 500 +REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 +REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES +REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 8.7 DEGREES +REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES +REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 52 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES +REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES +REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES +REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES +REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES +REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: TORSION ANGLES +REMARK 500 +REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: +REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; +REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) +REMARK 500 +REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- +REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 +REMARK 500 +REMARK 500 M RES CSSEQI PSI PHI +REMARK 500 ARG A 68 19.50 -141.12 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 525 +REMARK 525 SOLVENT +REMARK 525 +REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT +REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST +REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT +REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE +REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; +REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE +REMARK 525 NUMBER; I=INSERTION CODE): +REMARK 525 +REMARK 525 M RES CSSEQI +REMARK 525 HOH A 188 DISTANCE = 6.89 ANGSTROMS +REMARK 525 HOH A 189 DISTANCE = 6.32 ANGSTROMS +REMARK 525 HOH A 190 DISTANCE = 5.68 ANGSTROMS +REMARK 525 HOH A 228 DISTANCE = 6.51 ANGSTROMS +REMARK 525 HOH A 230 DISTANCE = 5.30 ANGSTROMS +REMARK 525 HOH A 243 DISTANCE = 5.19 ANGSTROMS +REMARK 525 HOH A 249 DISTANCE = 6.99 ANGSTROMS +REMARK 525 HOH A 258 DISTANCE = 6.92 ANGSTROMS +REMARK 525 HOH A 268 DISTANCE = 8.36 ANGSTROMS +REMARK 525 HOH A 278 DISTANCE = 6.81 ANGSTROMS +REMARK 525 HOH A 304 DISTANCE = 7.48 ANGSTROMS +REMARK 525 HOH A 305 DISTANCE = 6.21 ANGSTROMS +REMARK 525 HOH A 308 DISTANCE = 19.71 ANGSTROMS +DBREF 1HEL A 1 129 UNP P00698 LYSC_CHICK 19 147 +SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS +SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY +SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN +SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP +SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN +SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE +SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER +SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY +SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY +SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU +FORMUL 2 HOH *185(H2 O) +HELIX 1 H1 GLY A 4 GLY A 16 1 13 +HELIX 2 H2 LEU A 25 PHE A 34 1 10 +HELIX 3 H3 PRO A 79 LEU A 84 5 6 +HELIX 4 H4 ILE A 88 SER A 100 1 13 +HELIX 5 H5 GLY A 104 TRP A 108 5 5 +HELIX 6 H6 VAL A 109 ARG A 114 1 6 +HELIX 7 H7 VAL A 120 ILE A 124 5 5 +SHEET 1 S1 3 ALA A 42 ASN A 46 0 +SHEET 2 S1 3 GLY A 49 GLY A 54 -1 O SER A 50 N ASN A 46 +SHEET 3 S1 3 LEU A 56 SER A 60 -1 O SER A 60 N THR A 51 +SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.99 +SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.11 +SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.00 +SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.10 +CRYST1 79.100 79.100 37.900 90.00 90.00 90.00 P 43 21 2 8 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.012642 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.012642 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.026385 0.00000 +ATOM 1 N LYS A 1 3.294 10.164 10.266 1.00 11.18 N +ATOM 2 CA LYS A 1 2.388 10.533 9.168 1.00 9.68 C +ATOM 3 C LYS A 1 2.438 12.049 8.889 1.00 14.00 C +ATOM 4 O LYS A 1 2.406 12.898 9.815 1.00 14.00 O +ATOM 5 CB LYS A 1 0.949 10.101 9.559 1.00 13.29 C +ATOM 6 CG LYS A 1 -0.050 10.621 8.573 1.00 13.52 C +ATOM 7 CD LYS A 1 -1.425 10.081 8.720 1.00 22.15 C +ATOM 8 CE LYS A 1 -2.370 10.773 7.722 1.00 20.23 C +ATOM 9 NZ LYS A 1 -3.776 10.439 7.933 1.00 68.72 N +ATOM 10 N VAL A 2 2.552 12.428 7.626 1.00 10.17 N +ATOM 11 CA VAL A 2 2.524 13.840 7.282 1.00 10.02 C +ATOM 12 C VAL A 2 1.120 14.180 6.770 1.00 27.84 C +ATOM 13 O VAL A 2 0.737 13.798 5.675 1.00 22.87 O +ATOM 14 CB VAL A 2 3.529 14.264 6.240 1.00 9.00 C +ATOM 15 CG1 VAL A 2 3.313 15.765 5.983 1.00 11.37 C +ATOM 16 CG2 VAL A 2 4.928 14.016 6.810 1.00 10.57 C +ATOM 17 N PHE A 3 0.333 14.851 7.573 1.00 16.35 N +ATOM 18 CA PHE A 3 -1.021 15.173 7.169 1.00 15.34 C +ATOM 19 C PHE A 3 -1.097 16.285 6.126 1.00 14.79 C +ATOM 20 O PHE A 3 -0.261 17.203 6.054 1.00 14.99 O +ATOM 21 CB PHE A 3 -1.867 15.710 8.361 1.00 14.03 C +ATOM 22 CG PHE A 3 -2.412 14.638 9.295 1.00 16.41 C +ATOM 23 CD1 PHE A 3 -1.575 14.049 10.240 1.00 14.44 C +ATOM 24 CD2 PHE A 3 -3.757 14.285 9.274 1.00 18.12 C +ATOM 25 CE1 PHE A 3 -2.065 13.116 11.135 1.00 11.11 C +ATOM 26 CE2 PHE A 3 -4.263 13.332 10.178 1.00 32.24 C +ATOM 27 CZ PHE A 3 -3.413 12.758 11.132 1.00 14.31 C +ATOM 28 N GLY A 4 -2.229 16.228 5.393 1.00 15.47 N +ATOM 29 CA GLY A 4 -2.645 17.273 4.511 1.00 13.97 C +ATOM 30 C GLY A 4 -3.456 18.261 5.350 1.00 10.95 C +ATOM 31 O GLY A 4 -4.070 17.876 6.282 1.00 16.45 O +ATOM 32 N ARG A 5 -3.414 19.518 5.009 1.00 14.28 N +ATOM 33 CA ARG A 5 -4.106 20.560 5.674 1.00 11.63 C +ATOM 34 C ARG A 5 -5.540 20.226 5.992 1.00 21.37 C +ATOM 35 O ARG A 5 -5.963 20.258 7.138 1.00 9.74 O +ATOM 36 CB ARG A 5 -3.952 21.857 4.900 1.00 13.31 C +ATOM 37 CG ARG A 5 -4.508 23.053 5.610 1.00 13.02 C +ATOM 38 CD ARG A 5 -4.414 24.335 4.775 1.00 19.72 C +ATOM 39 NE ARG A 5 -5.013 24.223 3.447 1.00 23.52 N +ATOM 40 CZ ARG A 5 -6.287 24.522 3.048 1.00 40.17 C +ATOM 41 NH1 ARG A 5 -7.248 25.009 3.841 1.00 17.54 N +ATOM 42 NH2 ARG A 5 -6.619 24.303 1.767 1.00 33.21 N +ATOM 43 N CYS A 6 -6.327 19.866 4.967 1.00 15.04 N +ATOM 44 CA CYS A 6 -7.767 19.572 5.189 1.00 12.93 C +ATOM 45 C CYS A 6 -7.997 18.269 5.916 1.00 5.10 C +ATOM 46 O CYS A 6 -8.992 18.125 6.630 1.00 13.60 O +ATOM 47 CB CYS A 6 -8.607 19.637 3.859 1.00 16.72 C +ATOM 48 SG CYS A 6 -8.669 21.273 3.104 1.00 16.68 S +ATOM 49 N GLU A 7 -7.142 17.274 5.653 1.00 7.34 N +ATOM 50 CA GLU A 7 -7.309 15.981 6.323 1.00 10.86 C +ATOM 51 C GLU A 7 -7.129 16.181 7.848 1.00 17.71 C +ATOM 52 O GLU A 7 -7.835 15.638 8.657 1.00 14.19 O +ATOM 53 CB GLU A 7 -6.187 15.048 5.880 1.00 16.19 C +ATOM 54 CG GLU A 7 -6.206 13.614 6.496 1.00 16.67 C +ATOM 55 CD GLU A 7 -4.952 12.864 6.030 1.00 32.91 C +ATOM 56 OE1 GLU A 7 -4.003 13.411 5.480 1.00 18.18 O +ATOM 57 OE2 GLU A 7 -4.992 11.578 6.219 1.00 28.07 O +ATOM 58 N LEU A 8 -6.148 16.987 8.221 1.00 14.04 N +ATOM 59 CA LEU A 8 -5.919 17.285 9.637 1.00 8.65 C +ATOM 60 C LEU A 8 -7.068 18.103 10.254 1.00 10.08 C +ATOM 61 O LEU A 8 -7.500 17.827 11.353 1.00 15.66 O +ATOM 62 CB LEU A 8 -4.607 18.084 9.809 1.00 14.88 C +ATOM 63 CG LEU A 8 -4.384 18.432 11.299 1.00 12.61 C +ATOM 64 CD1 LEU A 8 -4.110 17.104 12.053 1.00 12.51 C +ATOM 65 CD2 LEU A 8 -3.147 19.299 11.372 1.00 13.98 C +ATOM 66 N ALA A 9 -7.524 19.122 9.561 1.00 11.92 N +ATOM 67 CA ALA A 9 -8.664 19.896 9.982 1.00 10.97 C +ATOM 68 C ALA A 9 -9.841 18.971 10.304 1.00 15.73 C +ATOM 69 O ALA A 9 -10.469 19.046 11.359 1.00 13.41 O +ATOM 70 CB ALA A 9 -9.039 21.012 8.954 1.00 8.88 C +ATOM 71 N ALA A 10 -10.124 18.049 9.425 1.00 12.11 N +ATOM 72 CA ALA A 10 -11.262 17.129 9.595 1.00 12.19 C +ATOM 73 C ALA A 10 -11.034 16.206 10.780 1.00 18.02 C +ATOM 74 O ALA A 10 -11.932 15.902 11.522 1.00 17.70 O +ATOM 75 CB ALA A 10 -11.457 16.297 8.313 1.00 14.75 C +ATOM 76 N ALA A 11 -9.815 15.771 10.988 1.00 14.94 N +ATOM 77 CA ALA A 11 -9.544 14.908 12.136 1.00 12.19 C +ATOM 78 C ALA A 11 -9.651 15.641 13.494 1.00 7.51 C +ATOM 79 O ALA A 11 -10.088 15.066 14.457 1.00 12.99 O +ATOM 80 CB ALA A 11 -8.153 14.250 12.041 1.00 15.76 C +ATOM 81 N MET A 12 -9.107 16.884 13.529 1.00 10.71 N +ATOM 82 CA MET A 12 -9.160 17.683 14.710 1.00 12.27 C +ATOM 83 C MET A 12 -10.599 17.988 15.028 1.00 16.76 C +ATOM 84 O MET A 12 -10.964 17.966 16.195 1.00 17.43 O +ATOM 85 CB MET A 12 -8.385 18.996 14.563 1.00 6.96 C +ATOM 86 CG MET A 12 -6.872 18.717 14.593 1.00 7.53 C +ATOM 87 SD MET A 12 -5.971 20.286 14.351 1.00 16.25 S +ATOM 88 CE MET A 12 -4.392 19.972 15.137 1.00 11.48 C +ATOM 89 N LYS A 13 -11.421 18.239 13.985 1.00 11.66 N +ATOM 90 CA LYS A 13 -12.844 18.554 14.146 1.00 12.77 C +ATOM 91 C LYS A 13 -13.552 17.402 14.762 1.00 17.21 C +ATOM 92 O LYS A 13 -14.278 17.533 15.704 1.00 15.75 O +ATOM 93 CB LYS A 13 -13.505 18.908 12.852 1.00 14.38 C +ATOM 94 CG LYS A 13 -14.874 19.457 13.096 1.00 16.88 C +ATOM 95 CD LYS A 13 -15.519 20.062 11.867 1.00 19.73 C +ATOM 96 CE LYS A 13 -17.062 20.060 11.971 1.00 41.06 C +ATOM 97 NZ LYS A 13 -17.725 20.836 10.899 1.00 61.80 N +ATOM 98 N ARG A 14 -13.273 16.240 14.220 1.00 21.68 N +ATOM 99 CA ARG A 14 -13.878 15.021 14.667 1.00 17.17 C +ATOM 100 C ARG A 14 -13.480 14.746 16.099 1.00 27.88 C +ATOM 101 O ARG A 14 -14.217 14.129 16.823 1.00 17.70 O +ATOM 102 CB ARG A 14 -13.448 13.876 13.756 1.00 23.48 C +ATOM 103 CG ARG A 14 -14.102 12.553 14.162 1.00 51.76 C +ATOM 104 CD ARG A 14 -13.875 11.424 13.160 1.00 52.15 C +ATOM 105 NE ARG A 14 -12.616 10.730 13.354 1.00 61.79 N +ATOM 106 CZ ARG A 14 -12.406 9.681 14.156 1.00 47.00 C +ATOM 107 NH1 ARG A 14 -13.357 9.121 14.898 1.00 35.04 N +ATOM 108 NH2 ARG A 14 -11.177 9.169 14.196 1.00 55.70 N +ATOM 109 N HIS A 15 -12.300 15.219 16.498 1.00 20.13 N +ATOM 110 CA HIS A 15 -11.791 15.016 17.846 1.00 14.58 C +ATOM 111 C HIS A 15 -12.221 16.074 18.888 1.00 18.83 C +ATOM 112 O HIS A 15 -11.689 16.060 19.970 1.00 22.76 O +ATOM 113 CB HIS A 15 -10.268 14.799 17.851 1.00 23.09 C +ATOM 114 CG HIS A 15 -9.906 13.364 17.563 1.00 21.53 C +ATOM 115 ND1 HIS A 15 -9.721 12.896 16.256 1.00 28.28 N +ATOM 116 CD2 HIS A 15 -9.723 12.308 18.413 1.00 30.99 C +ATOM 117 CE1 HIS A 15 -9.422 11.580 16.350 1.00 20.50 C +ATOM 118 NE2 HIS A 15 -9.412 11.213 17.627 1.00 42.34 N +ATOM 119 N GLY A 16 -13.146 16.952 18.551 1.00 14.90 N +ATOM 120 CA GLY A 16 -13.687 17.956 19.401 1.00 16.84 C +ATOM 121 C GLY A 16 -12.871 19.227 19.554 1.00 23.06 C +ATOM 122 O GLY A 16 -13.121 20.016 20.460 1.00 19.24 O +ATOM 123 N LEU A 17 -11.922 19.491 18.685 1.00 14.25 N +ATOM 124 CA LEU A 17 -11.134 20.695 18.826 1.00 10.83 C +ATOM 125 C LEU A 17 -11.728 21.961 18.295 1.00 16.61 C +ATOM 126 O LEU A 17 -11.276 23.016 18.657 1.00 18.63 O +ATOM 127 CB LEU A 17 -9.749 20.538 18.218 1.00 14.80 C +ATOM 128 CG LEU A 17 -8.792 19.745 19.031 1.00 19.84 C +ATOM 129 CD1 LEU A 17 -7.483 19.876 18.293 1.00 22.16 C +ATOM 130 CD2 LEU A 17 -8.675 20.282 20.474 1.00 15.82 C +ATOM 131 N ASP A 18 -12.704 21.930 17.405 1.00 18.32 N +ATOM 132 CA ASP A 18 -13.261 23.178 16.884 1.00 18.68 C +ATOM 133 C ASP A 18 -13.986 23.912 17.979 1.00 19.05 C +ATOM 134 O ASP A 18 -14.952 23.375 18.512 1.00 21.74 O +ATOM 135 CB ASP A 18 -14.275 23.002 15.717 1.00 25.90 C +ATOM 136 CG ASP A 18 -14.712 24.288 15.010 1.00 37.66 C +ATOM 137 OD1 ASP A 18 -14.134 25.393 15.038 1.00 26.98 O +ATOM 138 OD2 ASP A 18 -15.751 24.055 14.248 1.00 63.41 O +ATOM 139 N ASN A 19 -13.542 25.130 18.229 1.00 12.22 N +ATOM 140 CA ASN A 19 -14.046 26.010 19.253 1.00 9.99 C +ATOM 141 C ASN A 19 -13.851 25.507 20.671 1.00 15.97 C +ATOM 142 O ASN A 19 -14.534 25.975 21.595 1.00 18.10 O +ATOM 143 CB ASN A 19 -15.518 26.259 19.032 1.00 20.32 C +ATOM 144 CG ASN A 19 -15.706 27.052 17.774 1.00 40.03 C +ATOM 145 OD1 ASN A 19 -15.227 28.183 17.693 1.00 57.25 O +ATOM 146 ND2 ASN A 19 -16.402 26.456 16.811 1.00 40.09 N +ATOM 147 N TYR A 20 -12.956 24.552 20.827 1.00 12.49 N +ATOM 148 CA TYR A 20 -12.652 24.027 22.106 1.00 8.91 C +ATOM 149 C TYR A 20 -12.037 25.159 22.929 1.00 19.06 C +ATOM 150 O TYR A 20 -10.978 25.687 22.602 1.00 16.99 O +ATOM 151 CB TYR A 20 -11.717 22.810 22.005 1.00 17.23 C +ATOM 152 CG TYR A 20 -11.532 22.151 23.355 1.00 13.76 C +ATOM 153 CD1 TYR A 20 -12.444 21.206 23.832 1.00 17.40 C +ATOM 154 CD2 TYR A 20 -10.475 22.556 24.184 1.00 24.53 C +ATOM 155 CE1 TYR A 20 -12.311 20.657 25.111 1.00 20.84 C +ATOM 156 CE2 TYR A 20 -10.331 22.023 25.461 1.00 16.26 C +ATOM 157 CZ TYR A 20 -11.259 21.078 25.922 1.00 35.41 C +ATOM 158 OH TYR A 20 -11.104 20.560 27.183 1.00 29.68 O +ATOM 159 N ARG A 21 -12.721 25.593 23.977 1.00 19.00 N +ATOM 160 CA ARG A 21 -12.250 26.715 24.791 1.00 15.05 C +ATOM 161 C ARG A 21 -12.264 27.987 24.017 1.00 8.63 C +ATOM 162 O ARG A 21 -11.450 28.877 24.295 1.00 13.69 O +ATOM 163 CB ARG A 21 -10.847 26.601 25.387 1.00 18.33 C +ATOM 164 CG ARG A 21 -10.694 25.514 26.442 1.00 27.37 C +ATOM 165 CD ARG A 21 -11.577 25.864 27.598 1.00 40.81 C +ATOM 166 NE ARG A 21 -11.597 24.902 28.676 1.00 57.85 N +ATOM 167 CZ ARG A 21 -11.253 25.330 29.884 1.00 97.15 C +ATOM 168 NH1 ARG A 21 -10.859 26.593 30.049 1.00 63.15 N +ATOM 169 NH2 ARG A 21 -11.283 24.508 30.937 1.00 68.08 N +ATOM 170 N GLY A 22 -13.173 28.076 23.045 1.00 11.97 N +ATOM 171 CA GLY A 22 -13.290 29.312 22.253 1.00 13.56 C +ATOM 172 C GLY A 22 -12.276 29.499 21.125 1.00 15.57 C +ATOM 173 O GLY A 22 -12.274 30.537 20.508 1.00 15.13 O +ATOM 174 N TYR A 23 -11.414 28.511 20.863 1.00 17.25 N +ATOM 175 CA TYR A 23 -10.419 28.584 19.787 1.00 12.17 C +ATOM 176 C TYR A 23 -10.964 27.832 18.564 1.00 7.69 C +ATOM 177 O TYR A 23 -11.097 26.573 18.581 1.00 8.57 O +ATOM 178 CB TYR A 23 -9.059 27.910 20.217 1.00 11.16 C +ATOM 179 CG TYR A 23 -8.358 28.702 21.299 1.00 14.01 C +ATOM 180 CD1 TYR A 23 -7.560 29.766 20.910 1.00 10.23 C +ATOM 181 CD2 TYR A 23 -8.534 28.427 22.652 1.00 6.77 C +ATOM 182 CE1 TYR A 23 -6.879 30.557 21.846 1.00 9.23 C +ATOM 183 CE2 TYR A 23 -7.907 29.219 23.612 1.00 10.96 C +ATOM 184 CZ TYR A 23 -7.061 30.276 23.207 1.00 12.99 C +ATOM 185 OH TYR A 23 -6.411 31.069 24.111 1.00 13.78 O +ATOM 186 N SER A 24 -11.219 28.590 17.517 1.00 12.88 N +ATOM 187 CA SER A 24 -11.730 28.032 16.253 1.00 14.99 C +ATOM 188 C SER A 24 -10.726 27.075 15.616 1.00 20.42 C +ATOM 189 O SER A 24 -9.487 27.191 15.841 1.00 9.73 O +ATOM 190 CB SER A 24 -12.060 29.179 15.305 1.00 9.90 C +ATOM 191 OG SER A 24 -10.830 29.750 14.853 1.00 17.68 O +ATOM 192 N LEU A 25 -11.267 26.110 14.822 1.00 16.10 N +ATOM 193 CA LEU A 25 -10.460 25.111 14.092 1.00 11.40 C +ATOM 194 C LEU A 25 -9.205 25.683 13.438 1.00 11.44 C +ATOM 195 O LEU A 25 -8.145 25.073 13.536 1.00 10.56 O +ATOM 196 CB LEU A 25 -11.293 24.412 12.993 1.00 13.62 C +ATOM 197 CG LEU A 25 -10.826 23.089 12.491 1.00 16.00 C +ATOM 198 CD1 LEU A 25 -10.359 22.212 13.644 1.00 15.17 C +ATOM 199 CD2 LEU A 25 -12.018 22.437 11.805 1.00 15.75 C +ATOM 200 N GLY A 26 -9.311 26.836 12.758 1.00 10.18 N +ATOM 201 CA GLY A 26 -8.169 27.388 12.084 1.00 7.13 C +ATOM 202 C GLY A 26 -6.984 27.643 12.997 1.00 9.12 C +ATOM 203 O GLY A 26 -5.854 27.610 12.555 1.00 12.61 O +ATOM 204 N ASN A 27 -7.232 27.928 14.280 1.00 10.01 N +ATOM 205 CA ASN A 27 -6.132 28.159 15.255 1.00 10.13 C +ATOM 206 C ASN A 27 -5.317 26.889 15.464 1.00 2.57 C +ATOM 207 O ASN A 27 -4.057 26.899 15.477 1.00 7.08 O +ATOM 208 CB ASN A 27 -6.688 28.636 16.631 1.00 9.13 C +ATOM 209 CG ASN A 27 -7.131 30.092 16.624 1.00 4.84 C +ATOM 210 OD1 ASN A 27 -6.292 30.979 16.582 1.00 9.37 O +ATOM 211 ND2 ASN A 27 -8.466 30.324 16.587 1.00 8.00 N +ATOM 212 N TRP A 28 -6.033 25.791 15.639 1.00 5.40 N +ATOM 213 CA TRP A 28 -5.402 24.497 15.879 1.00 5.45 C +ATOM 214 C TRP A 28 -4.584 24.047 14.657 1.00 6.38 C +ATOM 215 O TRP A 28 -3.510 23.501 14.767 1.00 7.31 O +ATOM 216 CB TRP A 28 -6.482 23.490 16.237 1.00 7.31 C +ATOM 217 CG TRP A 28 -7.149 23.849 17.539 1.00 7.66 C +ATOM 218 CD1 TRP A 28 -8.351 24.415 17.748 1.00 11.80 C +ATOM 219 CD2 TRP A 28 -6.540 23.691 18.841 1.00 9.47 C +ATOM 220 NE1 TRP A 28 -8.575 24.567 19.117 1.00 11.48 N +ATOM 221 CE2 TRP A 28 -7.475 24.139 19.807 1.00 9.56 C +ATOM 222 CE3 TRP A 28 -5.321 23.121 19.249 1.00 10.24 C +ATOM 223 CZ2 TRP A 28 -7.187 24.066 21.210 1.00 11.03 C +ATOM 224 CZ3 TRP A 28 -5.059 23.060 20.609 1.00 20.66 C +ATOM 225 CH2 TRP A 28 -5.985 23.551 21.560 1.00 9.06 C +ATOM 226 N VAL A 29 -5.166 24.262 13.469 1.00 3.89 N +ATOM 227 CA VAL A 29 -4.458 23.870 12.217 1.00 5.65 C +ATOM 228 C VAL A 29 -3.242 24.746 11.972 1.00 2.99 C +ATOM 229 O VAL A 29 -2.170 24.273 11.571 1.00 7.90 O +ATOM 230 CB VAL A 29 -5.456 23.881 11.020 1.00 7.66 C +ATOM 231 CG1 VAL A 29 -4.630 23.646 9.743 1.00 13.23 C +ATOM 232 CG2 VAL A 29 -6.516 22.751 11.149 1.00 6.73 C +ATOM 233 N CYS A 30 -3.372 26.060 12.262 1.00 2.63 N +ATOM 234 CA CYS A 30 -2.281 26.976 12.125 1.00 7.05 C +ATOM 235 C CYS A 30 -1.151 26.582 13.072 1.00 10.47 C +ATOM 236 O CYS A 30 0.054 26.552 12.766 1.00 4.93 O +ATOM 237 CB CYS A 30 -2.756 28.428 12.303 1.00 2.61 C +ATOM 238 SG CYS A 30 -1.467 29.667 12.134 1.00 10.20 S +ATOM 239 N ALA A 31 -1.521 26.283 14.306 1.00 9.82 N +ATOM 240 CA ALA A 31 -0.491 25.884 15.276 1.00 15.61 C +ATOM 241 C ALA A 31 0.235 24.607 14.849 1.00 5.07 C +ATOM 242 O ALA A 31 1.464 24.554 14.987 1.00 9.27 O +ATOM 243 CB ALA A 31 -1.089 25.781 16.704 1.00 7.85 C +ATOM 244 N ALA A 32 -0.483 23.609 14.315 1.00 7.79 N +ATOM 245 CA ALA A 32 0.162 22.357 13.855 1.00 8.61 C +ATOM 246 C ALA A 32 1.085 22.594 12.673 1.00 7.90 C +ATOM 247 O ALA A 32 2.197 22.050 12.585 1.00 9.35 O +ATOM 248 CB ALA A 32 -0.823 21.268 13.540 1.00 10.83 C +ATOM 249 N LYS A 33 0.653 23.463 11.786 1.00 7.35 N +ATOM 250 CA LYS A 33 1.542 23.795 10.635 1.00 6.50 C +ATOM 251 C LYS A 33 2.867 24.333 11.097 1.00 6.89 C +ATOM 252 O LYS A 33 3.936 23.889 10.727 1.00 10.45 O +ATOM 253 CB LYS A 33 0.863 24.886 9.776 1.00 10.32 C +ATOM 254 CG LYS A 33 1.793 25.437 8.676 1.00 13.52 C +ATOM 255 CD LYS A 33 1.927 24.485 7.491 1.00 19.87 C +ATOM 256 CE LYS A 33 3.138 24.764 6.621 1.00 27.04 C +ATOM 257 NZ LYS A 33 3.217 23.793 5.511 1.00 45.44 N +ATOM 258 N PHE A 34 2.807 25.345 11.961 1.00 9.24 N +ATOM 259 CA PHE A 34 4.029 25.958 12.436 1.00 8.96 C +ATOM 260 C PHE A 34 4.846 25.192 13.455 1.00 16.48 C +ATOM 261 O PHE A 34 6.039 25.360 13.540 1.00 14.96 O +ATOM 262 CB PHE A 34 3.856 27.469 12.721 1.00 9.21 C +ATOM 263 CG PHE A 34 3.417 28.201 11.426 1.00 11.78 C +ATOM 264 CD1 PHE A 34 4.231 28.189 10.282 1.00 11.49 C +ATOM 265 CD2 PHE A 34 2.212 28.933 11.385 1.00 12.86 C +ATOM 266 CE1 PHE A 34 3.830 28.854 9.136 1.00 12.74 C +ATOM 267 CE2 PHE A 34 1.803 29.618 10.224 1.00 13.38 C +ATOM 268 CZ PHE A 34 2.627 29.554 9.090 1.00 13.39 C +ATOM 269 N GLU A 35 4.201 24.324 14.225 1.00 9.90 N +ATOM 270 CA GLU A 35 4.889 23.543 15.263 1.00 11.92 C +ATOM 271 C GLU A 35 5.641 22.352 14.706 1.00 13.79 C +ATOM 272 O GLU A 35 6.781 22.129 15.054 1.00 8.23 O +ATOM 273 CB GLU A 35 3.839 23.026 16.259 1.00 6.00 C +ATOM 274 CG GLU A 35 3.409 24.107 17.322 1.00 11.89 C +ATOM 275 CD GLU A 35 4.516 24.690 18.200 1.00 12.03 C +ATOM 276 OE1 GLU A 35 5.640 24.296 18.226 1.00 12.97 O +ATOM 277 OE2 GLU A 35 4.167 25.730 18.876 1.00 13.03 O +ATOM 278 N SER A 36 4.983 21.591 13.819 1.00 8.49 N +ATOM 279 CA SER A 36 5.541 20.369 13.283 1.00 8.82 C +ATOM 280 C SER A 36 5.483 20.189 11.756 1.00 10.13 C +ATOM 281 O SER A 36 5.800 19.070 11.251 1.00 14.88 O +ATOM 282 CB SER A 36 4.684 19.256 13.831 1.00 7.77 C +ATOM 283 OG SER A 36 3.330 19.336 13.297 1.00 8.30 O +ATOM 284 N ASN A 37 4.975 21.223 11.050 1.00 11.55 N +ATOM 285 CA ASN A 37 4.752 21.103 9.605 1.00 8.89 C +ATOM 286 C ASN A 37 3.825 19.918 9.321 1.00 14.33 C +ATOM 287 O ASN A 37 3.972 19.215 8.320 1.00 14.19 O +ATOM 288 CB ASN A 37 6.061 21.002 8.788 1.00 20.93 C +ATOM 289 CG ASN A 37 5.851 21.458 7.334 1.00 25.83 C +ATOM 290 OD1 ASN A 37 5.061 22.365 7.057 1.00 26.84 O +ATOM 291 ND2 ASN A 37 6.474 20.759 6.397 1.00 52.87 N +ATOM 292 N PHE A 38 2.864 19.696 10.220 1.00 7.19 N +ATOM 293 CA PHE A 38 1.862 18.625 10.075 1.00 11.76 C +ATOM 294 C PHE A 38 2.411 17.214 10.168 1.00 10.63 C +ATOM 295 O PHE A 38 1.747 16.276 9.742 1.00 9.49 O +ATOM 296 CB PHE A 38 1.092 18.696 8.696 1.00 8.56 C +ATOM 297 CG PHE A 38 0.280 19.956 8.505 1.00 13.59 C +ATOM 298 CD1 PHE A 38 -0.367 20.558 9.597 1.00 8.45 C +ATOM 299 CD2 PHE A 38 0.112 20.532 7.255 1.00 17.61 C +ATOM 300 CE1 PHE A 38 -1.146 21.685 9.432 1.00 11.53 C +ATOM 301 CE2 PHE A 38 -0.664 21.687 7.081 1.00 17.65 C +ATOM 302 CZ PHE A 38 -1.316 22.268 8.162 1.00 13.17 C +ATOM 303 N ASN A 39 3.667 17.073 10.600 1.00 8.40 N +ATOM 304 CA ASN A 39 4.271 15.737 10.699 1.00 6.01 C +ATOM 305 C ASN A 39 4.101 15.211 12.158 1.00 6.81 C +ATOM 306 O ASN A 39 4.597 15.858 13.147 1.00 11.41 O +ATOM 307 CB ASN A 39 5.776 15.925 10.373 1.00 6.39 C +ATOM 308 CG ASN A 39 6.552 14.636 10.450 1.00 6.34 C +ATOM 309 OD1 ASN A 39 5.992 13.541 10.684 1.00 10.75 O +ATOM 310 ND2 ASN A 39 7.832 14.764 10.100 1.00 13.88 N +ATOM 311 N THR A 40 3.430 14.054 12.314 1.00 8.05 N +ATOM 312 CA THR A 40 3.222 13.509 13.676 1.00 10.13 C +ATOM 313 C THR A 40 4.525 13.041 14.358 1.00 8.64 C +ATOM 314 O THR A 40 4.546 12.831 15.542 1.00 12.11 O +ATOM 315 CB THR A 40 2.279 12.302 13.663 1.00 12.49 C +ATOM 316 OG1 THR A 40 2.862 11.250 12.880 1.00 10.89 O +ATOM 317 CG2 THR A 40 0.843 12.666 13.219 1.00 9.90 C +ATOM 318 N GLN A 41 5.594 12.819 13.559 1.00 6.61 N +ATOM 319 CA GLN A 41 6.860 12.308 14.019 1.00 3.67 C +ATOM 320 C GLN A 41 7.861 13.372 14.433 1.00 4.66 C +ATOM 321 O GLN A 41 8.986 13.051 14.864 1.00 8.80 O +ATOM 322 CB GLN A 41 7.463 11.344 12.979 1.00 9.30 C +ATOM 323 CG GLN A 41 6.598 10.100 12.797 1.00 12.21 C +ATOM 324 CD GLN A 41 7.402 8.999 12.104 1.00 22.47 C +ATOM 325 OE1 GLN A 41 8.254 8.393 12.763 1.00 16.54 O +ATOM 326 NE2 GLN A 41 7.257 8.847 10.744 1.00 13.11 N +ATOM 327 N ALA A 42 7.460 14.657 14.305 1.00 6.51 N +ATOM 328 CA ALA A 42 8.376 15.748 14.672 1.00 8.14 C +ATOM 329 C ALA A 42 8.824 15.710 16.237 1.00 11.70 C +ATOM 330 O ALA A 42 8.005 15.547 17.165 1.00 5.54 O +ATOM 331 CB ALA A 42 7.744 17.108 14.349 1.00 8.97 C +ATOM 332 N THR A 43 10.132 15.865 16.445 1.00 7.08 N +ATOM 333 CA THR A 43 10.705 15.992 17.773 1.00 10.42 C +ATOM 334 C THR A 43 11.694 17.112 17.692 1.00 11.09 C +ATOM 335 O THR A 43 12.280 17.411 16.646 1.00 12.80 O +ATOM 336 CB THR A 43 11.362 14.748 18.354 1.00 13.93 C +ATOM 337 OG1 THR A 43 12.360 14.429 17.435 1.00 11.09 O +ATOM 338 CG2 THR A 43 10.420 13.567 18.530 1.00 7.58 C +ATOM 339 N ASN A 44 11.894 17.801 18.808 1.00 10.77 N +ATOM 340 CA ASN A 44 12.828 18.909 18.863 1.00 6.02 C +ATOM 341 C ASN A 44 13.258 19.036 20.281 1.00 16.51 C +ATOM 342 O ASN A 44 12.426 19.127 21.185 1.00 11.61 O +ATOM 343 CB ASN A 44 12.171 20.225 18.473 1.00 13.37 C +ATOM 344 CG ASN A 44 11.932 20.272 16.966 1.00 55.95 C +ATOM 345 OD1 ASN A 44 12.883 20.299 16.146 1.00 30.16 O +ATOM 346 ND2 ASN A 44 10.659 20.233 16.594 1.00 20.67 N +ATOM 347 N ARG A 45 14.545 19.035 20.479 1.00 13.41 N +ATOM 348 CA ARG A 45 15.061 19.112 21.827 1.00 12.01 C +ATOM 349 C ARG A 45 15.250 20.555 22.252 1.00 20.93 C +ATOM 350 O ARG A 45 15.601 21.418 21.435 1.00 20.22 O +ATOM 351 CB ARG A 45 16.408 18.438 21.953 1.00 19.70 C +ATOM 352 CG ARG A 45 16.935 18.714 23.338 1.00 35.82 C +ATOM 353 CD ARG A 45 16.730 17.468 24.141 1.00 27.63 C +ATOM 354 NE ARG A 45 17.249 16.408 23.330 1.00 67.37 N +ATOM 355 CZ ARG A 45 18.249 15.588 23.641 1.00 91.84 C +ATOM 356 NH1 ARG A 45 18.868 15.589 24.830 1.00 36.08 N +ATOM 357 NH2 ARG A 45 18.624 14.698 22.716 1.00 64.26 N +ATOM 358 N ASN A 46 15.056 20.796 23.543 1.00 12.63 N +ATOM 359 CA ASN A 46 15.247 22.135 24.062 1.00 12.92 C +ATOM 360 C ASN A 46 16.508 22.245 24.900 1.00 8.11 C +ATOM 361 O ASN A 46 17.149 21.253 25.274 1.00 15.77 O +ATOM 362 CB ASN A 46 13.989 22.699 24.735 1.00 11.70 C +ATOM 363 CG ASN A 46 12.659 22.418 24.007 1.00 21.14 C +ATOM 364 OD1 ASN A 46 11.762 21.669 24.459 1.00 23.29 O +ATOM 365 ND2 ASN A 46 12.508 23.062 22.886 1.00 24.99 N +ATOM 366 N THR A 47 16.906 23.489 25.146 1.00 23.92 N +ATOM 367 CA THR A 47 18.108 23.768 25.931 1.00 39.90 C +ATOM 368 C THR A 47 17.996 23.269 27.358 1.00 25.44 C +ATOM 369 O THR A 47 18.958 22.798 27.923 1.00 34.24 O +ATOM 370 CB THR A 47 18.506 25.250 25.905 1.00 47.42 C +ATOM 371 OG1 THR A 47 17.376 26.053 26.142 1.00 38.53 O +ATOM 372 CG2 THR A 47 19.115 25.572 24.552 1.00 58.08 C +ATOM 373 N ASP A 48 16.797 23.339 27.935 1.00 20.62 N +ATOM 374 CA ASP A 48 16.626 22.832 29.261 1.00 9.90 C +ATOM 375 C ASP A 48 16.700 21.306 29.306 1.00 19.23 C +ATOM 376 O ASP A 48 16.586 20.723 30.361 1.00 22.36 O +ATOM 377 CB ASP A 48 15.349 23.377 29.887 1.00 14.78 C +ATOM 378 CG ASP A 48 14.119 22.821 29.267 1.00 19.04 C +ATOM 379 OD1 ASP A 48 14.160 21.981 28.422 1.00 28.31 O +ATOM 380 OD2 ASP A 48 13.002 23.315 29.717 1.00 28.61 O +ATOM 381 N GLY A 49 16.883 20.637 28.166 1.00 17.28 N +ATOM 382 CA GLY A 49 16.950 19.205 28.182 1.00 10.24 C +ATOM 383 C GLY A 49 15.608 18.534 27.977 1.00 14.24 C +ATOM 384 O GLY A 49 15.499 17.291 27.852 1.00 13.58 O +ATOM 385 N SER A 50 14.564 19.331 27.973 1.00 9.07 N +ATOM 386 CA SER A 50 13.311 18.716 27.712 1.00 7.32 C +ATOM 387 C SER A 50 13.217 18.531 26.131 1.00 11.52 C +ATOM 388 O SER A 50 14.085 19.016 25.374 1.00 13.96 O +ATOM 389 CB SER A 50 12.113 19.490 28.182 1.00 4.67 C +ATOM 390 OG SER A 50 12.074 20.716 27.461 1.00 9.76 O +ATOM 391 N THR A 51 12.150 17.857 25.646 1.00 11.43 N +ATOM 392 CA THR A 51 11.958 17.610 24.179 1.00 9.12 C +ATOM 393 C THR A 51 10.485 17.806 23.917 1.00 16.87 C +ATOM 394 O THR A 51 9.677 17.499 24.825 1.00 8.33 O +ATOM 395 CB THR A 51 12.363 16.177 23.757 1.00 5.49 C +ATOM 396 OG1 THR A 51 13.711 15.986 24.120 1.00 6.88 O +ATOM 397 CG2 THR A 51 12.234 15.930 22.227 1.00 7.94 C +ATOM 398 N ASP A 52 10.158 18.354 22.701 1.00 9.46 N +ATOM 399 CA ASP A 52 8.767 18.608 22.181 1.00 5.88 C +ATOM 400 C ASP A 52 8.451 17.463 21.198 1.00 5.87 C +ATOM 401 O ASP A 52 9.311 17.033 20.476 1.00 5.53 O +ATOM 402 CB ASP A 52 8.717 19.972 21.485 1.00 6.73 C +ATOM 403 CG ASP A 52 9.014 21.046 22.449 1.00 17.46 C +ATOM 404 OD1 ASP A 52 8.778 20.978 23.593 1.00 16.69 O +ATOM 405 OD2 ASP A 52 9.531 22.065 21.923 1.00 28.92 O +ATOM 406 N TYR A 53 7.279 16.908 21.280 1.00 7.33 N +ATOM 407 CA TYR A 53 6.899 15.745 20.548 1.00 9.37 C +ATOM 408 C TYR A 53 5.580 15.922 19.790 1.00 13.52 C +ATOM 409 O TYR A 53 4.554 16.399 20.326 1.00 7.94 O +ATOM 410 CB TYR A 53 6.630 14.562 21.517 1.00 7.91 C +ATOM 411 CG TYR A 53 7.865 14.099 22.242 1.00 6.82 C +ATOM 412 CD1 TYR A 53 8.335 14.742 23.399 1.00 8.88 C +ATOM 413 CD2 TYR A 53 8.618 13.027 21.749 1.00 6.30 C +ATOM 414 CE1 TYR A 53 9.548 14.382 24.006 1.00 1.83 C +ATOM 415 CE2 TYR A 53 9.846 12.646 22.351 1.00 10.07 C +ATOM 416 CZ TYR A 53 10.229 13.264 23.534 1.00 8.70 C +ATOM 417 OH TYR A 53 11.374 12.889 24.151 1.00 12.40 O +ATOM 418 N GLY A 54 5.598 15.446 18.516 1.00 11.04 N +ATOM 419 CA GLY A 54 4.390 15.347 17.710 1.00 7.71 C +ATOM 420 C GLY A 54 3.939 16.599 17.020 1.00 3.67 C +ATOM 421 O GLY A 54 4.535 17.621 17.017 1.00 8.49 O +ATOM 422 N ILE A 55 2.748 16.458 16.496 1.00 11.91 N +ATOM 423 CA ILE A 55 2.096 17.435 15.686 1.00 7.88 C +ATOM 424 C ILE A 55 1.893 18.749 16.386 1.00 10.21 C +ATOM 425 O ILE A 55 1.904 19.805 15.761 1.00 9.17 O +ATOM 426 CB ILE A 55 0.838 16.805 15.068 1.00 19.48 C +ATOM 427 CG1 ILE A 55 0.390 17.438 13.734 1.00 15.27 C +ATOM 428 CG2 ILE A 55 -0.262 16.528 16.106 1.00 16.63 C +ATOM 429 CD1 ILE A 55 -0.353 16.483 12.846 1.00 21.60 C +ATOM 430 N LEU A 56 1.765 18.677 17.706 1.00 9.90 N +ATOM 431 CA LEU A 56 1.584 19.877 18.488 1.00 7.23 C +ATOM 432 C LEU A 56 2.735 20.173 19.390 1.00 18.66 C +ATOM 433 O LEU A 56 2.660 21.074 20.200 1.00 10.73 O +ATOM 434 CB LEU A 56 0.216 19.957 19.205 1.00 11.28 C +ATOM 435 CG LEU A 56 -0.990 20.157 18.283 1.00 12.31 C +ATOM 436 CD1 LEU A 56 -2.255 19.795 19.036 1.00 11.09 C +ATOM 437 CD2 LEU A 56 -1.074 21.607 17.850 1.00 11.43 C +ATOM 438 N GLN A 57 3.804 19.441 19.202 1.00 7.01 N +ATOM 439 CA GLN A 57 5.029 19.733 19.898 1.00 9.13 C +ATOM 440 C GLN A 57 4.883 19.918 21.451 1.00 11.13 C +ATOM 441 O GLN A 57 5.272 20.968 22.020 1.00 12.02 O +ATOM 442 CB GLN A 57 5.767 20.937 19.263 1.00 10.29 C +ATOM 443 CG GLN A 57 6.362 20.658 17.863 1.00 6.27 C +ATOM 444 CD GLN A 57 7.544 19.747 17.936 1.00 2.25 C +ATOM 445 OE1 GLN A 57 8.676 20.257 18.147 1.00 7.47 O +ATOM 446 NE2 GLN A 57 7.279 18.413 17.746 1.00 7.69 N +ATOM 447 N ILE A 58 4.303 18.898 22.061 1.00 9.58 N +ATOM 448 CA ILE A 58 4.031 18.814 23.487 1.00 12.88 C +ATOM 449 C ILE A 58 5.301 18.482 24.282 1.00 14.09 C +ATOM 450 O ILE A 58 6.055 17.583 23.982 1.00 10.65 O +ATOM 451 CB ILE A 58 2.839 17.923 23.711 1.00 12.15 C +ATOM 452 CG1 ILE A 58 1.599 18.614 23.110 1.00 12.61 C +ATOM 453 CG2 ILE A 58 2.704 17.544 25.215 1.00 12.37 C +ATOM 454 CD1 ILE A 58 0.329 17.770 23.138 1.00 17.22 C +ATOM 455 N ASN A 59 5.556 19.297 25.282 1.00 11.07 N +ATOM 456 CA ASN A 59 6.797 19.305 26.034 1.00 6.68 C +ATOM 457 C ASN A 59 6.893 18.239 27.099 1.00 8.46 C +ATOM 458 O ASN A 59 5.904 18.002 27.761 1.00 12.15 O +ATOM 459 CB ASN A 59 7.045 20.721 26.565 1.00 7.94 C +ATOM 460 CG ASN A 59 8.434 20.839 27.178 1.00 12.92 C +ATOM 461 OD1 ASN A 59 8.578 20.809 28.411 1.00 30.15 O +ATOM 462 ND2 ASN A 59 9.469 20.939 26.342 1.00 15.71 N +ATOM 463 N SER A 60 8.096 17.590 27.218 1.00 8.63 N +ATOM 464 CA SER A 60 8.333 16.496 28.162 1.00 11.30 C +ATOM 465 C SER A 60 8.586 17.015 29.647 1.00 7.42 C +ATOM 466 O SER A 60 8.559 16.218 30.620 1.00 18.39 O +ATOM 467 CB SER A 60 9.448 15.619 27.698 1.00 9.31 C +ATOM 468 OG SER A 60 10.642 16.390 27.790 1.00 9.01 O +ATOM 469 N ARG A 61 8.806 18.347 29.787 1.00 11.96 N +ATOM 470 CA ARG A 61 8.981 18.933 31.125 1.00 18.58 C +ATOM 471 C ARG A 61 7.701 18.806 31.935 1.00 21.66 C +ATOM 472 O ARG A 61 7.730 18.363 33.063 1.00 24.43 O +ATOM 473 CB ARG A 61 9.507 20.347 31.068 1.00 19.81 C +ATOM 474 CG ARG A 61 9.259 21.125 32.338 1.00 40.52 C +ATOM 475 CD ARG A 61 10.511 21.648 33.063 1.00 30.90 C +ATOM 476 NE ARG A 61 11.777 21.523 32.353 1.00 58.97 N +ATOM 477 CZ ARG A 61 12.722 20.587 32.539 1.00 70.61 C +ATOM 478 NH1 ARG A 61 12.610 19.570 33.413 1.00 68.85 N +ATOM 479 NH2 ARG A 61 13.829 20.673 31.795 1.00 56.33 N +ATOM 480 N TRP A 62 6.542 19.071 31.329 1.00 12.69 N +ATOM 481 CA TRP A 62 5.279 18.955 32.026 1.00 10.92 C +ATOM 482 C TRP A 62 4.281 17.916 31.682 1.00 19.26 C +ATOM 483 O TRP A 62 3.526 17.478 32.563 1.00 19.01 O +ATOM 484 CB TRP A 62 4.455 20.234 31.875 1.00 14.48 C +ATOM 485 CG TRP A 62 5.346 21.376 31.920 1.00 34.77 C +ATOM 486 CD1 TRP A 62 5.937 21.965 30.857 1.00 48.56 C +ATOM 487 CD2 TRP A 62 5.859 21.980 33.091 1.00 34.03 C +ATOM 488 NE1 TRP A 62 6.753 22.970 31.303 1.00 60.61 N +ATOM 489 CE2 TRP A 62 6.730 22.995 32.671 1.00 37.59 C +ATOM 490 CE3 TRP A 62 5.619 21.790 34.443 1.00 44.85 C +ATOM 491 CZ2 TRP A 62 7.373 23.823 33.582 1.00 74.91 C +ATOM 492 CZ3 TRP A 62 6.254 22.606 35.347 1.00 49.52 C +ATOM 493 CH2 TRP A 62 7.122 23.609 34.923 1.00 52.73 C +ATOM 494 N TRP A 63 4.152 17.600 30.385 1.00 11.21 N +ATOM 495 CA TRP A 63 3.036 16.858 29.848 1.00 9.63 C +ATOM 496 C TRP A 63 3.155 15.396 29.592 1.00 4.89 C +ATOM 497 O TRP A 63 2.183 14.725 29.581 1.00 11.10 O +ATOM 498 CB TRP A 63 2.652 17.635 28.566 1.00 6.50 C +ATOM 499 CG TRP A 63 2.429 19.101 28.874 1.00 5.59 C +ATOM 500 CD1 TRP A 63 3.223 20.140 28.615 1.00 15.86 C +ATOM 501 CD2 TRP A 63 1.364 19.632 29.695 1.00 11.68 C +ATOM 502 NE1 TRP A 63 2.675 21.309 29.075 1.00 15.89 N +ATOM 503 CE2 TRP A 63 1.567 21.028 29.780 1.00 12.27 C +ATOM 504 CE3 TRP A 63 0.230 19.055 30.324 1.00 14.52 C +ATOM 505 CZ2 TRP A 63 0.682 21.862 30.488 1.00 10.75 C +ATOM 506 CZ3 TRP A 63 -0.678 19.891 30.985 1.00 10.21 C +ATOM 507 CH2 TRP A 63 -0.421 21.271 31.057 1.00 13.33 C +ATOM 508 N CYS A 64 4.324 14.905 29.353 1.00 8.53 N +ATOM 509 CA CYS A 64 4.448 13.469 29.032 1.00 14.18 C +ATOM 510 C CYS A 64 5.785 12.968 29.569 1.00 8.75 C +ATOM 511 O CYS A 64 6.694 13.742 29.793 1.00 11.88 O +ATOM 512 CB CYS A 64 4.366 13.241 27.432 1.00 12.87 C +ATOM 513 SG CYS A 64 5.695 14.086 26.427 1.00 9.81 S +ATOM 514 N ASN A 65 5.913 11.651 29.720 1.00 9.55 N +ATOM 515 CA ASN A 65 7.127 11.114 30.200 1.00 16.84 C +ATOM 516 C ASN A 65 7.999 10.547 29.073 1.00 4.97 C +ATOM 517 O ASN A 65 7.529 9.623 28.435 1.00 10.83 O +ATOM 518 CB ASN A 65 6.809 9.953 31.188 1.00 9.17 C +ATOM 519 CG ASN A 65 8.120 9.322 31.715 1.00 22.59 C +ATOM 520 OD1 ASN A 65 9.033 10.017 32.182 1.00 21.36 O +ATOM 521 ND2 ASN A 65 8.276 8.015 31.524 1.00 36.98 N +ATOM 522 N ASP A 66 9.254 10.993 28.982 1.00 7.66 N +ATOM 523 CA ASP A 66 10.153 10.434 27.995 1.00 14.97 C +ATOM 524 C ASP A 66 11.354 9.742 28.601 1.00 23.09 C +ATOM 525 O ASP A 66 12.237 9.341 27.867 1.00 9.43 O +ATOM 526 CB ASP A 66 10.641 11.448 26.948 1.00 13.58 C +ATOM 527 CG ASP A 66 11.480 12.554 27.535 1.00 11.41 C +ATOM 528 OD1 ASP A 66 11.787 12.613 28.717 1.00 18.43 O +ATOM 529 OD2 ASP A 66 11.850 13.432 26.659 1.00 10.72 O +ATOM 530 N GLY A 67 11.395 9.644 29.920 1.00 14.60 N +ATOM 531 CA GLY A 67 12.449 8.941 30.665 1.00 9.04 C +ATOM 532 C GLY A 67 13.738 9.677 30.697 1.00 13.04 C +ATOM 533 O GLY A 67 14.726 9.165 31.164 1.00 23.22 O +ATOM 534 N ARG A 68 13.787 10.891 30.194 1.00 8.50 N +ATOM 535 CA ARG A 68 15.089 11.512 30.237 1.00 11.50 C +ATOM 536 C ARG A 68 15.046 12.949 30.560 1.00 11.49 C +ATOM 537 O ARG A 68 15.995 13.645 30.281 1.00 17.90 O +ATOM 538 CB ARG A 68 15.872 11.277 28.959 1.00 18.67 C +ATOM 539 CG ARG A 68 15.218 11.867 27.707 1.00 21.19 C +ATOM 540 CD ARG A 68 16.251 12.103 26.592 1.00 19.51 C +ATOM 541 NE ARG A 68 15.790 12.984 25.527 1.00 20.38 N +ATOM 542 CZ ARG A 68 16.264 12.978 24.248 1.00 29.94 C +ATOM 543 NH1 ARG A 68 17.253 12.102 23.926 1.00 13.00 N +ATOM 544 NH2 ARG A 68 15.787 13.865 23.293 1.00 13.47 N +ATOM 545 N THR A 69 13.937 13.376 31.145 1.00 12.12 N +ATOM 546 CA THR A 69 13.674 14.782 31.586 1.00 17.22 C +ATOM 547 C THR A 69 13.372 14.770 33.144 1.00 15.41 C +ATOM 548 O THR A 69 12.260 14.526 33.618 1.00 19.26 O +ATOM 549 CB THR A 69 12.464 15.410 30.798 1.00 12.81 C +ATOM 550 OG1 THR A 69 12.589 15.107 29.412 1.00 17.25 O +ATOM 551 CG2 THR A 69 12.392 16.932 30.990 1.00 8.98 C +ATOM 552 N PRO A 70 14.431 14.960 33.874 1.00 30.00 N +ATOM 553 CA PRO A 70 14.563 14.964 35.315 1.00 31.13 C +ATOM 554 C PRO A 70 13.654 16.003 35.904 1.00 43.01 C +ATOM 555 O PRO A 70 13.699 17.188 35.594 1.00 37.19 O +ATOM 556 CB PRO A 70 16.056 15.221 35.541 1.00 43.11 C +ATOM 557 CG PRO A 70 16.728 15.203 34.148 1.00 49.23 C +ATOM 558 CD PRO A 70 15.635 15.319 33.119 1.00 44.60 C +ATOM 559 N GLY A 71 12.698 15.573 36.672 1.00 29.79 N +ATOM 560 CA GLY A 71 11.785 16.609 37.130 1.00 38.84 C +ATOM 561 C GLY A 71 10.547 16.728 36.220 1.00 34.52 C +ATOM 562 O GLY A 71 9.750 17.644 36.328 1.00 53.49 O +ATOM 563 N SER A 72 10.339 15.797 35.324 1.00 30.26 N +ATOM 564 CA SER A 72 9.157 15.860 34.502 1.00 32.28 C +ATOM 565 C SER A 72 7.906 15.615 35.374 1.00 22.29 C +ATOM 566 O SER A 72 7.914 14.715 36.197 1.00 26.48 O +ATOM 567 CB SER A 72 9.249 14.700 33.473 1.00 31.83 C +ATOM 568 OG SER A 72 8.038 14.552 32.612 1.00 33.11 O +ATOM 569 N ARG A 73 6.801 16.311 35.113 1.00 20.31 N +ATOM 570 CA ARG A 73 5.550 16.055 35.819 1.00 12.77 C +ATOM 571 C ARG A 73 4.564 15.081 35.174 1.00 35.87 C +ATOM 572 O ARG A 73 3.662 14.597 35.845 1.00 50.20 O +ATOM 573 CB ARG A 73 4.830 17.322 36.128 1.00 19.66 C +ATOM 574 CG ARG A 73 5.605 18.165 37.124 1.00 35.18 C +ATOM 575 CD ARG A 73 4.864 19.471 37.396 1.00 86.10 C +ATOM 576 NE ARG A 73 4.736 19.744 38.823 1.00 80.19 N +ATOM 577 CZ ARG A 73 4.227 20.854 39.398 1.00 81.09 C +ATOM 578 NH1 ARG A 73 3.742 21.891 38.705 1.00 81.15 N +ATOM 579 NH2 ARG A 73 4.215 20.930 40.739 1.00 71.03 N +ATOM 580 N ASN A 74 4.668 14.781 33.896 1.00 18.76 N +ATOM 581 CA ASN A 74 3.715 13.833 33.313 1.00 10.40 C +ATOM 582 C ASN A 74 2.194 14.147 33.501 1.00 8.97 C +ATOM 583 O ASN A 74 1.355 13.278 33.697 1.00 15.29 O +ATOM 584 CB ASN A 74 4.053 12.334 33.426 1.00 16.10 C +ATOM 585 CG ASN A 74 3.479 11.413 32.309 1.00 15.75 C +ATOM 586 OD1 ASN A 74 2.928 11.864 31.297 1.00 22.77 O +ATOM 587 ND2 ASN A 74 3.593 10.101 32.490 1.00 17.62 N +ATOM 588 N LEU A 75 1.851 15.405 33.334 1.00 13.92 N +ATOM 589 CA LEU A 75 0.471 15.774 33.458 1.00 16.58 C +ATOM 590 C LEU A 75 -0.505 15.089 32.565 1.00 21.84 C +ATOM 591 O LEU A 75 -1.654 14.976 32.957 1.00 22.99 O +ATOM 592 CB LEU A 75 0.245 17.277 33.466 1.00 17.10 C +ATOM 593 CG LEU A 75 0.919 17.845 34.715 1.00 30.53 C +ATOM 594 CD1 LEU A 75 0.889 19.358 34.725 1.00 35.25 C +ATOM 595 CD2 LEU A 75 0.238 17.306 35.969 1.00 21.06 C +ATOM 596 N CYS A 76 -0.146 14.663 31.359 1.00 18.42 N +ATOM 597 CA CYS A 76 -1.153 13.970 30.513 1.00 10.67 C +ATOM 598 C CYS A 76 -1.137 12.463 30.738 1.00 12.68 C +ATOM 599 O CYS A 76 -1.935 11.725 30.131 1.00 17.21 O +ATOM 600 CB CYS A 76 -1.094 14.295 28.984 1.00 9.97 C +ATOM 601 SG CYS A 76 -1.329 16.050 28.713 1.00 13.70 S +ATOM 602 N ASN A 77 -0.194 12.038 31.586 1.00 14.93 N +ATOM 603 CA ASN A 77 -0.117 10.607 31.926 1.00 19.18 C +ATOM 604 C ASN A 77 0.099 9.697 30.747 1.00 21.40 C +ATOM 605 O ASN A 77 -0.626 8.715 30.538 1.00 17.53 O +ATOM 606 CB ASN A 77 -1.421 10.174 32.620 1.00 36.06 C +ATOM 607 CG ASN A 77 -1.361 8.783 33.215 1.00 80.95 C +ATOM 608 OD1 ASN A 77 -2.358 8.042 33.188 1.00 78.33 O +ATOM 609 ND2 ASN A 77 -0.186 8.412 33.715 1.00 38.97 N +ATOM 610 N ILE A 78 1.114 10.006 29.979 1.00 14.33 N +ATOM 611 CA ILE A 78 1.373 9.191 28.838 1.00 11.33 C +ATOM 612 C ILE A 78 2.873 9.258 28.499 1.00 13.41 C +ATOM 613 O ILE A 78 3.568 10.265 28.718 1.00 12.78 O +ATOM 614 CB ILE A 78 0.764 9.855 27.598 1.00 15.98 C +ATOM 615 CG1 ILE A 78 0.764 11.376 27.743 1.00 20.19 C +ATOM 616 CG2 ILE A 78 -0.461 9.195 26.985 1.00 25.51 C +ATOM 617 CD1 ILE A 78 0.735 12.094 26.406 1.00 31.88 C +ATOM 618 N PRO A 79 3.343 8.210 27.843 1.00 14.97 N +ATOM 619 CA PRO A 79 4.715 8.229 27.362 1.00 12.65 C +ATOM 620 C PRO A 79 4.738 9.234 26.187 1.00 10.18 C +ATOM 621 O PRO A 79 3.762 9.304 25.359 1.00 11.71 O +ATOM 622 CB PRO A 79 4.962 6.830 26.843 1.00 11.25 C +ATOM 623 CG PRO A 79 3.631 6.096 26.844 1.00 17.21 C +ATOM 624 CD PRO A 79 2.621 6.951 27.581 1.00 9.85 C +ATOM 625 N CYS A 80 5.798 10.020 26.078 1.00 11.09 N +ATOM 626 CA CYS A 80 5.870 11.003 24.969 1.00 5.24 C +ATOM 627 C CYS A 80 5.782 10.359 23.546 1.00 8.89 C +ATOM 628 O CYS A 80 5.284 10.950 22.568 1.00 11.52 O +ATOM 629 CB CYS A 80 7.126 11.894 25.061 1.00 7.40 C +ATOM 630 SG CYS A 80 7.251 12.847 26.592 1.00 9.47 S +ATOM 631 N SER A 81 6.259 9.115 23.442 1.00 9.85 N +ATOM 632 CA SER A 81 6.242 8.432 22.154 1.00 7.67 C +ATOM 633 C SER A 81 4.815 8.223 21.687 1.00 15.55 C +ATOM 634 O SER A 81 4.554 8.156 20.510 1.00 15.82 O +ATOM 635 CB SER A 81 6.995 7.111 22.234 1.00 15.31 C +ATOM 636 OG SER A 81 6.295 6.245 23.119 1.00 17.97 O +ATOM 637 N ALA A 82 3.857 8.169 22.598 1.00 11.39 N +ATOM 638 CA ALA A 82 2.452 8.033 22.185 1.00 14.65 C +ATOM 639 C ALA A 82 2.000 9.216 21.325 1.00 20.26 C +ATOM 640 O ALA A 82 1.033 9.113 20.571 1.00 22.13 O +ATOM 641 CB ALA A 82 1.481 8.009 23.384 1.00 17.51 C +ATOM 642 N LEU A 83 2.659 10.349 21.528 1.00 9.56 N +ATOM 643 CA LEU A 83 2.329 11.589 20.867 1.00 12.01 C +ATOM 644 C LEU A 83 2.834 11.627 19.385 1.00 18.14 C +ATOM 645 O LEU A 83 2.626 12.620 18.685 1.00 12.31 O +ATOM 646 CB LEU A 83 2.986 12.761 21.651 1.00 15.90 C +ATOM 647 CG LEU A 83 2.370 12.966 23.055 1.00 9.43 C +ATOM 648 CD1 LEU A 83 3.076 14.069 23.849 1.00 12.61 C +ATOM 649 CD2 LEU A 83 0.843 13.174 22.965 1.00 15.37 C +ATOM 650 N LEU A 84 3.542 10.556 18.940 1.00 13.34 N +ATOM 651 CA LEU A 84 4.131 10.512 17.618 1.00 11.55 C +ATOM 652 C LEU A 84 3.361 9.657 16.630 1.00 16.60 C +ATOM 653 O LEU A 84 3.704 9.570 15.475 1.00 22.63 O +ATOM 654 CB LEU A 84 5.630 10.044 17.645 1.00 7.92 C +ATOM 655 CG LEU A 84 6.546 10.859 18.552 1.00 18.00 C +ATOM 656 CD1 LEU A 84 7.978 10.414 18.359 1.00 17.76 C +ATOM 657 CD2 LEU A 84 6.513 12.306 18.116 1.00 8.41 C +ATOM 658 N SER A 85 2.332 9.023 17.096 1.00 15.68 N +ATOM 659 CA SER A 85 1.485 8.148 16.333 1.00 22.63 C +ATOM 660 C SER A 85 0.792 8.827 15.194 1.00 14.76 C +ATOM 661 O SER A 85 0.519 10.007 15.280 1.00 16.99 O +ATOM 662 CB SER A 85 0.376 7.776 17.295 1.00 16.59 C +ATOM 663 OG SER A 85 -0.373 6.761 16.741 1.00 23.89 O +ATOM 664 N SER A 86 0.371 8.039 14.186 1.00 19.04 N +ATOM 665 CA SER A 86 -0.430 8.505 13.025 1.00 17.09 C +ATOM 666 C SER A 86 -1.827 8.884 13.487 1.00 21.77 C +ATOM 667 O SER A 86 -2.481 9.696 12.857 1.00 24.42 O +ATOM 668 CB SER A 86 -0.584 7.358 12.026 1.00 21.75 C +ATOM 669 OG SER A 86 0.687 7.146 11.467 1.00 50.53 O +ATOM 670 N ASP A 87 -2.288 8.227 14.575 1.00 13.55 N +ATOM 671 CA ASP A 87 -3.611 8.483 15.195 1.00 14.83 C +ATOM 672 C ASP A 87 -3.426 9.673 16.162 1.00 16.43 C +ATOM 673 O ASP A 87 -2.640 9.585 17.147 1.00 17.32 O +ATOM 674 CB ASP A 87 -4.025 7.244 15.987 1.00 17.38 C +ATOM 675 CG ASP A 87 -5.365 7.435 16.676 1.00 36.42 C +ATOM 676 OD1 ASP A 87 -5.875 8.512 16.868 1.00 21.05 O +ATOM 677 OD2 ASP A 87 -5.952 6.315 17.005 1.00 56.25 O +ATOM 678 N ILE A 88 -4.037 10.803 15.879 1.00 12.05 N +ATOM 679 CA ILE A 88 -3.749 11.974 16.722 1.00 17.85 C +ATOM 680 C ILE A 88 -4.490 12.067 18.055 1.00 12.40 C +ATOM 681 O ILE A 88 -4.393 13.081 18.780 1.00 11.64 O +ATOM 682 CB ILE A 88 -4.014 13.293 15.954 1.00 16.92 C +ATOM 683 CG1 ILE A 88 -5.565 13.392 15.634 1.00 15.36 C +ATOM 684 CG2 ILE A 88 -3.104 13.384 14.694 1.00 18.11 C +ATOM 685 CD1 ILE A 88 -6.065 14.738 15.196 1.00 20.80 C +ATOM 686 N THR A 89 -5.257 11.069 18.381 1.00 13.72 N +ATOM 687 CA THR A 89 -6.058 11.103 19.584 1.00 12.45 C +ATOM 688 C THR A 89 -5.326 11.520 20.907 1.00 8.02 C +ATOM 689 O THR A 89 -5.777 12.403 21.614 1.00 14.43 O +ATOM 690 CB THR A 89 -6.717 9.735 19.716 1.00 18.11 C +ATOM 691 OG1 THR A 89 -7.492 9.539 18.564 1.00 18.36 O +ATOM 692 CG2 THR A 89 -7.642 9.724 20.953 1.00 16.37 C +ATOM 693 N ALA A 90 -4.186 10.900 21.216 1.00 10.40 N +ATOM 694 CA ALA A 90 -3.483 11.250 22.444 1.00 14.23 C +ATOM 695 C ALA A 90 -2.971 12.685 22.412 1.00 17.47 C +ATOM 696 O ALA A 90 -2.981 13.344 23.413 1.00 10.92 O +ATOM 697 CB ALA A 90 -2.331 10.290 22.751 1.00 15.55 C +ATOM 698 N SER A 91 -2.504 13.185 21.257 1.00 8.67 N +ATOM 699 CA SER A 91 -2.032 14.567 21.163 1.00 7.03 C +ATOM 700 C SER A 91 -3.155 15.522 21.418 1.00 6.83 C +ATOM 701 O SER A 91 -3.033 16.547 22.059 1.00 13.20 O +ATOM 702 CB SER A 91 -1.445 14.870 19.783 1.00 7.71 C +ATOM 703 OG SER A 91 -0.111 14.402 19.670 1.00 11.50 O +ATOM 704 N VAL A 92 -4.289 15.234 20.839 1.00 9.57 N +ATOM 705 CA VAL A 92 -5.449 16.101 21.004 1.00 7.79 C +ATOM 706 C VAL A 92 -5.938 16.148 22.488 1.00 10.65 C +ATOM 707 O VAL A 92 -6.254 17.195 23.018 1.00 12.26 O +ATOM 708 CB VAL A 92 -6.523 15.597 19.994 1.00 23.58 C +ATOM 709 CG1 VAL A 92 -7.936 16.117 20.303 1.00 19.93 C +ATOM 710 CG2 VAL A 92 -6.110 15.987 18.555 1.00 17.17 C +ATOM 711 N ASN A 93 -6.047 14.973 23.140 1.00 10.03 N +ATOM 712 CA ASN A 93 -6.511 14.862 24.536 1.00 24.44 C +ATOM 713 C ASN A 93 -5.602 15.647 25.472 1.00 10.79 C +ATOM 714 O ASN A 93 -6.049 16.390 26.310 1.00 15.54 O +ATOM 715 CB ASN A 93 -6.580 13.395 24.989 1.00 13.16 C +ATOM 716 CG ASN A 93 -7.781 12.668 24.406 1.00 15.37 C +ATOM 717 OD1 ASN A 93 -7.842 11.422 24.426 1.00 35.75 O +ATOM 718 ND2 ASN A 93 -8.682 13.436 23.835 1.00 16.65 N +ATOM 719 N CYS A 94 -4.284 15.477 25.249 1.00 10.49 N +ATOM 720 CA CYS A 94 -3.267 16.178 25.984 1.00 7.62 C +ATOM 721 C CYS A 94 -3.353 17.649 25.690 1.00 17.58 C +ATOM 722 O CYS A 94 -3.298 18.462 26.598 1.00 9.76 O +ATOM 723 CB CYS A 94 -1.875 15.620 25.709 1.00 5.33 C +ATOM 724 SG CYS A 94 -0.613 16.312 26.762 1.00 13.87 S +ATOM 725 N ALA A 95 -3.546 18.041 24.407 1.00 7.01 N +ATOM 726 CA ALA A 95 -3.656 19.481 24.142 1.00 8.80 C +ATOM 727 C ALA A 95 -4.864 20.156 24.849 1.00 8.68 C +ATOM 728 O ALA A 95 -4.867 21.353 25.215 1.00 11.44 O +ATOM 729 CB ALA A 95 -3.774 19.698 22.627 1.00 6.34 C +ATOM 730 N LYS A 96 -5.932 19.405 24.966 1.00 9.62 N +ATOM 731 CA LYS A 96 -7.108 19.927 25.596 1.00 9.41 C +ATOM 732 C LYS A 96 -6.804 20.229 27.091 1.00 11.43 C +ATOM 733 O LYS A 96 -7.271 21.199 27.627 1.00 15.34 O +ATOM 734 CB LYS A 96 -8.195 18.868 25.472 1.00 12.74 C +ATOM 735 CG LYS A 96 -8.927 18.820 24.137 1.00 9.62 C +ATOM 736 CD LYS A 96 -9.976 17.699 24.147 1.00 14.08 C +ATOM 737 CE LYS A 96 -10.973 17.784 22.960 1.00 16.34 C +ATOM 738 NZ LYS A 96 -11.641 16.485 22.720 1.00 20.55 N +ATOM 739 N LYS A 97 -5.944 19.447 27.750 1.00 13.54 N +ATOM 740 CA LYS A 97 -5.538 19.706 29.158 1.00 14.41 C +ATOM 741 C LYS A 97 -4.672 20.981 29.209 1.00 13.37 C +ATOM 742 O LYS A 97 -4.809 21.878 30.014 1.00 13.38 O +ATOM 743 CB LYS A 97 -4.710 18.544 29.689 1.00 10.77 C +ATOM 744 CG LYS A 97 -5.493 17.342 30.140 1.00 32.04 C +ATOM 745 CD LYS A 97 -6.434 17.637 31.297 1.00 45.76 C +ATOM 746 CE LYS A 97 -7.073 16.369 31.886 1.00 70.47 C +ATOM 747 NZ LYS A 97 -8.523 16.232 31.620 1.00 59.21 N +ATOM 748 N ILE A 98 -3.760 21.072 28.264 1.00 12.65 N +ATOM 749 CA ILE A 98 -2.856 22.204 28.161 1.00 10.78 C +ATOM 750 C ILE A 98 -3.607 23.536 27.991 1.00 8.94 C +ATOM 751 O ILE A 98 -3.322 24.532 28.701 1.00 12.98 O +ATOM 752 CB ILE A 98 -1.778 22.026 27.022 1.00 17.91 C +ATOM 753 CG1 ILE A 98 -0.899 20.798 27.234 1.00 15.21 C +ATOM 754 CG2 ILE A 98 -0.932 23.292 26.811 1.00 10.73 C +ATOM 755 CD1 ILE A 98 -0.035 20.440 26.059 1.00 5.59 C +ATOM 756 N VAL A 99 -4.497 23.570 26.973 1.00 12.61 N +ATOM 757 CA VAL A 99 -5.194 24.822 26.643 1.00 14.92 C +ATOM 758 C VAL A 99 -6.158 25.244 27.757 1.00 17.60 C +ATOM 759 O VAL A 99 -6.529 26.431 27.844 1.00 21.46 O +ATOM 760 CB VAL A 99 -5.863 24.788 25.223 1.00 7.93 C +ATOM 761 CG1 VAL A 99 -7.102 23.930 25.230 1.00 13.13 C +ATOM 762 CG2 VAL A 99 -6.203 26.159 24.648 1.00 14.05 C +ATOM 763 N SER A 100 -6.529 24.274 28.623 1.00 14.94 N +ATOM 764 CA SER A 100 -7.469 24.559 29.728 1.00 23.99 C +ATOM 765 C SER A 100 -6.810 25.233 30.952 1.00 23.57 C +ATOM 766 O SER A 100 -7.460 25.872 31.759 1.00 30.51 O +ATOM 767 CB SER A 100 -8.109 23.250 30.148 1.00 15.96 C +ATOM 768 OG SER A 100 -9.019 22.837 29.120 1.00 33.46 O +ATOM 769 N ASP A 101 -5.495 25.061 30.981 1.00 27.50 N +ATOM 770 CA ASP A 101 -4.485 25.414 31.955 1.00 38.61 C +ATOM 771 C ASP A 101 -4.239 26.879 32.265 1.00 31.46 C +ATOM 772 O ASP A 101 -3.422 27.194 33.137 1.00 49.53 O +ATOM 773 CB ASP A 101 -3.173 24.648 31.624 1.00 32.62 C +ATOM 774 CG ASP A 101 -2.133 24.566 32.715 1.00 66.21 C +ATOM 775 OD1 ASP A 101 -2.482 23.821 33.747 1.00 53.53 O +ATOM 776 OD2 ASP A 101 -1.045 25.095 32.609 1.00 62.33 O +ATOM 777 N GLY A 102 -4.876 27.820 31.617 1.00 31.57 N +ATOM 778 CA GLY A 102 -4.525 29.170 32.093 1.00 42.83 C +ATOM 779 C GLY A 102 -4.082 30.192 31.049 1.00 56.99 C +ATOM 780 O GLY A 102 -4.713 31.264 30.990 1.00 31.68 O +ATOM 781 N ASN A 103 -2.979 29.915 30.284 1.00 23.55 N +ATOM 782 CA ASN A 103 -2.573 30.864 29.246 1.00 11.97 C +ATOM 783 C ASN A 103 -3.176 30.497 27.876 1.00 9.86 C +ATOM 784 O ASN A 103 -2.905 31.106 26.860 1.00 13.84 O +ATOM 785 CB ASN A 103 -1.070 31.114 29.177 1.00 17.92 C +ATOM 786 CG ASN A 103 -0.638 31.476 30.587 1.00 65.73 C +ATOM 787 OD1 ASN A 103 0.384 30.993 31.105 1.00 74.71 O +ATOM 788 ND2 ASN A 103 -1.509 32.224 31.271 1.00 54.30 N +ATOM 789 N GLY A 104 -4.070 29.522 27.865 1.00 10.94 N +ATOM 790 CA GLY A 104 -4.733 29.138 26.601 1.00 18.78 C +ATOM 791 C GLY A 104 -3.725 28.668 25.570 1.00 8.28 C +ATOM 792 O GLY A 104 -2.766 27.947 25.892 1.00 12.01 O +ATOM 793 N MET A 105 -3.906 29.119 24.313 1.00 13.56 N +ATOM 794 CA MET A 105 -3.014 28.684 23.198 1.00 9.18 C +ATOM 795 C MET A 105 -1.637 29.372 23.232 1.00 8.69 C +ATOM 796 O MET A 105 -0.727 29.013 22.506 1.00 9.67 O +ATOM 797 CB MET A 105 -3.739 28.882 21.838 1.00 3.51 C +ATOM 798 CG MET A 105 -4.790 27.788 21.646 1.00 9.82 C +ATOM 799 SD MET A 105 -5.184 27.455 19.852 1.00 12.90 S +ATOM 800 CE MET A 105 -3.617 26.757 19.326 1.00 6.80 C +ATOM 801 N ASN A 106 -1.509 30.373 24.105 1.00 7.08 N +ATOM 802 CA ASN A 106 -0.270 31.037 24.269 1.00 4.32 C +ATOM 803 C ASN A 106 0.809 30.046 24.765 1.00 8.04 C +ATOM 804 O ASN A 106 2.030 30.336 24.608 1.00 11.37 O +ATOM 805 CB ASN A 106 -0.396 32.190 25.241 1.00 12.62 C +ATOM 806 CG ASN A 106 -1.239 33.309 24.682 1.00 16.51 C +ATOM 807 OD1 ASN A 106 -0.864 33.972 23.658 1.00 9.88 O +ATOM 808 ND2 ASN A 106 -2.372 33.492 25.355 1.00 15.30 N +ATOM 809 N ALA A 107 0.360 28.870 25.250 1.00 8.10 N +ATOM 810 CA ALA A 107 1.308 27.840 25.625 1.00 10.48 C +ATOM 811 C ALA A 107 2.113 27.450 24.395 1.00 16.77 C +ATOM 812 O ALA A 107 3.191 26.948 24.511 1.00 16.10 O +ATOM 813 CB ALA A 107 0.585 26.599 26.143 1.00 11.40 C +ATOM 814 N TRP A 108 1.577 27.639 23.205 1.00 10.51 N +ATOM 815 CA TRP A 108 2.303 27.285 21.966 1.00 9.27 C +ATOM 816 C TRP A 108 2.970 28.504 21.404 1.00 9.11 C +ATOM 817 O TRP A 108 2.312 29.428 20.865 1.00 9.30 O +ATOM 818 CB TRP A 108 1.398 26.569 20.912 1.00 4.39 C +ATOM 819 CG TRP A 108 1.005 25.176 21.256 1.00 2.06 C +ATOM 820 CD1 TRP A 108 1.760 24.069 21.021 1.00 10.56 C +ATOM 821 CD2 TRP A 108 -0.146 24.722 21.926 1.00 4.61 C +ATOM 822 NE1 TRP A 108 1.131 22.972 21.471 1.00 11.23 N +ATOM 823 CE2 TRP A 108 -0.048 23.321 22.045 1.00 11.25 C +ATOM 824 CE3 TRP A 108 -1.256 25.348 22.436 1.00 8.16 C +ATOM 825 CZ2 TRP A 108 -1.038 22.520 22.626 1.00 7.13 C +ATOM 826 CZ3 TRP A 108 -2.220 24.549 23.074 1.00 13.29 C +ATOM 827 CH2 TRP A 108 -2.156 23.123 23.101 1.00 8.74 C +ATOM 828 N VAL A 109 4.320 28.523 21.508 1.00 10.59 N +ATOM 829 CA VAL A 109 5.046 29.672 21.044 1.00 10.72 C +ATOM 830 C VAL A 109 4.800 30.025 19.545 1.00 7.07 C +ATOM 831 O VAL A 109 4.617 31.199 19.228 1.00 12.32 O +ATOM 832 CB VAL A 109 6.549 29.491 21.342 1.00 15.75 C +ATOM 833 CG1 VAL A 109 7.068 28.242 20.605 1.00 38.18 C +ATOM 834 CG2 VAL A 109 7.327 30.751 20.898 1.00 17.01 C +ATOM 835 N ALA A 110 4.761 28.998 18.662 1.00 7.28 N +ATOM 836 CA ALA A 110 4.506 29.281 17.232 1.00 14.92 C +ATOM 837 C ALA A 110 3.122 29.845 17.031 1.00 12.74 C +ATOM 838 O ALA A 110 2.902 30.659 16.125 1.00 13.19 O +ATOM 839 CB ALA A 110 4.783 28.117 16.262 1.00 12.16 C +ATOM 840 N TRP A 111 2.190 29.398 17.892 1.00 7.58 N +ATOM 841 CA TRP A 111 0.821 29.901 17.789 1.00 5.91 C +ATOM 842 C TRP A 111 0.815 31.399 18.100 1.00 9.06 C +ATOM 843 O TRP A 111 0.249 32.308 17.369 1.00 6.22 O +ATOM 844 CB TRP A 111 -0.240 29.136 18.618 1.00 6.54 C +ATOM 845 CG TRP A 111 -1.589 29.763 18.461 1.00 9.13 C +ATOM 846 CD1 TRP A 111 -2.510 29.517 17.447 1.00 5.89 C +ATOM 847 CD2 TRP A 111 -2.190 30.781 19.295 1.00 10.48 C +ATOM 848 NE1 TRP A 111 -3.642 30.322 17.597 1.00 5.88 N +ATOM 849 CE2 TRP A 111 -3.471 31.090 18.728 1.00 5.72 C +ATOM 850 CE3 TRP A 111 -1.805 31.432 20.511 1.00 4.95 C +ATOM 851 CZ2 TRP A 111 -4.306 32.057 19.314 1.00 13.37 C +ATOM 852 CZ3 TRP A 111 -2.658 32.382 21.061 1.00 6.90 C +ATOM 853 CH2 TRP A 111 -3.906 32.666 20.489 1.00 4.12 C +ATOM 854 N ARG A 112 1.497 31.701 19.218 1.00 7.90 N +ATOM 855 CA ARG A 112 1.527 33.107 19.659 1.00 11.81 C +ATOM 856 C ARG A 112 2.221 34.013 18.630 1.00 9.34 C +ATOM 857 O ARG A 112 1.746 35.118 18.330 1.00 9.72 O +ATOM 858 CB ARG A 112 2.215 33.175 21.040 1.00 18.21 C +ATOM 859 CG ARG A 112 2.053 34.513 21.722 1.00 52.15 C +ATOM 860 CD ARG A 112 2.813 34.593 23.056 1.00 27.12 C +ATOM 861 NE ARG A 112 3.479 33.351 23.413 1.00 52.40 N +ATOM 862 CZ ARG A 112 4.785 33.247 23.639 1.00 49.41 C +ATOM 863 NH1 ARG A 112 5.612 34.286 23.535 1.00 53.98 N +ATOM 864 NH2 ARG A 112 5.274 32.058 23.981 1.00 51.24 N +ATOM 865 N ASN A 113 3.331 33.501 18.078 1.00 8.96 N +ATOM 866 CA ASN A 113 4.132 34.283 17.152 1.00 15.60 C +ATOM 867 C ASN A 113 3.657 34.303 15.695 1.00 17.72 C +ATOM 868 O ASN A 113 3.919 35.261 14.974 1.00 16.73 O +ATOM 869 CB ASN A 113 5.657 33.938 17.244 1.00 8.06 C +ATOM 870 CG ASN A 113 6.192 34.297 18.636 1.00 11.97 C +ATOM 871 OD1 ASN A 113 5.714 35.228 19.278 1.00 19.44 O +ATOM 872 ND2 ASN A 113 7.179 33.595 19.091 1.00 9.04 N +ATOM 873 N ARG A 114 2.964 33.273 15.287 1.00 7.06 N +ATOM 874 CA ARG A 114 2.604 33.129 13.873 1.00 11.57 C +ATOM 875 C ARG A 114 1.171 33.002 13.552 1.00 19.78 C +ATOM 876 O ARG A 114 0.827 33.118 12.375 1.00 14.27 O +ATOM 877 CB ARG A 114 3.309 31.830 13.395 1.00 8.51 C +ATOM 878 CG ARG A 114 4.766 31.877 13.898 1.00 21.43 C +ATOM 879 CD ARG A 114 5.833 31.132 13.125 1.00 27.54 C +ATOM 880 NE ARG A 114 5.898 31.278 11.660 1.00 16.59 N +ATOM 881 CZ ARG A 114 6.631 30.413 10.970 1.00 12.23 C +ATOM 882 NH1 ARG A 114 7.271 29.439 11.649 1.00 11.43 N +ATOM 883 NH2 ARG A 114 6.744 30.477 9.659 1.00 12.83 N +ATOM 884 N CYS A 115 0.351 32.723 14.572 1.00 5.86 N +ATOM 885 CA CYS A 115 -1.055 32.487 14.333 1.00 8.05 C +ATOM 886 C CYS A 115 -1.937 33.541 14.914 1.00 18.18 C +ATOM 887 O CYS A 115 -2.914 34.024 14.264 1.00 11.36 O +ATOM 888 CB CYS A 115 -1.488 31.114 14.872 1.00 7.31 C +ATOM 889 SG CYS A 115 -0.553 29.849 14.022 1.00 10.81 S +ATOM 890 N LYS A 116 -1.630 33.796 16.196 1.00 10.46 N +ATOM 891 CA LYS A 116 -2.372 34.723 16.976 1.00 9.75 C +ATOM 892 C LYS A 116 -2.562 36.032 16.228 1.00 9.63 C +ATOM 893 O LYS A 116 -1.583 36.599 15.729 1.00 13.85 O +ATOM 894 CB LYS A 116 -1.716 34.948 18.335 1.00 12.72 C +ATOM 895 CG LYS A 116 -2.557 35.791 19.284 1.00 7.87 C +ATOM 896 CD LYS A 116 -1.809 35.938 20.635 1.00 15.62 C +ATOM 897 CE LYS A 116 -2.607 36.597 21.773 1.00 17.04 C +ATOM 898 NZ LYS A 116 -1.889 36.524 23.073 1.00 11.32 N +ATOM 899 N GLY A 117 -3.862 36.462 16.131 1.00 9.19 N +ATOM 900 CA GLY A 117 -4.213 37.737 15.493 1.00 22.87 C +ATOM 901 C GLY A 117 -4.091 37.759 13.972 1.00 33.97 C +ATOM 902 O GLY A 117 -4.044 38.799 13.371 1.00 28.79 O +ATOM 903 N THR A 118 -4.019 36.612 13.340 1.00 15.57 N +ATOM 904 CA THR A 118 -3.940 36.537 11.885 1.00 20.24 C +ATOM 905 C THR A 118 -5.285 35.977 11.407 1.00 18.25 C +ATOM 906 O THR A 118 -6.080 35.563 12.249 1.00 18.09 O +ATOM 907 CB THR A 118 -2.747 35.680 11.439 1.00 13.62 C +ATOM 908 OG1 THR A 118 -3.060 34.321 11.639 1.00 12.88 O +ATOM 909 CG2 THR A 118 -1.455 36.072 12.193 1.00 12.89 C +ATOM 910 N ASP A 119 -5.573 35.973 10.102 1.00 20.97 N +ATOM 911 CA ASP A 119 -6.848 35.408 9.620 1.00 17.43 C +ATOM 912 C ASP A 119 -6.693 33.892 9.567 1.00 19.50 C +ATOM 913 O ASP A 119 -6.430 33.280 8.509 1.00 24.87 O +ATOM 914 CB ASP A 119 -7.228 35.933 8.234 1.00 27.62 C +ATOM 915 CG ASP A 119 -8.359 35.154 7.625 1.00 57.62 C +ATOM 916 OD1 ASP A 119 -9.168 34.529 8.288 1.00 36.72 O +ATOM 917 OD2 ASP A 119 -8.349 35.190 6.315 1.00 41.26 O +ATOM 918 N VAL A 120 -6.836 33.291 10.750 1.00 20.10 N +ATOM 919 CA VAL A 120 -6.637 31.835 10.895 1.00 24.77 C +ATOM 920 C VAL A 120 -7.664 31.011 10.149 1.00 16.15 C +ATOM 921 O VAL A 120 -7.486 29.777 9.914 1.00 13.85 O +ATOM 922 CB VAL A 120 -6.476 31.372 12.367 1.00 15.61 C +ATOM 923 CG1 VAL A 120 -5.271 32.055 13.060 1.00 17.17 C +ATOM 924 CG2 VAL A 120 -7.761 31.691 13.097 1.00 18.96 C +ATOM 925 N GLN A 121 -8.761 31.679 9.776 1.00 18.05 N +ATOM 926 CA GLN A 121 -9.808 30.981 9.039 1.00 20.34 C +ATOM 927 C GLN A 121 -9.285 30.499 7.694 1.00 14.19 C +ATOM 928 O GLN A 121 -9.831 29.566 7.093 1.00 15.61 O +ATOM 929 CB GLN A 121 -10.896 31.993 8.746 1.00 39.58 C +ATOM 930 CG GLN A 121 -12.076 31.743 9.628 1.00 39.30 C +ATOM 931 CD GLN A 121 -13.286 31.887 8.785 1.00 58.93 C +ATOM 932 OE1 GLN A 121 -13.734 30.908 8.174 1.00 64.91 O +ATOM 933 NE2 GLN A 121 -13.757 33.131 8.683 1.00 55.29 N +ATOM 934 N ALA A 122 -8.222 31.161 7.229 1.00 14.53 N +ATOM 935 CA ALA A 122 -7.588 30.777 5.964 1.00 13.31 C +ATOM 936 C ALA A 122 -7.152 29.312 5.955 1.00 18.32 C +ATOM 937 O ALA A 122 -7.123 28.622 4.924 1.00 14.96 O +ATOM 938 CB ALA A 122 -6.378 31.657 5.724 1.00 18.92 C +ATOM 939 N TRP A 123 -6.792 28.829 7.138 1.00 14.16 N +ATOM 940 CA TRP A 123 -6.304 27.460 7.305 1.00 21.27 C +ATOM 941 C TRP A 123 -7.326 26.369 7.031 1.00 12.05 C +ATOM 942 O TRP A 123 -6.976 25.209 6.736 1.00 15.94 O +ATOM 943 CB TRP A 123 -5.545 27.274 8.649 1.00 14.43 C +ATOM 944 CG TRP A 123 -4.302 28.098 8.663 1.00 16.32 C +ATOM 945 CD1 TRP A 123 -4.115 29.310 9.238 1.00 16.23 C +ATOM 946 CD2 TRP A 123 -3.066 27.733 8.045 1.00 6.26 C +ATOM 947 NE1 TRP A 123 -2.826 29.737 8.996 1.00 13.70 N +ATOM 948 CE2 TRP A 123 -2.184 28.799 8.248 1.00 10.20 C +ATOM 949 CE3 TRP A 123 -2.680 26.618 7.323 1.00 14.76 C +ATOM 950 CZ2 TRP A 123 -0.873 28.742 7.761 1.00 21.80 C +ATOM 951 CZ3 TRP A 123 -1.413 26.574 6.804 1.00 21.47 C +ATOM 952 CH2 TRP A 123 -0.520 27.623 7.023 1.00 22.40 C +ATOM 953 N ILE A 124 -8.590 26.696 7.126 1.00 10.36 N +ATOM 954 CA ILE A 124 -9.573 25.659 6.831 1.00 14.89 C +ATOM 955 C ILE A 124 -10.353 25.927 5.530 1.00 16.52 C +ATOM 956 O ILE A 124 -11.277 25.213 5.172 1.00 16.40 O +ATOM 957 CB ILE A 124 -10.480 25.421 8.019 1.00 15.33 C +ATOM 958 CG1 ILE A 124 -11.016 26.778 8.456 1.00 15.55 C +ATOM 959 CG2 ILE A 124 -9.624 24.846 9.164 1.00 15.50 C +ATOM 960 CD1 ILE A 124 -12.489 26.742 8.908 1.00 32.95 C +ATOM 961 N ARG A 125 -9.977 27.003 4.848 1.00 17.59 N +ATOM 962 CA ARG A 125 -10.598 27.366 3.586 1.00 26.87 C +ATOM 963 C ARG A 125 -10.424 26.259 2.569 1.00 18.05 C +ATOM 964 O ARG A 125 -9.339 25.658 2.433 1.00 24.03 O +ATOM 965 CB ARG A 125 -10.123 28.708 3.068 1.00 29.23 C +ATOM 966 CG ARG A 125 -10.586 29.089 1.669 1.00 46.98 C +ATOM 967 CD ARG A 125 -10.321 30.571 1.370 1.00 51.79 C +ATOM 968 NE ARG A 125 -8.921 30.857 1.669 1.00 80.40 N +ATOM 969 CZ ARG A 125 -7.924 30.424 0.892 1.00 80.57 C +ATOM 970 NH1 ARG A 125 -8.167 29.752 -0.234 1.00 50.97 N +ATOM 971 NH2 ARG A 125 -6.657 30.677 1.239 1.00 73.99 N +ATOM 972 N GLY A 126 -11.581 25.957 1.917 1.00 23.54 N +ATOM 973 CA GLY A 126 -11.741 24.959 0.858 1.00 15.85 C +ATOM 974 C GLY A 126 -11.903 23.570 1.356 1.00 22.07 C +ATOM 975 O GLY A 126 -11.988 22.638 0.564 1.00 33.97 O +ATOM 976 N CYS A 127 -11.912 23.409 2.685 1.00 12.41 N +ATOM 977 CA CYS A 127 -12.009 22.059 3.164 1.00 10.52 C +ATOM 978 C CYS A 127 -13.442 21.578 3.291 1.00 13.96 C +ATOM 979 O CYS A 127 -14.383 22.316 3.676 1.00 19.22 O +ATOM 980 CB CYS A 127 -11.259 21.795 4.516 1.00 16.08 C +ATOM 981 SG CYS A 127 -9.562 22.365 4.503 1.00 17.92 S +ATOM 982 N ARG A 128 -13.609 20.299 3.023 1.00 19.23 N +ATOM 983 CA ARG A 128 -14.929 19.757 3.200 1.00 29.52 C +ATOM 984 C ARG A 128 -15.116 19.387 4.645 1.00 19.23 C +ATOM 985 O ARG A 128 -14.626 18.345 5.078 1.00 29.24 O +ATOM 986 CB ARG A 128 -15.159 18.511 2.363 1.00 35.15 C +ATOM 987 CG ARG A 128 -16.602 18.043 2.481 1.00 32.92 C +ATOM 988 CD ARG A 128 -16.961 17.187 1.277 1.00 38.70 C +ATOM 989 NE ARG A 128 -15.779 16.498 0.721 1.00 50.55 N +ATOM 990 CZ ARG A 128 -15.503 16.208 -0.581 1.00 55.70 C +ATOM 991 NH1 ARG A 128 -16.293 16.551 -1.610 1.00 46.94 N +ATOM 992 NH2 ARG A 128 -14.377 15.541 -0.856 1.00 48.25 N +ATOM 993 N LEU A 129 -15.775 20.226 5.404 1.00 22.75 N +ATOM 994 CA LEU A 129 -15.976 19.869 6.811 1.00 33.38 C +ATOM 995 C LEU A 129 -17.449 19.906 7.141 1.00 72.70 C +ATOM 996 O LEU A 129 -18.191 20.465 6.277 1.00 49.87 O +ATOM 997 CB LEU A 129 -15.235 20.742 7.845 1.00 23.67 C +ATOM 998 CG LEU A 129 -13.711 20.917 7.641 1.00 28.34 C +ATOM 999 CD1 LEU A 129 -13.308 22.315 8.150 1.00 36.38 C +ATOM 1000 CD2 LEU A 129 -12.970 19.868 8.434 1.00 43.93 C +ATOM 1001 OXT LEU A 129 -17.769 19.416 8.251 1.00 70.56 O +TER 1002 LEU A 129 +HETATM 1003 O HOH A 131 10.467 23.310 29.307 1.00 39.80 O +HETATM 1004 O HOH A 132 -1.176 15.339 1.263 1.00 49.26 O +HETATM 1005 O HOH A 133 -2.951 23.272 0.888 1.00 44.65 O +HETATM 1006 O HOH A 134 1.217 11.752 36.245 1.00 47.43 O +HETATM 1007 O HOH A 135 -5.565 19.565 2.145 1.00 30.47 O +HETATM 1008 O HOH A 136 -8.561 15.857 2.186 1.00 67.45 O +HETATM 1009 O HOH A 137 -11.371 18.534 1.797 1.00 29.55 O +HETATM 1010 O HOH A 138 -5.769 17.371 2.752 1.00 20.51 O +HETATM 1011 O HOH A 139 -1.154 20.600 3.261 1.00 38.26 O +HETATM 1012 O HOH A 140 -14.391 27.317 2.971 1.00 41.99 O +HETATM 1013 O HOH A 141 9.925 21.314 4.349 1.00 72.67 O +HETATM 1014 O HOH A 142 -3.255 29.381 4.245 1.00 58.91 O +HETATM 1015 O HOH A 143 -1.469 12.396 4.494 1.00 45.35 O +HETATM 1016 O HOH A 144 1.369 18.410 4.770 1.00 33.99 O +HETATM 1017 O HOH A 145 -13.995 24.766 5.080 1.00 22.81 O +HETATM 1018 O HOH A 146 -11.877 17.908 5.201 1.00 33.63 O +HETATM 1019 O HOH A 147 3.579 19.755 5.269 1.00 28.71 O +HETATM 1020 O HOH A 148 -0.938 23.757 3.720 1.00 71.21 O +HETATM 1021 O HOH A 149 2.851 10.418 5.675 1.00 22.01 O +HETATM 1022 O HOH A 150 6.153 10.387 6.792 1.00 23.16 O +HETATM 1023 O HOH A 151 -4.154 33.433 7.551 1.00 36.56 O +HETATM 1024 O HOH A 152 -2.892 31.523 5.422 1.00 70.64 O +HETATM 1025 O HOH A 153 8.184 17.799 8.234 1.00 52.27 O +HETATM 1026 O HOH A 154 7.851 28.286 8.261 1.00 20.33 O +HETATM 1027 O HOH A 155 -0.327 32.726 8.576 1.00 42.08 O +HETATM 1028 O HOH A 156 -7.096 11.131 8.405 1.00 40.02 O +HETATM 1029 O HOH A 157 -3.462 37.549 8.393 1.00 46.77 O +HETATM 1030 O HOH A 158 -8.809 13.307 8.142 1.00 30.47 O +HETATM 1031 O HOH A 159 -0.082 35.568 8.883 1.00 34.44 O +HETATM 1032 O HOH A 160 5.759 11.110 9.448 1.00 12.55 O +HETATM 1033 O HOH A 161 1.655 33.826 9.694 1.00 24.07 O +HETATM 1034 O HOH A 162 -2.547 32.477 9.746 1.00 26.29 O +HETATM 1035 O HOH A 163 4.474 33.152 9.881 1.00 17.58 O +HETATM 1036 O HOH A 164 3.338 7.494 10.654 1.00 33.32 O +HETATM 1037 O HOH A 165 8.193 18.034 10.710 1.00 21.87 O +HETATM 1038 O HOH A 166 7.329 25.034 11.046 1.00 35.50 O +HETATM 1039 O HOH A 167 -14.609 15.459 10.822 1.00 40.68 O +HETATM 1040 O HOH A 168 -10.475 34.131 10.612 1.00 52.70 O +HETATM 1041 O HOH A 169 2.254 4.105 11.205 1.00 64.88 O +HETATM 1042 O HOH A 170 8.719 22.583 10.964 1.00 48.95 O +HETATM 1043 O HOH A 171 -11.115 29.055 11.946 1.00 14.76 O +HETATM 1044 O HOH A 172 -13.874 27.050 11.990 1.00 53.84 O +HETATM 1045 O HOH A 173 -5.674 10.727 13.313 1.00 39.68 O +HETATM 1046 O HOH A 174 -11.999 31.072 12.630 1.00 63.32 O +HETATM 1047 O HOH A 175 -17.134 26.536 21.794 1.00 62.44 O +HETATM 1048 O HOH A 176 10.318 19.087 12.648 1.00 26.21 O +HETATM 1049 O HOH A 177 -6.214 5.635 13.140 1.00 68.62 O +HETATM 1050 O HOH A 178 4.038 7.633 13.524 1.00 23.33 O +HETATM 1051 O HOH A 179 -3.450 4.975 13.407 1.00 49.46 O +HETATM 1052 O HOH A 180 -7.339 10.569 14.831 1.00 42.40 O +HETATM 1053 O HOH A 181 7.627 28.588 14.215 1.00 19.60 O +HETATM 1054 O HOH A 182 1.193 5.002 14.601 1.00 41.13 O +HETATM 1055 O HOH A 183 -8.623 6.412 17.116 1.00 59.00 O +HETATM 1056 O HOH A 184 9.260 21.322 13.868 1.00 48.09 O +HETATM 1057 O HOH A 185 -16.033 21.080 23.763 1.00 60.47 O +HETATM 1058 O HOH A 186 11.590 13.479 14.940 1.00 13.69 O +HETATM 1059 O HOH A 187 -6.668 35.428 15.178 1.00 31.78 O +HETATM 1060 O HOH A 188 -4.892 -0.201 15.033 1.00 72.09 O +HETATM 1061 O HOH A 189 1.858 30.674 4.862 1.00 56.21 O +HETATM 1062 O HOH A 190 -10.895 36.814 14.982 1.00 35.20 O +HETATM 1063 O HOH A 191 0.992 36.275 15.433 1.00 18.46 O +HETATM 1064 O HOH A 192 4.392 4.463 15.873 1.00 37.98 O +HETATM 1065 O HOH A 193 -9.880 33.178 15.826 1.00 28.17 O +HETATM 1066 O HOH A 194 9.025 23.955 15.613 1.00 37.22 O +HETATM 1067 O HOH A 195 -7.206 38.395 16.256 1.00 55.89 O +HETATM 1068 O HOH A 196 -0.377 36.589 25.905 1.00 34.65 O +HETATM 1069 O HOH A 197 -14.982 19.034 22.737 1.00 64.15 O +HETATM 1070 O HOH A 198 -0.223 12.099 16.607 1.00 28.04 O +HETATM 1071 O HOH A 199 -6.317 33.838 16.796 1.00 22.79 O +HETATM 1072 O HOH A 200 8.078 31.375 16.915 1.00 10.01 O +HETATM 1073 O HOH A 201 1.489 13.820 17.020 1.00 21.39 O +HETATM 1074 O HOH A 202 9.131 28.844 17.354 1.00 52.49 O +HETATM 1075 O HOH A 203 14.994 15.102 18.263 1.00 53.36 O +HETATM 1076 O HOH A 204 15.333 22.227 18.703 1.00 50.97 O +HETATM 1077 O HOH A 205 16.093 18.390 18.034 1.00 33.35 O +HETATM 1078 O HOH A 206 3.768 6.469 18.636 1.00 38.13 O +HETATM 1079 O HOH A 207 -13.347 18.342 27.796 1.00 58.07 O +HETATM 1080 O HOH A 208 -14.200 9.443 18.914 1.00 81.98 O +HETATM 1081 O HOH A 209 9.257 22.574 18.988 1.00 22.39 O +HETATM 1082 O HOH A 210 4.907 37.823 19.024 1.00 41.16 O +HETATM 1083 O HOH A 211 -1.433 4.723 19.249 1.00 62.14 O +HETATM 1084 O HOH A 212 -1.071 11.315 19.089 1.00 15.91 O +HETATM 1085 O HOH A 213 -3.235 8.498 19.677 1.00 21.40 O +HETATM 1086 O HOH A 214 7.620 25.081 19.861 1.00 35.14 O +HETATM 1087 O HOH A 215 1.711 16.542 19.779 1.00 9.12 O +HETATM 1088 O HOH A 216 11.204 23.310 20.531 1.00 44.08 O +HETATM 1089 O HOH A 217 -0.792 7.051 20.523 1.00 25.44 O +HETATM 1090 O HOH A 219 -11.306 12.254 20.909 1.00 58.87 O +HETATM 1091 O HOH A 220 -15.497 22.071 20.968 1.00 42.59 O +HETATM 1092 O HOH A 221 -14.046 13.904 22.148 1.00 59.61 O +HETATM 1093 O HOH A 222 5.919 23.529 21.973 1.00 36.31 O +HETATM 1094 O HOH A 223 5.611 26.207 22.382 1.00 26.89 O +HETATM 1095 O HOH A 224 8.793 23.775 23.737 1.00 53.46 O +HETATM 1096 O HOH A 225 -14.958 24.195 25.086 1.00 26.18 O +HETATM 1097 O HOH A 226 -14.258 17.077 24.576 1.00 42.15 O +HETATM 1098 O HOH A 227 3.901 21.949 25.503 1.00 15.15 O +HETATM 1099 O HOH A 228 -17.138 15.370 26.017 1.00 64.87 O +HETATM 1100 O HOH A 229 1.041 39.543 25.118 1.00 75.63 O +HETATM 1101 O HOH A 230 -18.171 19.097 19.147 1.00 58.24 O +HETATM 1102 O HOH A 231 19.800 18.720 25.766 1.00 41.96 O +HETATM 1103 O HOH A 232 13.910 14.986 26.681 1.00 11.69 O +HETATM 1104 O HOH A 233 4.284 26.127 26.885 1.00 44.36 O +HETATM 1105 O HOH A 234 14.969 25.124 27.122 1.00 37.22 O +HETATM 1106 O HOH A 235 19.235 28.375 27.869 1.00 51.94 O +HETATM 1107 O HOH A 236 -8.227 15.787 27.736 1.00 28.71 O +HETATM 1108 O HOH A 237 11.129 29.398 26.784 1.00 53.97 O +HETATM 1109 O HOH A 238 -2.152 26.984 28.613 1.00 25.16 O +HETATM 1110 O HOH A 239 -12.126 14.584 29.332 1.00 70.39 O +HETATM 1111 O HOH A 240 -6.410 28.639 29.739 1.00 33.78 O +HETATM 1112 O HOH A 241 -9.363 18.929 29.236 1.00 54.93 O +HETATM 1113 O HOH A 242 7.290 6.035 29.744 1.00 44.70 O +HETATM 1114 O HOH A 243 0.532 4.323 25.856 1.00 66.97 O +HETATM 1115 O HOH A 244 -5.527 11.769 31.278 1.00 52.96 O +HETATM 1116 O HOH A 245 9.709 13.211 30.865 1.00 15.87 O +HETATM 1117 O HOH A 246 -5.539 14.098 29.938 1.00 63.37 O +HETATM 1118 O HOH A 247 2.285 7.164 31.744 1.00 42.72 O +HETATM 1119 O HOH A 249 2.557 37.778 32.502 1.00 60.66 O +HETATM 1120 O HOH A 250 11.653 11.933 32.683 1.00 24.19 O +HETATM 1121 O HOH A 251 -2.007 6.140 23.286 1.00 48.50 O +HETATM 1122 O HOH A 252 7.578 12.160 33.759 1.00 39.59 O +HETATM 1123 O HOH A 253 14.454 7.531 33.771 1.00 35.83 O +HETATM 1124 O HOH A 254 -3.513 31.619 34.652 1.00 56.09 O +HETATM 1125 O HOH A 255 13.552 10.709 34.982 1.00 58.90 O +HETATM 1126 O HOH A 256 -0.456 24.995 36.970 1.00 68.09 O +HETATM 1127 O HOH A 257 -2.238 9.934 2.797 1.00 67.44 O +HETATM 1128 O HOH A 258 -7.483 20.739 37.397 1.00 68.20 O +HETATM 1129 O HOH A 259 16.885 30.334 28.147 1.00 50.66 O +HETATM 1130 O HOH A 260 -2.189 19.144 1.123 1.00 56.23 O +HETATM 1131 O HOH A 263 5.554 35.805 21.621 1.00 47.47 O +HETATM 1132 O HOH A 264 0.167 38.321 22.074 1.00 63.57 O +HETATM 1133 O HOH A 265 2.643 23.311 24.222 1.00 37.06 O +HETATM 1134 O HOH A 266 -3.261 12.368 26.079 1.00 36.01 O +HETATM 1135 O HOH A 267 -8.163 28.523 28.227 1.00 31.53 O +HETATM 1136 O HOH A 268 11.314 34.308 29.649 1.00 69.35 O +HETATM 1137 O HOH A 269 -8.925 18.710 -0.425 1.00 67.80 O +HETATM 1138 O HOH A 270 1.106 7.975 2.503 1.00 57.87 O +HETATM 1139 O HOH A 271 3.658 14.557 2.346 1.00 58.10 O +HETATM 1140 O HOH A 272 5.462 18.910 4.058 1.00 56.45 O +HETATM 1141 O HOH A 273 -12.194 34.778 7.299 1.00 56.09 O +HETATM 1142 O HOH A 274 -1.696 6.065 8.495 1.00 68.76 O +HETATM 1143 O HOH A 275 -12.182 12.057 9.624 1.00 89.37 O +HETATM 1144 O HOH A 276 -17.165 32.342 9.988 1.00 67.99 O +HETATM 1145 O HOH A 277 -0.310 4.774 9.964 1.00 51.58 O +HETATM 1146 O HOH A 278 -18.106 6.723 19.155 1.00 64.11 O +HETATM 1147 O HOH A 279 -10.523 7.855 18.757 1.00 55.12 O +HETATM 1148 O HOH A 280 -5.786 9.627 24.788 1.00 56.60 O +HETATM 1149 O HOH A 281 4.973 30.366 26.631 1.00 56.27 O +HETATM 1150 O HOH A 282 -14.163 23.294 27.041 1.00 80.21 O +HETATM 1151 O HOH A 283 4.190 23.920 28.202 1.00 47.07 O +HETATM 1152 O HOH A 284 1.927 24.235 28.261 1.00 53.05 O +HETATM 1153 O HOH A 285 8.469 24.914 28.323 1.00 76.29 O +HETATM 1154 O HOH A 286 0.504 26.234 30.223 1.00 48.47 O +HETATM 1155 O HOH A 287 4.961 6.376 30.326 1.00 57.17 O +HETATM 1156 O HOH A 288 -9.395 28.233 30.605 1.00 55.86 O +HETATM 1157 O HOH A 289 -7.403 29.010 31.768 1.00 58.13 O +HETATM 1158 O HOH A 290 17.262 22.252 32.977 1.00 32.13 O +HETATM 1159 O HOH A 291 -13.958 24.749 32.936 1.00 40.16 O +HETATM 1160 O HOH A 292 11.050 6.576 33.893 1.00 53.38 O +HETATM 1161 O HOH A 293 -6.940 30.679 34.967 1.00 57.95 O +HETATM 1162 O HOH A 294 -7.751 19.631 32.932 1.00 55.95 O +HETATM 1163 O HOH A 295 -11.917 25.473 35.232 1.00 70.62 O +HETATM 1164 O HOH A 296 -0.614 22.162 37.001 1.00 49.79 O +HETATM 1165 O HOH A 297 -5.763 25.243 36.097 1.00 78.09 O +HETATM 1166 O HOH A 298 -0.024 14.493 36.828 1.00 63.91 O +HETATM 1167 O HOH A 299 0.443 17.296 2.028 1.00 52.55 O +HETATM 1168 O HOH A 300 1.738 27.507 3.463 1.00 74.82 O +HETATM 1169 O HOH A 301 3.836 11.760 3.259 1.00 57.42 O +HETATM 1170 O HOH A 302 -9.211 4.115 14.687 1.00 48.13 O +HETATM 1171 O HOH A 303 16.205 21.210 16.009 1.00 69.59 O +HETATM 1172 O HOH A 304 -14.845 6.428 21.717 1.00 61.77 O +HETATM 1173 O HOH A 305 -13.311 8.488 24.665 1.00 62.09 O +HETATM 1174 O HOH A 306 8.880 27.820 26.816 1.00 71.28 O +HETATM 1175 O HOH A 307 0.932 10.327 2.387 1.00 62.28 O +HETATM 1176 O HOH A 308 -32.793 6.518 16.878 1.00 55.27 O +HETATM 1177 O HOH A 309 -10.109 33.422 4.951 1.00 51.37 O +HETATM 1178 O HOH A 310 -6.930 35.720 3.927 1.00 68.08 O +HETATM 1179 O HOH A 311 -1.458 29.021 31.741 1.00 71.39 O +HETATM 1180 O HOH A 312 -7.776 27.408 33.976 1.00 51.50 O +HETATM 1181 O HOH A 313 2.002 13.196 3.708 1.00 54.99 O +HETATM 1182 O HOH A 314 7.005 28.792 27.719 1.00 69.52 O +HETATM 1183 O HOH A 315 -14.736 20.042 16.788 1.00 37.49 O +HETATM 1184 O HOH A 316 17.457 15.414 26.607 1.00 36.58 O +HETATM 1185 O HOH A 317 1.388 37.676 19.438 1.00 42.27 O +HETATM 1186 O HOH A 318 12.884 12.733 37.805 0.50 65.31 O +HETATM 1187 O HOH A 319 7.795 26.278 15.645 1.00 44.16 O +CONECT 48 981 +CONECT 238 889 +CONECT 513 630 +CONECT 601 724 +CONECT 630 513 +CONECT 724 601 +CONECT 889 238 +CONECT 981 48 +MASTER 294 0 0 7 3 0 0 6 1186 1 8 10 +END diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map new file mode 100644 index 00000000..3c638013 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/map.map @@ -0,0 +1,1275 @@ + CONTACT MAPS FROM PDB FILES + + This software is written by: + Rodrigo Azevedo Moreira da Silva + + Copyright (c) 2020 - IPPT-PAN + Institute of Fundamental Techonological Research + Polish Academy of Sciences + MIT LICENSE, check out LICENSE for more informations. + +Reading file: ../aa.pdb +pdb natoms: 1001 +pdb nresidues: 129 +Memory usage: 6.38 MB +UNMAPPED ATOM LEU OXT +Fibonacci grid: 610 +ALPHA: 1.24 +WATER_RADIUS: 2.80 + +Residue-Residue Contacts + +ID - atom identification +I1,I2 - serial residue id +AA - 3-letter code of aminoacid +C - chain +I(PDB) - residue number in PDB file +DCA - distance between CA +CMs - OV , CSU , oCSU , rCSU + (CSU does not take into account chemical properties of atoms) +rCSU - net contact from rCSU +Count - number of contacts between residues +MODEL - model number + + ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count Model +============================================================================================ +R 1 1 LYS A 1 2 VAL A 2 3.8094 1 1 1 1 11 369 0 +R 2 1 LYS A 1 3 PHE A 3 6.0948 1 1 1 0 -13 106 0 +R 3 1 LYS A 1 7 GLU A 7 11.4807 1 1 1 1 121 225 0 +R 4 1 LYS A 1 38 PHE A 38 8.1596 1 1 0 0 -12 12 0 +R 5 1 LYS A 1 39 ASN A 39 5.7421 1 0 0 0 0 0 0 +R 6 1 LYS A 1 40 THR A 40 5.4657 1 1 1 1 222 238 0 +R 7 1 LYS A 1 41 GLN A 41 6.8324 1 1 0 0 -112 118 0 +R 8 1 LYS A 1 86 SER A 86 5.1894 1 1 1 0 -53 161 0 +R 9 2 VAL A 2 1 LYS A 1 3.8094 1 1 0 0 -21 386 0 +R 10 2 VAL A 2 3 PHE A 3 3.7890 1 1 1 0 -32 413 0 +R 11 2 VAL A 2 4 GLY A 4 6.7958 0 1 1 1 10 14 0 +R 12 2 VAL A 2 7 GLU A 7 10.1090 0 1 0 0 -12 12 0 +R 13 2 VAL A 2 37 ASN A 37 7.9443 0 1 0 0 -75 75 0 +R 14 2 VAL A 2 38 PHE A 38 5.5799 1 1 1 0 -20 27 0 +R 15 2 VAL A 2 39 ASN A 39 4.2809 1 1 1 0 -13 121 0 +R 16 3 PHE A 3 1 LYS A 1 6.0948 1 1 1 0 -49 77 0 +R 17 3 PHE A 3 2 VAL A 2 3.7890 1 1 0 0 -25 380 0 +R 18 3 PHE A 3 4 GLY A 4 3.7566 1 1 1 0 -9 362 0 +R 19 3 PHE A 3 7 GLU A 7 6.3959 1 1 1 1 27 66 0 +R 20 3 PHE A 3 8 LEU A 8 5.8772 1 1 1 1 71 144 0 +R 21 3 PHE A 3 11 ALA A 11 9.8683 1 1 1 1 35 35 0 +R 22 3 PHE A 3 38 PHE A 38 5.3547 1 1 1 0 -112 144 0 +R 23 3 PHE A 3 40 THR A 40 7.9444 1 1 1 1 133 133 0 +R 24 3 PHE A 3 55 ILE A 55 9.3473 1 1 1 1 35 35 0 +R 25 3 PHE A 3 86 SER A 86 8.8941 1 1 0 0 -65 65 0 +R 26 3 PHE A 3 88 ILE A 88 10.4372 1 1 1 1 102 102 0 +R 27 4 GLY A 4 2 VAL A 2 6.7958 0 1 1 1 6 11 0 +R 28 4 GLY A 4 3 PHE A 3 3.7566 1 1 0 0 -1 353 0 +R 29 4 GLY A 4 5 ARG A 5 3.7804 1 1 1 1 24 382 0 +R 30 4 GLY A 4 6 CYS A 6 5.6551 1 1 0 0 0 9 0 +R 31 4 GLY A 4 7 GLU A 7 5.1677 1 1 1 1 39 78 0 +R 32 4 GLY A 4 8 LEU A 8 6.0824 1 1 1 1 97 105 0 +R 33 4 GLY A 4 38 PHE A 38 7.2869 0 1 0 0 0 2 0 +R 34 5 ARG A 5 3 PHE A 3 6.3853 0 1 1 1 10 10 0 +R 35 5 ARG A 5 4 GLY A 4 3.7804 1 1 0 0 0 324 0 +R 36 5 ARG A 5 6 CYS A 6 3.8229 1 1 1 1 16 405 0 +R 37 5 ARG A 5 7 GLU A 7 5.6256 1 0 0 0 0 0 0 +R 38 5 ARG A 5 8 LEU A 8 5.4514 1 1 0 0 -5 5 0 +R 39 5 ARG A 5 9 ALA A 9 6.3068 1 1 1 1 111 121 0 +R 40 5 ARG A 5 29 VAL A 29 7.3410 1 0 0 0 0 0 0 +R 41 5 ARG A 5 38 PHE A 38 7.6636 1 1 1 1 72 111 0 +R 42 5 ARG A 5 122 ALA A 122 10.7979 1 1 1 1 15 21 0 +R 43 5 ARG A 5 123 TRP A 123 7.4230 1 1 1 1 80 312 0 +R 44 5 ARG A 5 124 ILE A 124 7.5648 1 0 0 0 0 0 0 +R 45 5 ARG A 5 125 ARG A 125 9.6347 1 1 1 1 135 211 0 +R 46 5 ARG A 5 126 GLY A 126 10.0418 0 1 0 0 -1 13 0 +R 47 5 ARG A 5 127 CYS A 127 8.4264 1 1 0 0 0 21 0 +R 48 6 CYS A 6 4 GLY A 4 5.6551 1 1 0 0 0 2 0 +R 49 6 CYS A 6 5 ARG A 5 3.8229 1 1 0 0 -20 442 0 +R 50 6 CYS A 6 7 GLU A 7 3.7935 1 1 1 0 -3 369 0 +R 51 6 CYS A 6 8 LEU A 8 5.3320 1 0 0 0 0 0 0 +R 52 6 CYS A 6 9 ALA A 9 4.8870 1 0 0 0 0 0 0 +R 53 6 CYS A 6 10 ALA A 10 6.1316 1 1 1 1 85 131 0 +R 54 6 CYS A 6 126 GLY A 126 7.9731 0 1 0 0 0 12 0 +R 55 6 CYS A 6 127 CYS A 127 5.3179 1 1 1 1 23 264 0 +R 56 6 CYS A 6 128 ARG A 128 7.4354 0 1 0 0 -14 14 0 +R 57 7 GLU A 7 1 LYS A 1 11.4807 1 1 1 1 153 207 0 +R 58 7 GLU A 7 2 VAL A 2 10.1090 0 1 0 0 -7 7 0 +R 59 7 GLU A 7 3 PHE A 3 6.3959 1 1 1 1 29 30 0 +R 60 7 GLU A 7 4 GLY A 4 5.1677 1 1 1 1 95 139 0 +R 61 7 GLU A 7 5 ARG A 5 5.6256 1 0 0 0 0 0 0 +R 62 7 GLU A 7 6 CYS A 6 3.7935 1 1 1 0 -23 363 0 +R 63 7 GLU A 7 8 LEU A 8 3.8230 1 1 1 1 10 347 0 +R 64 7 GLU A 7 9 ALA A 9 5.5273 1 0 0 0 0 0 0 +R 65 7 GLU A 7 10 ALA A 10 5.2583 1 1 1 1 2 28 0 +R 66 7 GLU A 7 11 ALA A 11 6.3196 1 1 1 1 115 119 0 +R 67 8 LEU A 8 3 PHE A 3 5.8772 1 1 1 1 56 64 0 +R 68 8 LEU A 8 4 GLY A 4 6.0824 1 1 1 0 -47 63 0 +R 69 8 LEU A 8 5 ARG A 5 5.4514 1 1 0 0 -5 5 0 +R 70 8 LEU A 8 6 CYS A 6 5.3320 1 0 0 0 0 0 0 +R 71 8 LEU A 8 7 GLU A 7 3.8230 1 1 0 0 -20 356 0 +R 72 8 LEU A 8 9 ALA A 9 3.8041 1 1 1 1 10 355 0 +R 73 8 LEU A 8 10 ALA A 10 5.3454 1 0 0 0 0 0 0 +R 74 8 LEU A 8 11 ALA A 11 5.0036 1 0 0 0 0 0 0 +R 75 8 LEU A 8 12 MET A 12 6.0331 1 1 1 1 189 211 0 +R 76 8 LEU A 8 29 VAL A 29 7.2217 0 1 1 1 1 1 0 +R 77 8 LEU A 8 32 ALA A 32 8.9719 1 1 1 1 78 78 0 +R 78 8 LEU A 8 38 PHE A 38 7.9077 1 1 1 1 168 168 0 +R 79 8 LEU A 8 55 ILE A 55 10.0426 1 1 1 1 102 102 0 +R 80 8 LEU A 8 88 ILE A 88 9.1166 1 1 1 1 16 16 0 +R 81 9 ALA A 9 5 ARG A 5 6.3068 1 1 1 0 -49 77 0 +R 82 9 ALA A 9 6 CYS A 6 4.8870 1 1 0 0 -20 30 0 +R 83 9 ALA A 9 7 GLU A 7 5.5273 1 0 0 0 0 0 0 +R 84 9 ALA A 9 8 LEU A 8 3.8041 1 1 0 0 -13 342 0 +R 85 9 ALA A 9 10 ALA A 10 3.8152 1 1 1 1 4 325 0 +R 86 9 ALA A 9 11 ALA A 11 5.5040 1 0 0 0 0 0 0 +R 87 9 ALA A 9 12 MET A 12 5.2438 1 0 0 0 0 0 0 +R 88 9 ALA A 9 13 LYS A 13 6.0508 1 1 1 1 121 177 0 +R 89 9 ALA A 9 25 LEU A 25 6.8785 1 1 0 0 -1 1 0 +R 90 9 ALA A 9 29 VAL A 29 6.2031 1 1 1 1 65 103 0 +R 91 9 ALA A 9 124 ILE A 124 6.6308 1 1 1 1 91 91 0 +R 92 9 ALA A 9 129 LEU A 129 7.9700 1 1 1 1 31 31 0 +R 93 10 ALA A 10 6 CYS A 6 6.1316 1 1 1 0 -57 71 0 +R 94 10 ALA A 10 7 GLU A 7 5.2583 1 1 1 0 -14 35 0 +R 95 10 ALA A 10 8 LEU A 8 5.3454 1 0 0 0 0 0 0 +R 96 10 ALA A 10 9 ALA A 9 3.8152 1 1 0 0 -12 348 0 +R 97 10 ALA A 10 11 ALA A 11 3.7870 1 1 1 1 4 363 0 +R 98 10 ALA A 10 12 MET A 12 5.5577 1 0 0 0 0 0 0 +R 99 10 ALA A 10 13 LYS A 13 5.0244 1 1 0 0 -2 3 0 +R 100 10 ALA A 10 14 ARG A 14 6.0838 1 1 1 1 85 143 0 +R 101 10 ALA A 10 128 ARG A 128 7.8262 0 1 0 0 -37 37 0 +R 102 10 ALA A 10 129 LEU A 129 6.1221 1 1 1 1 42 83 0 +R 103 11 ALA A 11 3 PHE A 3 9.8683 1 1 1 1 49 49 0 +R 104 11 ALA A 11 7 GLU A 7 6.3196 1 1 1 0 -44 76 0 +R 105 11 ALA A 11 8 LEU A 8 5.0036 1 1 0 0 -13 13 0 +R 106 11 ALA A 11 9 ALA A 9 5.5040 1 0 0 0 0 0 0 +R 107 11 ALA A 11 10 ALA A 10 3.7870 1 1 0 0 -22 362 0 +R 108 11 ALA A 11 12 MET A 12 3.8044 1 1 1 1 4 329 0 +R 109 11 ALA A 11 13 LYS A 13 5.3126 1 0 0 0 0 0 0 +R 110 11 ALA A 11 14 ARG A 14 5.0202 1 1 0 0 -15 41 0 +R 111 11 ALA A 11 15 HIS A 15 6.1372 1 1 1 1 176 196 0 +R 112 11 ALA A 11 88 ILE A 88 7.9512 1 1 1 1 91 91 0 +R 113 12 MET A 12 8 LEU A 8 6.0331 1 1 1 1 81 189 0 +R 114 12 MET A 12 9 ALA A 9 5.2438 1 1 0 0 -12 12 0 +R 115 12 MET A 12 10 ALA A 10 5.5577 1 0 0 0 0 0 0 +R 116 12 MET A 12 11 ALA A 11 3.8044 1 1 0 0 -10 337 0 +R 117 12 MET A 12 13 LYS A 13 3.8273 1 1 1 0 0 351 0 +R 118 12 MET A 12 14 ARG A 14 5.4173 1 0 0 0 0 0 0 +R 119 12 MET A 12 15 HIS A 15 4.8856 1 1 1 1 55 59 0 +R 120 12 MET A 12 16 GLY A 16 6.5249 1 1 1 1 1 1 0 +R 121 12 MET A 12 17 LEU A 17 5.4690 1 1 1 1 162 162 0 +R 122 12 MET A 12 25 LEU A 25 7.5662 1 1 1 1 34 34 0 +R 123 12 MET A 12 28 TRP A 28 7.8689 1 1 1 0 -80 205 0 +R 124 12 MET A 12 29 VAL A 29 8.1611 1 1 0 0 0 12 0 +R 125 12 MET A 12 32 ALA A 32 10.4631 1 1 1 1 31 31 0 +R 126 12 MET A 12 55 ILE A 55 11.3010 0 1 1 1 3 3 0 +R 127 12 MET A 12 56 LEU A 56 11.5983 1 1 1 1 52 52 0 +R 128 12 MET A 12 88 ILE A 88 8.1191 1 1 1 1 12 26 0 +R 129 13 LYS A 13 9 ALA A 9 6.0508 1 1 1 0 -47 63 0 +R 130 13 LYS A 13 10 ALA A 10 5.0244 1 1 0 0 -13 13 0 +R 131 13 LYS A 13 11 ALA A 11 5.3126 1 0 0 0 0 0 0 +R 132 13 LYS A 13 12 MET A 12 3.8273 1 1 0 0 -22 349 0 +R 133 13 LYS A 13 14 ARG A 14 3.7179 1 1 1 1 4 358 0 +R 134 13 LYS A 13 15 HIS A 15 5.2265 1 0 0 0 0 0 0 +R 135 13 LYS A 13 16 GLY A 16 5.3557 1 1 1 1 71 90 0 +R 136 13 LYS A 13 18 ASP A 18 5.3900 1 1 1 1 51 92 0 +R 137 13 LYS A 13 25 LEU A 25 6.9771 1 1 1 1 52 74 0 +R 138 13 LYS A 13 129 LEU A 129 8.0834 1 1 1 1 59 161 0 +R 139 14 ARG A 14 10 ALA A 10 6.0838 1 1 1 0 -54 66 0 +R 140 14 ARG A 14 11 ALA A 11 5.0202 1 1 1 0 -14 33 0 +R 141 14 ARG A 14 12 MET A 12 5.4173 1 0 0 0 0 0 0 +R 142 14 ARG A 14 13 LYS A 13 3.7179 1 1 1 0 -16 374 0 +R 143 14 ARG A 14 15 HIS A 15 3.8028 1 1 1 0 -115 484 0 +R 144 14 ARG A 14 16 GLY A 16 5.5733 1 1 1 1 11 16 0 +R 145 14 ARG A 14 89 THR A 89 10.0339 0 1 1 1 12 12 0 +R 146 15 HIS A 15 11 ALA A 11 6.1372 1 1 1 1 67 117 0 +R 147 15 HIS A 15 12 MET A 12 4.8856 1 1 0 0 -6 6 0 +R 148 15 HIS A 15 13 LYS A 13 5.2265 1 0 0 0 0 0 0 +R 149 15 HIS A 15 14 ARG A 14 3.8028 1 1 1 0 -121 524 0 +R 150 15 HIS A 15 16 GLY A 16 3.8284 1 1 1 1 25 263 0 +R 151 15 HIS A 15 17 LEU A 17 5.8003 1 0 0 0 0 0 0 +R 152 15 HIS A 15 87 ASP A 87 10.7991 0 1 0 0 -1 1 0 +R 153 15 HIS A 15 88 ILE A 88 8.6713 1 1 1 1 35 53 0 +R 154 15 HIS A 15 89 THR A 89 7.1554 1 1 1 1 53 244 0 +R 155 15 HIS A 15 92 VAL A 92 7.1674 1 1 1 1 71 71 0 +R 156 15 HIS A 15 93 ASN A 93 8.5240 0 1 0 0 -5 5 0 +R 157 15 HIS A 15 96 LYS A 96 10.3010 1 1 1 1 191 193 0 +R 158 16 GLY A 16 12 MET A 12 6.5249 1 0 0 0 0 0 0 +R 159 16 GLY A 16 13 LYS A 13 5.3557 1 1 1 1 11 44 0 +R 160 16 GLY A 16 14 ARG A 14 5.5733 1 1 1 1 2 14 0 +R 161 16 GLY A 16 15 HIS A 15 3.8284 1 1 0 0 -32 379 0 +R 162 16 GLY A 16 17 LEU A 17 3.7882 1 1 1 1 23 340 0 +R 163 16 GLY A 16 18 ASP A 18 5.8126 1 1 1 0 -8 32 0 +R 164 16 GLY A 16 20 TYR A 20 6.7265 1 1 0 0 -129 130 0 +R 165 16 GLY A 16 96 LYS A 96 9.2491 1 1 0 0 0 24 0 +R 166 17 LEU A 17 12 MET A 12 5.4690 1 1 1 1 110 161 0 +R 167 17 LEU A 17 15 HIS A 15 5.8003 1 0 0 0 0 0 0 +R 168 17 LEU A 17 16 GLY A 16 3.7882 1 1 0 0 -18 366 0 +R 169 17 LEU A 17 18 ASP A 18 3.8027 1 1 1 1 12 357 0 +R 170 17 LEU A 17 19 ASN A 19 6.0755 1 1 1 1 30 30 0 +R 171 17 LEU A 17 20 TYR A 20 4.9158 1 1 1 1 43 43 0 +R 172 17 LEU A 17 28 TRP A 28 7.4830 1 1 1 1 217 217 0 +R 173 17 LEU A 17 92 VAL A 92 7.6268 1 1 1 1 89 89 0 +R 174 17 LEU A 17 96 LYS A 96 7.9140 1 1 1 1 155 155 0 +R 175 18 ASP A 18 13 LYS A 13 5.3900 1 1 1 1 2 165 0 +R 176 18 ASP A 18 16 GLY A 16 5.8126 1 1 0 0 -28 33 0 +R 177 18 ASP A 18 17 LEU A 17 3.8027 1 1 0 0 -35 354 0 +R 178 18 ASP A 18 19 ASN A 19 3.7747 1 1 1 1 115 510 0 +R 179 18 ASP A 18 20 TYR A 20 5.3255 1 1 1 1 5 6 0 +R 180 18 ASP A 18 24 SER A 24 5.1287 1 1 0 0 0 12 0 +R 181 18 ASP A 18 25 LEU A 25 4.4020 1 1 1 1 152 244 0 +R 182 19 ASN A 19 17 LEU A 17 6.0755 1 0 0 0 0 0 0 +R 183 19 ASN A 19 18 ASP A 18 3.7747 1 1 1 1 107 498 0 +R 184 19 ASN A 19 20 TYR A 20 3.7437 1 1 1 1 17 326 0 +R 185 19 ASN A 19 21 ARG A 21 5.8645 1 1 1 1 9 9 0 +R 186 19 ASN A 19 22 GLY A 22 4.5249 1 1 1 1 59 129 0 +R 187 19 ASN A 19 23 TYR A 23 4.4795 1 1 1 1 32 73 0 +R 188 19 ASN A 19 24 SER A 24 4.2956 1 1 1 1 9 109 0 +R 189 20 TYR A 20 16 GLY A 16 6.7265 1 1 0 0 -86 87 0 +R 190 20 TYR A 20 17 LEU A 17 4.9158 1 1 1 0 -66 84 0 +R 191 20 TYR A 20 18 ASP A 18 5.3255 1 1 0 0 0 9 0 +R 192 20 TYR A 20 19 ASN A 19 3.7437 1 1 0 0 -19 347 0 +R 193 20 TYR A 20 21 ARG A 21 3.8205 1 1 1 1 84 506 0 +R 194 20 TYR A 20 22 GLY A 22 5.3254 1 1 1 1 3 3 0 +R 195 20 TYR A 20 23 TYR A 23 5.5795 1 1 1 1 12 68 0 +R 196 20 TYR A 20 96 LYS A 96 7.7283 1 1 1 0 0 186 0 +R 197 20 TYR A 20 97 LYS A 97 10.9092 0 1 1 1 1 2 0 +R 198 20 TYR A 20 99 VAL A 99 8.7657 1 1 1 1 64 64 0 +R 199 20 TYR A 20 100 SER A 100 9.2326 1 1 1 1 87 87 0 +R 200 21 ARG A 21 19 ASN A 19 5.8645 1 1 1 1 10 10 0 +R 201 21 ARG A 21 20 TYR A 20 3.8205 1 1 1 1 40 461 0 +R 202 21 ARG A 21 22 GLY A 22 3.7772 1 1 1 1 13 344 0 +R 203 21 ARG A 21 23 TYR A 23 5.6467 1 1 1 0 -14 110 0 +R 204 21 ARG A 21 99 VAL A 99 7.5366 1 1 1 1 39 39 0 +R 205 21 ARG A 21 100 SER A 100 7.2028 1 1 1 1 180 220 0 +R 206 22 GLY A 22 19 ASN A 19 4.5249 1 1 1 1 6 85 0 +R 207 22 GLY A 22 20 TYR A 20 5.3254 1 0 0 0 0 0 0 +R 208 22 GLY A 22 21 ARG A 21 3.7772 1 1 0 0 -33 385 0 +R 209 22 GLY A 22 23 TYR A 23 3.8541 1 1 1 1 5 337 0 +R 210 22 GLY A 22 24 SER A 24 6.3302 1 1 1 1 23 31 0 +R 211 22 GLY A 22 27 ASN A 27 10.0766 0 1 1 1 5 5 0 +R 212 23 TYR A 23 19 ASN A 19 4.4795 1 1 1 1 110 110 0 +R 213 23 TYR A 23 20 TYR A 20 5.5795 1 1 0 0 -29 29 0 +R 214 23 TYR A 23 21 ARG A 21 5.6467 1 1 1 0 -120 126 0 +R 215 23 TYR A 23 22 GLY A 22 3.8541 1 1 0 0 -27 365 0 +R 216 23 TYR A 23 24 SER A 24 3.8095 1 1 1 1 20 358 0 +R 217 23 TYR A 23 25 LEU A 25 6.6706 1 0 0 0 0 0 0 +R 218 23 TYR A 23 27 ASN A 27 6.2528 1 1 0 0 -2 10 0 +R 219 23 TYR A 23 28 TRP A 28 7.5595 1 1 1 0 -54 94 0 +R 220 23 TYR A 23 99 VAL A 99 9.4052 1 1 1 1 96 96 0 +R 221 23 TYR A 23 103 ASN A 103 12.4992 0 1 1 1 16 16 0 +R 222 23 TYR A 23 104 GLY A 104 8.8920 1 1 0 0 0 47 0 +R 223 23 TYR A 23 105 MET A 105 8.1535 1 1 1 1 150 217 0 +R 224 23 TYR A 23 106 ASN A 106 11.3626 0 1 1 1 16 16 0 +R 225 23 TYR A 23 111 TRP A 111 11.4919 1 1 1 1 60 94 0 +R 226 24 SER A 24 18 ASP A 18 5.1287 1 1 0 0 0 35 0 +R 227 24 SER A 24 19 ASN A 19 4.2956 1 1 0 0 0 57 0 +R 228 24 SER A 24 22 GLY A 22 6.3302 1 1 1 1 7 14 0 +R 229 24 SER A 24 23 TYR A 23 3.8095 1 1 0 0 -10 366 0 +R 230 24 SER A 24 25 LEU A 25 3.8490 1 1 1 1 26 309 0 +R 231 24 SER A 24 26 GLY A 26 5.5205 1 1 1 1 31 37 0 +R 232 24 SER A 24 27 ASN A 27 5.6877 1 1 1 1 232 265 0 +R 233 24 SER A 24 28 TRP A 28 7.2581 1 1 0 0 -1 1 0 +R 234 24 SER A 24 120 VAL A 120 8.3132 1 1 0 0 -53 53 0 +R 235 24 SER A 24 121 GLN A 121 8.0270 0 1 0 0 -4 47 0 +R 236 25 LEU A 25 9 ALA A 9 6.8785 1 1 0 0 -75 75 0 +R 237 25 LEU A 25 12 MET A 12 7.5662 1 1 1 1 156 156 0 +R 238 25 LEU A 25 13 LYS A 13 6.9771 1 1 1 1 48 80 0 +R 239 25 LEU A 25 18 ASP A 18 4.4020 1 1 1 0 -33 86 0 +R 240 25 LEU A 25 23 TYR A 23 6.6706 1 1 1 1 3 3 0 +R 241 25 LEU A 25 24 SER A 24 3.8490 1 1 0 0 0 326 0 +R 242 25 LEU A 25 26 GLY A 26 3.8034 1 1 1 1 10 356 0 +R 243 25 LEU A 25 27 ASN A 27 5.4198 1 0 0 0 0 0 0 +R 244 25 LEU A 25 28 TRP A 28 5.3994 1 1 1 1 77 86 0 +R 245 25 LEU A 25 29 VAL A 29 6.4093 1 1 1 1 54 54 0 +R 246 25 LEU A 25 124 ILE A 124 7.3355 1 1 1 1 57 57 0 +R 247 25 LEU A 25 129 LEU A 129 10.5318 1 1 1 1 126 126 0 +R 248 26 GLY A 26 24 SER A 24 5.5205 1 1 1 1 12 16 0 +R 249 26 GLY A 26 25 LEU A 25 3.8034 1 1 0 0 -35 364 0 +R 250 26 GLY A 26 27 ASN A 27 3.8470 1 1 1 1 17 323 0 +R 251 26 GLY A 26 28 TRP A 28 5.5151 1 0 0 0 0 0 0 +R 252 26 GLY A 26 29 VAL A 29 5.1152 1 0 0 0 0 0 0 +R 253 26 GLY A 26 30 CYS A 30 5.9025 1 1 1 1 93 175 0 +R 254 26 GLY A 26 120 VAL A 120 4.8514 1 1 0 0 -1 120 0 +R 255 26 GLY A 26 123 TRP A 123 5.1305 1 0 0 0 0 0 0 +R 256 26 GLY A 26 124 ILE A 124 5.7057 1 1 0 0 -9 65 0 +R 257 27 ASN A 27 22 GLY A 22 10.0766 0 1 1 1 5 5 0 +R 258 27 ASN A 27 23 TYR A 23 6.2528 1 1 0 0 -6 33 0 +R 259 27 ASN A 27 24 SER A 24 5.6877 1 1 1 1 101 219 0 +R 260 27 ASN A 27 25 LEU A 25 5.4198 1 0 0 0 0 0 0 +R 261 27 ASN A 27 26 GLY A 26 3.8470 1 1 0 0 -20 351 0 +R 262 27 ASN A 27 28 TRP A 28 3.7858 1 1 1 1 4 333 0 +R 263 27 ASN A 27 29 VAL A 29 5.5161 1 0 0 0 0 0 0 +R 264 27 ASN A 27 30 CYS A 30 5.1016 1 0 0 0 0 0 0 +R 265 27 ASN A 27 31 ALA A 31 6.0825 1 1 1 1 119 171 0 +R 266 27 ASN A 27 105 MET A 105 8.5492 1 1 0 0 0 46 0 +R 267 27 ASN A 27 111 TRP A 111 7.6026 1 1 1 1 40 192 0 +R 268 27 ASN A 27 116 LYS A 116 7.7579 0 1 0 0 0 1 0 +R 269 27 ASN A 27 120 VAL A 120 5.7252 1 1 0 0 -82 87 0 +R 270 28 TRP A 28 12 MET A 12 7.8689 1 1 0 0 -32 95 0 +R 271 28 TRP A 28 17 LEU A 17 7.4830 1 1 1 1 81 218 0 +R 272 28 TRP A 28 20 TYR A 20 9.5686 0 1 0 0 -7 7 0 +R 273 28 TRP A 28 23 TYR A 23 7.5595 1 1 1 1 44 60 0 +R 274 28 TRP A 28 24 SER A 24 7.2581 1 1 0 0 -47 49 0 +R 275 28 TRP A 28 25 LEU A 25 5.3994 1 1 0 0 -18 19 0 +R 276 28 TRP A 28 26 GLY A 26 5.5151 1 0 0 0 0 0 0 +R 277 28 TRP A 28 27 ASN A 27 3.7858 1 1 0 0 -7 345 0 +R 278 28 TRP A 28 29 VAL A 29 3.8333 1 1 1 1 2 334 0 +R 279 28 TRP A 28 30 CYS A 30 5.4753 1 0 0 0 0 0 0 +R 280 28 TRP A 28 31 ALA A 31 5.1386 1 1 0 0 -1 1 0 +R 281 28 TRP A 28 32 ALA A 32 6.2956 1 1 1 1 132 132 0 +R 282 28 TRP A 28 56 LEU A 56 8.7724 0 1 1 1 25 25 0 +R 283 28 TRP A 28 95 ALA A 95 9.8227 1 1 1 1 35 35 0 +R 284 28 TRP A 28 99 VAL A 99 10.7709 1 1 1 1 240 240 0 +R 285 28 TRP A 28 105 MET A 105 8.7636 1 1 1 1 15 21 0 +R 286 28 TRP A 28 108 TRP A 108 10.2074 1 1 1 1 113 113 0 +R 287 29 VAL A 29 5 ARG A 5 7.3410 1 1 1 1 10 12 0 +R 288 29 VAL A 29 9 ALA A 9 6.2031 1 1 1 1 17 175 0 +R 289 29 VAL A 29 12 MET A 12 8.1611 1 1 0 0 0 34 0 +R 290 29 VAL A 29 25 LEU A 25 6.4093 1 1 0 0 -65 65 0 +R 291 29 VAL A 29 26 GLY A 26 5.1152 1 1 0 0 -10 10 0 +R 292 29 VAL A 29 27 ASN A 27 5.5161 1 0 0 0 0 0 0 +R 293 29 VAL A 29 28 TRP A 28 3.8333 1 1 0 0 -22 358 0 +R 294 29 VAL A 29 30 CYS A 30 3.7941 1 1 1 1 9 357 0 +R 295 29 VAL A 29 31 ALA A 31 5.3991 1 0 0 0 0 0 0 +R 296 29 VAL A 29 32 ALA A 32 5.1300 1 1 0 0 0 3 0 +R 297 29 VAL A 29 33 LYS A 33 6.2055 1 1 1 1 115 115 0 +R 298 29 VAL A 29 38 PHE A 38 8.4877 1 1 1 1 96 98 0 +R 299 29 VAL A 29 123 TRP A 123 6.3580 1 1 1 1 61 107 0 +R 300 29 VAL A 29 124 ILE A 124 7.6402 1 1 1 1 1 1 0 +R 301 30 CYS A 30 26 GLY A 26 5.9025 1 1 1 0 -65 79 0 +R 302 30 CYS A 30 27 ASN A 27 5.1016 1 1 0 0 -6 6 0 +R 303 30 CYS A 30 28 TRP A 28 5.4753 1 0 0 0 0 0 0 +R 304 30 CYS A 30 29 VAL A 29 3.7941 1 1 0 0 -11 343 0 +R 305 30 CYS A 30 31 ALA A 31 3.7849 1 1 1 1 12 355 0 +R 306 30 CYS A 30 32 ALA A 32 5.5042 1 0 0 0 0 0 0 +R 307 30 CYS A 30 33 LYS A 33 5.1917 1 0 0 0 0 0 0 +R 308 30 CYS A 30 34 PHE A 34 6.3992 1 1 1 1 96 170 0 +R 309 30 CYS A 30 115 CYS A 115 6.0621 1 1 1 1 10 238 0 +R 310 30 CYS A 30 120 VAL A 120 6.6406 1 0 0 0 0 0 0 +R 311 30 CYS A 30 123 TRP A 123 6.2969 1 1 1 1 34 144 0 +R 312 31 ALA A 31 27 ASN A 27 6.0825 1 1 1 0 -56 76 0 +R 313 31 ALA A 31 28 TRP A 28 5.1386 1 1 0 0 -10 10 0 +R 314 31 ALA A 31 29 VAL A 29 5.3991 1 0 0 0 0 0 0 +R 315 31 ALA A 31 30 CYS A 30 3.7849 1 1 0 0 -23 359 0 +R 316 31 ALA A 31 32 ALA A 32 3.8582 1 1 1 1 13 328 0 +R 317 31 ALA A 31 33 LYS A 33 5.4805 1 0 0 0 0 0 0 +R 318 31 ALA A 31 34 PHE A 34 5.3387 1 0 0 0 0 0 0 +R 319 31 ALA A 31 35 GLU A 35 5.8673 1 1 1 1 124 185 0 +R 320 31 ALA A 31 56 LEU A 56 7.1209 1 1 1 1 34 34 0 +R 321 31 ALA A 31 105 MET A 105 8.7729 1 1 1 1 112 112 0 +R 322 31 ALA A 31 111 TRP A 111 4.9166 1 1 1 1 50 56 0 +R 323 31 ALA A 31 115 CYS A 115 6.6938 1 1 0 0 0 26 0 +R 324 32 ALA A 32 8 LEU A 8 8.9719 1 1 1 1 134 134 0 +R 325 32 ALA A 32 12 MET A 12 10.4631 1 1 1 1 13 13 0 +R 326 32 ALA A 32 28 TRP A 28 6.2956 1 1 1 0 -46 72 0 +R 327 32 ALA A 32 29 VAL A 29 5.1300 1 0 0 0 0 0 0 +R 328 32 ALA A 32 30 CYS A 30 5.5042 1 0 0 0 0 0 0 +R 329 32 ALA A 32 31 ALA A 31 3.8582 1 1 0 0 -16 344 0 +R 330 32 ALA A 32 33 LYS A 33 3.7869 1 1 1 1 4 369 0 +R 331 32 ALA A 32 34 PHE A 34 5.4712 1 0 0 0 0 0 0 +R 332 32 ALA A 32 35 GLU A 35 5.0728 1 0 0 0 0 0 0 +R 333 32 ALA A 32 36 SER A 36 5.7631 1 1 1 1 146 146 0 +R 334 32 ALA A 32 37 ASN A 37 6.3799 1 0 0 0 0 0 0 +R 335 32 ALA A 32 38 PHE A 38 5.5773 1 0 0 0 0 0 0 +R 336 32 ALA A 32 55 ILE A 55 5.5963 1 1 1 0 -45 95 0 +R 337 32 ALA A 32 56 LEU A 56 5.4440 1 1 0 0 0 1 0 +R 338 33 LYS A 33 29 VAL A 29 6.2055 1 1 1 0 -25 53 0 +R 339 33 LYS A 33 30 CYS A 30 5.1917 1 1 0 0 -38 38 0 +R 340 33 LYS A 33 31 ALA A 31 5.4805 1 0 0 0 0 0 0 +R 341 33 LYS A 33 32 ALA A 32 3.7869 1 1 0 0 -19 351 0 +R 342 33 LYS A 33 34 PHE A 34 3.7560 1 1 1 1 23 393 0 +R 343 33 LYS A 33 35 GLU A 35 5.7170 1 0 0 0 0 0 0 +R 344 33 LYS A 33 37 ASN A 37 4.3141 1 1 1 1 179 307 0 +R 345 33 LYS A 33 38 PHE A 38 5.2101 1 1 1 1 29 126 0 +R 346 33 LYS A 33 123 TRP A 123 9.2780 1 1 1 1 84 121 0 +R 347 34 PHE A 34 30 CYS A 30 6.3992 1 1 1 0 -61 103 0 +R 348 34 PHE A 34 31 ALA A 31 5.3387 1 0 0 0 0 0 0 +R 349 34 PHE A 34 32 ALA A 32 5.4712 1 0 0 0 0 0 0 +R 350 34 PHE A 34 33 LYS A 33 3.7560 1 1 1 1 17 445 0 +R 351 34 PHE A 34 35 GLU A 35 3.8162 1 1 1 0 -2 355 0 +R 352 34 PHE A 34 36 SER A 36 5.8515 1 0 0 0 0 0 0 +R 353 34 PHE A 34 37 ASN A 37 5.6664 0 1 1 1 3 4 0 +R 354 34 PHE A 34 110 ALA A 110 5.8542 1 1 1 1 62 120 0 +R 355 34 PHE A 34 114 ARG A 114 7.4511 1 1 1 0 -10 291 0 +R 356 34 PHE A 34 115 CYS A 115 8.4896 1 0 0 0 0 0 0 +R 357 34 PHE A 34 123 TRP A 123 11.6342 1 1 1 1 156 156 0 +R 358 35 GLU A 35 31 ALA A 31 5.8673 1 1 1 0 -85 95 0 +R 359 35 GLU A 35 32 ALA A 32 5.0728 1 0 0 0 0 0 0 +R 360 35 GLU A 35 33 LYS A 33 5.7170 1 0 0 0 0 0 0 +R 361 35 GLU A 35 34 PHE A 34 3.8162 1 1 0 0 -42 384 0 +R 362 35 GLU A 35 36 SER A 36 3.7973 1 1 1 0 -1 326 0 +R 363 35 GLU A 35 37 ASN A 37 6.1632 1 0 0 0 0 0 0 +R 364 35 GLU A 35 44 ASN A 44 9.8723 0 1 1 1 31 31 0 +R 365 35 GLU A 35 55 ILE A 55 6.7296 1 1 0 0 -54 54 0 +R 366 35 GLU A 35 56 LEU A 56 5.8960 1 0 0 0 0 0 0 +R 367 35 GLU A 35 57 GLN A 57 6.0016 1 1 1 0 -184 219 0 +R 368 35 GLU A 35 108 TRP A 108 8.1006 1 1 1 0 -6 162 0 +R 369 35 GLU A 35 109 VAL A 109 8.4267 0 1 1 0 -31 49 0 +R 370 35 GLU A 35 110 ALA A 110 6.0785 1 1 1 1 137 176 0 +R 371 36 SER A 36 32 ALA A 32 5.7631 1 1 1 1 38 38 0 +R 372 36 SER A 36 34 PHE A 34 5.8515 1 0 0 0 0 0 0 +R 373 36 SER A 36 35 GLU A 35 3.7973 1 1 0 0 -2 362 0 +R 374 36 SER A 36 37 ASN A 37 3.8326 1 1 1 0 -26 382 0 +R 375 36 SER A 36 38 PHE A 38 5.1834 1 1 1 1 48 48 0 +R 376 36 SER A 36 39 ASN A 39 5.4539 1 1 1 1 3 162 0 +R 377 36 SER A 36 42 ALA A 42 5.5964 1 1 0 0 -9 33 0 +R 378 36 SER A 36 44 ASN A 44 9.2935 0 1 0 0 0 1 0 +R 379 36 SER A 36 54 GLY A 54 6.7929 1 1 0 0 0 40 0 +R 380 36 SER A 36 55 ILE A 55 5.1236 1 1 1 1 79 149 0 +R 381 36 SER A 36 57 GLN A 57 6.6652 1 0 0 0 0 0 0 +R 382 37 ASN A 37 2 VAL A 2 7.9443 0 1 0 0 -59 59 0 +R 383 37 ASN A 37 32 ALA A 32 6.3799 1 0 0 0 0 0 0 +R 384 37 ASN A 37 33 LYS A 33 4.3141 1 1 1 1 185 288 0 +R 385 37 ASN A 37 34 PHE A 34 5.6664 0 1 0 0 0 1 0 +R 386 37 ASN A 37 35 GLU A 35 6.1632 1 1 0 0 0 1 0 +R 387 37 ASN A 37 36 SER A 36 3.8326 1 1 0 0 -43 379 0 +R 388 37 ASN A 37 38 PHE A 38 3.8358 1 1 1 0 -29 388 0 +R 389 37 ASN A 37 39 ASN A 39 5.4975 1 1 1 1 8 18 0 +R 390 38 PHE A 38 1 LYS A 1 8.1596 1 1 0 0 -12 12 0 +R 391 38 PHE A 38 2 VAL A 2 5.5799 1 1 1 1 1 1 0 +R 392 38 PHE A 38 3 PHE A 3 5.3547 1 1 1 0 -5 210 0 +R 393 38 PHE A 38 5 ARG A 5 7.6636 1 1 1 1 21 94 0 +R 394 38 PHE A 38 8 LEU A 8 7.9077 1 1 1 1 78 78 0 +R 395 38 PHE A 38 29 VAL A 29 8.4877 1 1 1 1 43 117 0 +R 396 38 PHE A 38 32 ALA A 32 5.5773 1 0 0 0 0 0 0 +R 397 38 PHE A 38 33 LYS A 33 5.2101 1 1 1 1 22 242 0 +R 398 38 PHE A 38 36 SER A 36 5.1834 1 1 1 1 10 38 0 +R 399 38 PHE A 38 37 ASN A 37 3.8358 1 1 0 0 -67 379 0 +R 400 38 PHE A 38 39 ASN A 39 3.8122 1 1 1 1 24 317 0 +R 401 38 PHE A 38 40 THR A 40 6.4024 1 0 0 0 0 0 0 +R 402 38 PHE A 38 55 ILE A 55 5.7406 1 1 0 0 -18 31 0 +R 403 39 ASN A 39 1 LYS A 1 5.7421 1 1 0 0 -31 40 0 +R 404 39 ASN A 39 2 VAL A 2 4.2809 1 1 1 0 -29 96 0 +R 405 39 ASN A 39 36 SER A 36 5.4539 1 1 1 0 -49 115 0 +R 406 39 ASN A 39 37 ASN A 37 5.4975 1 1 1 0 -4 11 0 +R 407 39 ASN A 39 38 PHE A 38 3.8122 1 1 0 0 -14 363 0 +R 408 39 ASN A 39 40 THR A 40 3.8635 1 1 1 1 36 366 0 +R 409 39 ASN A 39 41 GLN A 41 5.4299 1 1 1 1 18 147 0 +R 410 39 ASN A 39 42 ALA A 42 5.7128 1 1 1 0 -23 110 0 +R 411 39 ASN A 39 55 ILE A 55 5.6995 1 0 0 0 0 0 0 +R 412 40 THR A 40 1 LYS A 1 5.4657 1 1 1 1 155 157 0 +R 413 40 THR A 40 3 PHE A 3 7.9444 1 1 1 1 154 154 0 +R 414 40 THR A 40 38 PHE A 38 6.4024 1 0 0 0 0 0 0 +R 415 40 THR A 40 39 ASN A 39 3.8635 1 1 0 0 0 339 0 +R 416 40 THR A 40 41 GLN A 41 3.8464 1 1 1 1 19 306 0 +R 417 40 THR A 40 42 ALA A 42 5.7069 1 0 0 0 0 0 0 +R 418 40 THR A 40 54 GLY A 54 4.5843 1 1 0 0 0 16 0 +R 419 40 THR A 40 55 ILE A 55 4.5521 1 1 1 1 34 54 0 +R 420 40 THR A 40 84 LEU A 84 5.0346 1 1 1 1 14 184 0 +R 421 40 THR A 40 85 SER A 85 6.2303 1 1 1 0 -71 109 0 +R 422 40 THR A 40 86 SER A 86 6.2290 1 1 0 0 0 2 0 +R 423 40 THR A 40 88 ILE A 88 7.7607 1 1 1 1 13 13 0 +R 424 41 GLN A 41 1 LYS A 1 6.8324 1 1 0 0 -73 76 0 +R 425 41 GLN A 41 39 ASN A 39 5.4299 1 1 1 0 -31 58 0 +R 426 41 GLN A 41 40 THR A 40 3.8464 1 1 0 0 -62 409 0 +R 427 41 GLN A 41 42 ALA A 42 3.8155 1 1 1 1 13 356 0 +R 428 41 GLN A 41 43 THR A 43 6.5152 1 1 1 0 -18 80 0 +R 429 41 GLN A 41 84 LEU A 84 4.8606 1 1 1 0 -79 95 0 +R 430 42 ALA A 42 36 SER A 36 5.5964 1 1 0 0 -19 94 0 +R 431 42 ALA A 42 39 ASN A 39 5.7128 1 1 1 0 -69 103 0 +R 432 42 ALA A 42 40 THR A 40 5.7069 1 0 0 0 0 0 0 +R 433 42 ALA A 42 41 GLN A 41 3.8155 1 1 0 0 -24 359 0 +R 434 42 ALA A 42 43 THR A 43 3.8859 1 1 1 1 5 326 0 +R 435 42 ALA A 42 44 ASN A 44 6.8831 0 1 0 0 -17 17 0 +R 436 42 ALA A 42 53 TYR A 53 6.0588 1 0 0 0 0 0 0 +R 437 42 ALA A 42 54 GLY A 54 5.0278 1 1 1 1 192 192 0 +R 438 42 ALA A 42 57 GLN A 57 7.3752 1 1 1 0 -61 69 0 +R 439 42 ALA A 42 84 LEU A 84 7.3563 1 0 0 0 0 0 0 +R 440 43 THR A 43 41 GLN A 41 6.5152 1 1 1 0 -27 55 0 +R 441 43 THR A 43 42 ALA A 42 3.8859 1 1 0 0 -37 391 0 +R 442 43 THR A 43 44 ASN A 44 3.7688 1 1 1 1 13 431 0 +R 443 43 THR A 43 51 THR A 51 6.7249 1 1 0 0 -1 34 0 +R 444 43 THR A 43 52 ASP A 52 5.4799 1 1 0 0 0 18 0 +R 445 43 THR A 43 53 TYR A 53 4.7167 1 1 1 1 138 138 0 +R 446 43 THR A 43 57 GLN A 57 7.1223 1 0 0 0 0 0 0 +R 447 43 THR A 43 84 LEU A 84 8.5599 1 1 1 1 36 36 0 +R 448 44 ASN A 44 35 GLU A 35 9.8723 0 1 1 1 45 45 0 +R 449 44 ASN A 44 42 ALA A 42 6.8831 0 1 0 0 -12 12 0 +R 450 44 ASN A 44 43 THR A 43 3.7688 1 1 1 0 -15 451 0 +R 451 44 ASN A 44 45 ARG A 45 3.7166 1 1 1 0 0 387 0 +R 452 44 ASN A 44 46 ASN A 46 6.5794 0 1 0 0 -6 6 0 +R 453 44 ASN A 44 51 THR A 51 5.5411 1 0 0 0 0 0 0 +R 454 44 ASN A 44 52 ASP A 52 5.2528 1 1 1 1 122 156 0 +R 455 44 ASN A 44 57 GLN A 57 7.9104 1 1 1 1 80 172 0 +R 456 45 ARG A 45 44 ASN A 44 3.7166 1 1 1 0 -12 381 0 +R 457 45 ARG A 45 46 ASN A 46 3.7641 1 1 1 0 -19 425 0 +R 458 45 ARG A 45 47 THR A 47 6.9141 0 1 1 1 3 4 0 +R 459 45 ARG A 45 49 GLY A 49 6.6305 1 1 1 1 15 60 0 +R 460 45 ARG A 45 50 SER A 50 6.1524 1 1 0 0 0 71 0 +R 461 45 ARG A 45 51 THR A 51 4.1733 1 1 0 0 0 23 0 +R 462 45 ARG A 45 68 ARG A 68 11.3353 1 1 0 0 -168 229 0 +R 463 46 ASN A 46 44 ASN A 44 6.5794 0 1 1 0 -9 12 0 +R 464 46 ASN A 46 45 ARG A 45 3.7641 1 1 1 0 -43 445 0 +R 465 46 ASN A 46 47 THR A 47 3.7875 1 1 1 0 -14 376 0 +R 466 46 ASN A 46 48 ASP A 48 5.4237 1 1 0 0 -52 57 0 +R 467 46 ASN A 46 49 GLY A 49 5.3347 1 1 1 1 86 87 0 +R 468 46 ASN A 46 50 SER A 50 5.3628 1 1 1 1 25 51 0 +R 469 46 ASN A 46 51 THR A 51 5.5953 1 0 0 0 0 0 0 +R 470 46 ASN A 46 52 ASP A 52 7.6137 1 1 1 1 75 130 0 +R 471 46 ASN A 46 59 ASN A 59 9.1269 1 1 1 1 182 188 0 +R 472 47 THR A 47 46 ASN A 46 3.7875 1 1 1 0 -15 361 0 +R 473 47 THR A 47 48 ASP A 48 3.7632 1 1 1 1 28 353 0 +R 474 47 THR A 47 49 GLY A 49 5.2181 1 1 1 1 35 47 0 +R 475 48 ASP A 48 46 ASN A 46 5.4237 1 1 0 0 -19 25 0 +R 476 48 ASP A 48 47 THR A 47 3.7632 1 1 0 0 -29 389 0 +R 477 48 ASP A 48 49 GLY A 49 3.7979 1 1 1 1 21 317 0 +R 478 48 ASP A 48 50 SER A 50 5.5073 1 1 1 1 235 235 0 +R 479 48 ASP A 48 59 ASN A 59 10.9299 0 1 1 0 -2 6 0 +R 480 48 ASP A 48 61 ARG A 61 8.7820 1 1 1 1 155 237 0 +R 481 48 ASP A 48 69 THR A 69 8.8838 0 1 0 0 -1 1 0 +R 482 49 GLY A 49 45 ARG A 45 6.6305 1 1 0 0 0 89 0 +R 483 49 GLY A 49 46 ASN A 46 5.3347 1 1 1 1 19 57 0 +R 484 49 GLY A 49 47 THR A 47 5.2181 1 1 0 0 0 17 0 +R 485 49 GLY A 49 48 ASP A 48 3.7979 1 1 0 0 -29 387 0 +R 486 49 GLY A 49 50 SER A 50 3.7017 1 1 1 1 14 349 0 +R 487 49 GLY A 49 51 THR A 51 6.5946 0 1 1 1 2 2 0 +R 488 49 GLY A 49 68 ARG A 68 8.1773 0 1 0 0 -40 53 0 +R 489 49 GLY A 49 69 THR A 69 6.4717 0 1 1 1 69 70 0 +R 490 49 GLY A 49 70 PRO A 70 8.6350 0 1 0 0 0 6 0 +R 491 50 SER A 50 45 ARG A 45 6.1524 1 0 0 0 0 0 0 +R 492 50 SER A 50 46 ASN A 46 5.3628 1 1 1 1 179 179 0 +R 493 50 SER A 50 48 ASP A 48 5.5073 1 1 1 1 91 116 0 +R 494 50 SER A 50 49 GLY A 49 3.7017 1 1 0 0 -24 393 0 +R 495 50 SER A 50 51 THR A 51 3.9416 1 1 1 1 36 307 0 +R 496 50 SER A 50 59 ASN A 59 6.7524 1 1 1 1 104 162 0 +R 497 50 SER A 50 60 SER A 60 5.4691 1 1 0 0 0 67 0 +R 498 50 SER A 50 61 ARG A 61 5.5177 1 1 0 0 0 6 0 +R 499 50 SER A 50 69 THR A 69 5.5332 1 1 0 0 0 50 0 +R 500 51 THR A 51 43 THR A 43 6.7249 1 1 0 0 0 19 0 +R 501 51 THR A 51 44 ASN A 44 5.5411 1 1 0 0 -64 88 0 +R 502 51 THR A 51 45 ARG A 45 4.1733 1 1 0 0 0 2 0 +R 503 51 THR A 51 46 ASN A 46 5.5953 1 0 0 0 0 0 0 +R 504 51 THR A 51 50 SER A 50 3.9416 1 1 1 1 10 379 0 +R 505 51 THR A 51 52 ASP A 52 3.8949 1 1 1 0 -40 355 0 +R 506 51 THR A 51 53 TYR A 53 6.5005 1 1 1 1 70 146 0 +R 507 51 THR A 51 59 ASN A 59 5.7402 1 0 0 0 0 0 0 +R 508 51 THR A 51 60 SER A 60 5.4996 1 1 1 1 168 168 0 +R 509 51 THR A 51 66 ASP A 66 8.3256 1 0 0 0 0 0 0 +R 510 51 THR A 51 68 ARG A 68 9.1481 1 1 1 1 115 157 0 +R 511 52 ASP A 52 43 THR A 43 5.4799 1 1 0 0 0 12 0 +R 512 52 ASP A 52 44 ASN A 44 5.2528 1 1 1 1 110 126 0 +R 513 52 ASP A 52 46 ASN A 46 7.6137 1 1 1 1 134 134 0 +R 514 52 ASP A 52 51 THR A 51 3.8949 1 1 0 0 -5 337 0 +R 515 52 ASP A 52 53 TYR A 53 3.7885 1 1 1 1 18 345 0 +R 516 52 ASP A 52 57 GLN A 57 4.5222 1 1 0 0 -155 164 0 +R 517 52 ASP A 52 58 ILE A 58 4.9171 1 1 0 0 0 5 0 +R 518 52 ASP A 52 59 ASN A 59 4.3832 1 1 1 1 120 202 0 +R 519 53 TYR A 53 42 ALA A 42 6.0588 1 1 0 0 0 1 0 +R 520 53 TYR A 53 43 THR A 43 4.7167 1 1 1 1 111 111 0 +R 521 53 TYR A 53 51 THR A 51 6.5005 1 1 1 0 -111 172 0 +R 522 53 TYR A 53 52 ASP A 52 3.7885 1 1 0 0 -1 354 0 +R 523 53 TYR A 53 54 GLY A 54 3.8089 1 1 1 1 16 350 0 +R 524 53 TYR A 53 57 GLN A 57 4.4524 1 1 1 1 4 4 0 +R 525 53 TYR A 53 58 ILE A 58 5.1266 1 1 1 1 72 153 0 +R 526 53 TYR A 53 60 SER A 60 7.7842 1 0 0 0 0 0 0 +R 527 53 TYR A 53 64 CYS A 64 9.1195 1 0 0 0 0 0 0 +R 528 53 TYR A 53 66 ASP A 66 9.7084 1 1 1 1 80 176 0 +R 529 53 TYR A 53 68 ARG A 68 13.3743 0 1 1 1 27 30 0 +R 530 53 TYR A 53 80 CYS A 80 6.5643 1 1 1 1 41 211 0 +R 531 53 TYR A 53 81 SER A 81 7.5160 0 1 0 0 -4 10 0 +R 532 53 TYR A 53 83 LEU A 83 6.1854 1 1 1 0 -3 11 0 +R 533 53 TYR A 53 84 LEU A 84 6.6054 1 1 1 1 22 22 0 +R 534 54 GLY A 54 36 SER A 36 6.7929 1 1 0 0 0 9 0 +R 535 54 GLY A 54 39 ASN A 39 7.0228 0 1 0 0 0 5 0 +R 536 54 GLY A 54 40 THR A 40 4.5843 1 1 0 0 0 102 0 +R 537 54 GLY A 54 42 ALA A 42 5.0278 1 1 1 1 49 51 0 +R 538 54 GLY A 54 53 TYR A 53 3.8089 1 1 0 0 -7 353 0 +R 539 54 GLY A 54 55 ILE A 55 3.7039 1 1 1 1 29 356 0 +R 540 54 GLY A 54 56 LEU A 56 5.3851 1 1 0 0 0 1 0 +R 541 54 GLY A 54 57 GLN A 57 4.9429 1 1 1 1 146 146 0 +R 542 54 GLY A 54 83 LEU A 83 5.3232 1 1 0 0 0 41 0 +R 543 54 GLY A 54 84 LEU A 84 4.8428 1 1 0 0 -4 4 0 +R 544 55 ILE A 55 3 PHE A 3 9.3473 1 1 1 1 98 98 0 +R 545 55 ILE A 55 8 LEU A 8 10.0426 1 1 1 1 62 62 0 +R 546 55 ILE A 55 12 MET A 12 11.3010 0 1 1 1 2 2 0 +R 547 55 ILE A 55 32 ALA A 32 5.5963 1 1 1 1 39 91 0 +R 548 55 ILE A 55 35 GLU A 35 6.7296 1 1 0 0 -1 1 0 +R 549 55 ILE A 55 36 SER A 36 5.1236 1 1 1 1 50 166 0 +R 550 55 ILE A 55 38 PHE A 38 5.7406 1 1 0 0 -109 112 0 +R 551 55 ILE A 55 39 ASN A 39 5.6995 1 1 1 1 2 2 0 +R 552 55 ILE A 55 40 THR A 40 4.5521 1 1 1 1 15 24 0 +R 553 55 ILE A 55 54 GLY A 54 3.7039 1 1 0 0 0 341 0 +R 554 55 ILE A 55 56 LEU A 56 3.7519 1 1 1 1 25 367 0 +R 555 55 ILE A 55 57 GLN A 57 5.6235 1 0 0 0 0 0 0 +R 556 55 ILE A 55 88 ILE A 88 8.0660 1 1 1 1 37 37 0 +R 557 55 ILE A 55 91 SER A 91 7.4339 1 1 0 0 -81 118 0 +R 558 56 LEU A 56 12 MET A 12 11.5983 1 1 1 1 79 79 0 +R 559 56 LEU A 56 28 TRP A 28 8.7724 0 1 1 0 -1 19 0 +R 560 56 LEU A 56 31 ALA A 31 7.1209 1 1 1 1 70 70 0 +R 561 56 LEU A 56 32 ALA A 32 5.4440 1 1 1 0 -98 114 0 +R 562 56 LEU A 56 35 GLU A 35 5.8960 1 1 0 0 0 1 0 +R 563 56 LEU A 56 54 GLY A 54 5.3851 1 1 0 0 0 3 0 +R 564 56 LEU A 56 55 ILE A 55 3.7519 1 1 1 0 -20 429 0 +R 565 56 LEU A 56 57 GLN A 57 3.7252 1 1 1 1 12 337 0 +R 566 56 LEU A 56 58 ILE A 58 5.6664 1 1 1 1 37 37 0 +R 567 56 LEU A 56 91 SER A 91 6.9590 0 1 0 0 -29 32 0 +R 568 56 LEU A 56 92 VAL A 92 8.3697 0 1 0 0 0 1 0 +R 569 56 LEU A 56 95 ALA A 95 7.7189 1 1 1 1 140 140 0 +R 570 56 LEU A 56 108 TRP A 108 8.2153 1 1 1 1 131 203 0 +R 571 57 GLN A 57 35 GLU A 35 6.0016 1 1 0 0 -170 175 0 +R 572 57 GLN A 57 36 SER A 36 6.6652 1 0 0 0 0 0 0 +R 573 57 GLN A 57 42 ALA A 42 7.3752 1 1 1 1 118 142 0 +R 574 57 GLN A 57 43 THR A 43 7.1223 1 0 0 0 0 0 0 +R 575 57 GLN A 57 44 ASN A 44 7.9104 1 1 1 1 150 163 0 +R 576 57 GLN A 57 52 ASP A 52 4.5222 1 1 1 0 -86 120 0 +R 577 57 GLN A 57 53 TYR A 53 4.4524 1 1 0 0 0 5 0 +R 578 57 GLN A 57 54 GLY A 54 4.9429 1 1 1 1 108 124 0 +R 579 57 GLN A 57 55 ILE A 55 5.6235 1 0 0 0 0 0 0 +R 580 57 GLN A 57 56 LEU A 56 3.7252 1 1 0 0 -62 391 0 +R 581 57 GLN A 57 58 ILE A 58 3.8369 1 1 1 1 20 351 0 +R 582 57 GLN A 57 59 ASN A 59 6.4000 1 1 1 1 9 19 0 +R 583 57 GLN A 57 108 TRP A 108 8.2910 0 1 1 1 13 33 0 +R 584 58 ILE A 58 52 ASP A 52 4.9171 1 1 0 0 0 1 0 +R 585 58 ILE A 58 53 TYR A 53 5.1266 1 1 1 1 85 125 0 +R 586 58 ILE A 58 56 LEU A 56 5.6664 1 1 1 0 -21 50 0 +R 587 58 ILE A 58 57 GLN A 57 3.8369 1 1 0 0 -1 340 0 +R 588 58 ILE A 58 59 ASN A 59 3.7920 1 1 1 1 8 375 0 +R 589 58 ILE A 58 63 TRP A 63 6.7289 1 1 1 1 142 142 0 +R 590 58 ILE A 58 83 LEU A 83 7.8716 1 1 1 1 62 62 0 +R 591 58 ILE A 58 91 SER A 91 7.7587 1 1 0 0 -148 183 0 +R 592 58 ILE A 58 94 CYS A 94 8.1513 1 1 1 1 27 28 0 +R 593 58 ILE A 58 95 ALA A 95 7.7436 1 1 0 0 -3 9 0 +R 594 58 ILE A 58 98 ILE A 98 8.9872 1 1 1 1 91 96 0 +R 595 59 ASN A 59 46 ASN A 46 9.1269 1 1 1 1 18 18 0 +R 596 59 ASN A 59 48 ASP A 48 10.9299 0 1 1 1 4 7 0 +R 597 59 ASN A 59 50 SER A 50 6.7524 1 1 1 1 128 134 0 +R 598 59 ASN A 59 51 THR A 51 5.7402 1 0 0 0 0 0 0 +R 599 59 ASN A 59 52 ASP A 52 4.3832 1 1 1 1 78 125 0 +R 600 59 ASN A 59 57 GLN A 57 6.4000 1 1 0 0 -7 7 0 +R 601 59 ASN A 59 58 ILE A 58 3.7920 1 1 0 0 -9 353 0 +R 602 59 ASN A 59 60 SER A 60 3.8442 1 1 1 1 25 327 0 +R 603 59 ASN A 59 61 ARG A 61 5.5522 1 1 1 1 50 218 0 +R 604 59 ASN A 59 62 TRP A 62 6.1912 1 1 1 1 1 30 0 +R 605 59 ASN A 59 63 TRP A 63 5.8889 1 1 1 1 162 200 0 +R 606 60 SER A 60 50 SER A 50 5.4691 1 0 0 0 0 0 0 +R 607 60 SER A 60 51 THR A 51 5.4996 1 1 1 1 101 120 0 +R 608 60 SER A 60 53 TYR A 53 7.7842 1 0 0 0 0 0 0 +R 609 60 SER A 60 59 ASN A 59 3.8442 1 1 0 0 0 339 0 +R 610 60 SER A 60 61 ARG A 61 3.8908 1 1 1 1 17 283 0 +R 611 60 SER A 60 62 TRP A 62 5.5049 1 0 0 0 0 0 0 +R 612 60 SER A 60 64 CYS A 64 5.0013 1 1 0 0 -1 31 0 +R 613 60 SER A 60 66 ASP A 66 6.3315 1 1 0 0 0 125 0 +R 614 60 SER A 60 69 THR A 69 6.5717 1 1 1 1 101 105 0 +R 615 60 SER A 60 72 SER A 72 6.4249 1 1 1 1 199 206 0 +R 616 60 SER A 60 80 CYS A 80 6.8143 1 1 0 0 0 32 0 +R 617 61 ARG A 61 48 ASP A 48 8.7820 1 1 1 1 204 281 0 +R 618 61 ARG A 61 50 SER A 50 5.5177 1 1 0 0 0 4 0 +R 619 61 ARG A 61 59 ASN A 59 5.5522 1 1 1 0 -68 70 0 +R 620 61 ARG A 61 60 SER A 60 3.8908 1 1 1 0 -12 362 0 +R 621 61 ARG A 61 62 TRP A 62 3.8101 1 1 1 1 110 481 0 +R 622 61 ARG A 61 69 THR A 69 6.2823 1 1 0 0 -70 92 0 +R 623 61 ARG A 61 70 PRO A 70 8.0292 1 1 1 1 167 167 0 +R 624 61 ARG A 61 71 GLY A 71 7.0231 0 1 0 0 -2 17 0 +R 625 61 ARG A 61 72 SER A 72 4.5693 1 1 0 0 0 14 0 +R 626 61 ARG A 61 73 ARG A 73 6.4875 1 1 1 1 130 130 0 +R 627 62 TRP A 62 59 ASN A 59 6.1912 1 1 1 0 -15 51 0 +R 628 62 TRP A 62 60 SER A 60 5.5049 1 0 0 0 0 0 0 +R 629 62 TRP A 62 61 ARG A 61 3.8101 1 1 1 1 9 531 0 +R 630 62 TRP A 62 63 TRP A 63 3.7646 1 1 1 0 -14 426 0 +R 631 62 TRP A 62 64 CYS A 64 6.3048 1 1 0 0 0 3 0 +R 632 62 TRP A 62 73 ARG A 73 4.7823 1 1 1 0 -49 187 0 +R 633 62 TRP A 62 74 ASN A 74 5.5079 1 1 1 1 11 11 0 +R 634 62 TRP A 62 75 LEU A 75 5.9402 1 1 1 1 178 204 0 +R 635 63 TRP A 63 58 ILE A 58 6.7289 1 1 1 1 89 89 0 +R 636 63 TRP A 63 59 ASN A 59 5.8889 1 1 0 0 -69 69 0 +R 637 63 TRP A 63 62 TRP A 62 3.7646 1 1 1 0 -6 481 0 +R 638 63 TRP A 63 64 CYS A 64 3.7610 1 1 1 0 -5 343 0 +R 639 63 TRP A 63 74 ASN A 74 4.6495 1 0 0 0 0 0 0 +R 640 63 TRP A 63 75 LEU A 75 4.5592 1 1 1 1 117 117 0 +R 641 63 TRP A 63 76 CYS A 76 5.1313 1 1 1 1 103 169 0 +R 642 63 TRP A 63 78 ILE A 78 7.9100 1 0 0 0 0 0 0 +R 643 63 TRP A 63 94 CYS A 94 7.4243 1 1 0 0 0 1 0 +R 644 63 TRP A 63 97 LYS A 97 9.0609 1 1 1 1 22 24 0 +R 645 63 TRP A 63 98 ILE A 98 8.1327 1 1 1 1 99 261 0 +R 646 63 TRP A 63 101 ASP A 101 11.5849 1 1 0 0 -76 144 0 +R 647 63 TRP A 63 107 ALA A 107 11.8922 0 1 1 1 4 4 0 +R 648 64 CYS A 64 53 TYR A 53 9.1195 1 1 0 0 0 10 0 +R 649 64 CYS A 64 59 ASN A 59 6.9688 0 1 0 0 0 4 0 +R 650 64 CYS A 64 60 SER A 60 5.0013 1 1 0 0 -120 167 0 +R 651 64 CYS A 64 62 TRP A 62 6.3048 1 1 0 0 0 3 0 +R 652 64 CYS A 64 63 TRP A 63 3.7610 1 1 0 0 -18 385 0 +R 653 64 CYS A 64 65 ASN A 65 3.7533 1 1 1 1 19 339 0 +R 654 64 CYS A 64 72 SER A 72 7.6034 1 1 1 1 5 5 0 +R 655 64 CYS A 64 74 ASN A 74 4.3585 1 1 0 0 0 24 0 +R 656 64 CYS A 64 78 ILE A 78 5.2721 1 1 1 0 -50 52 0 +R 657 64 CYS A 64 79 PRO A 79 5.5062 1 0 0 0 0 0 0 +R 658 64 CYS A 64 80 CYS A 80 4.9610 1 1 0 0 0 244 0 +R 659 64 CYS A 64 83 LEU A 83 8.6424 1 1 1 1 39 94 0 +R 660 65 ASN A 65 64 CYS A 64 3.7533 1 1 0 0 0 356 0 +R 661 65 ASN A 65 66 ASP A 66 3.8054 1 1 1 1 25 333 0 +R 662 65 ASN A 65 67 GLY A 67 5.7673 1 1 1 1 35 159 0 +R 663 65 ASN A 65 72 SER A 72 6.7196 0 1 1 1 39 61 0 +R 664 65 ASN A 65 74 ASN A 74 5.3596 1 1 1 0 -106 121 0 +R 665 65 ASN A 65 78 ILE A 78 6.2178 1 1 1 1 4 14 0 +R 666 65 ASN A 65 79 PRO A 79 4.7112 1 1 1 0 -55 57 0 +R 667 65 ASN A 65 80 CYS A 80 5.3811 1 1 1 1 88 88 0 +R 668 66 ASP A 66 51 THR A 51 8.3256 1 1 0 0 0 7 0 +R 669 66 ASP A 66 53 TYR A 53 9.7084 1 1 1 1 36 176 0 +R 670 66 ASP A 66 60 SER A 60 6.3315 1 1 1 1 32 36 0 +R 671 66 ASP A 66 65 ASN A 65 3.8054 1 1 0 0 0 362 0 +R 672 66 ASP A 66 67 GLY A 67 3.8249 1 1 1 1 10 319 0 +R 673 66 ASP A 66 68 ARG A 68 5.5275 1 1 1 0 -7 127 0 +R 674 66 ASP A 66 69 THR A 69 6.6481 1 1 1 1 191 194 0 +R 675 66 ASP A 66 79 PRO A 79 5.9021 0 1 0 0 0 3 0 +R 676 66 ASP A 66 80 CYS A 80 5.2749 1 1 1 1 7 42 0 +R 677 66 ASP A 66 81 SER A 81 7.3090 0 1 0 0 -1 5 0 +R 678 67 GLY A 67 65 ASN A 65 5.7673 1 1 1 1 14 97 0 +R 679 67 GLY A 67 66 ASP A 66 3.8249 1 1 1 0 -35 376 0 +R 680 67 GLY A 67 68 ARG A 68 3.7098 1 1 1 1 4 349 0 +R 681 67 GLY A 67 69 THR A 69 6.0387 1 1 0 0 0 3 0 +R 682 68 ARG A 68 45 ARG A 45 11.3353 1 1 0 0 -233 270 0 +R 683 68 ARG A 68 49 GLY A 49 8.1773 0 1 0 0 -21 24 0 +R 684 68 ARG A 68 51 THR A 51 9.1481 1 1 1 1 73 136 0 +R 685 68 ARG A 68 53 TYR A 53 13.3743 0 1 1 1 8 18 0 +R 686 68 ARG A 68 66 ASP A 66 5.5275 1 1 1 0 -50 78 0 +R 687 68 ARG A 68 67 GLY A 67 3.7098 1 1 0 0 -29 397 0 +R 688 68 ARG A 68 69 THR A 69 3.8098 1 1 1 1 2 345 0 +R 689 68 ARG A 68 70 PRO A 70 6.1627 1 1 0 0 -60 79 0 +R 690 69 THR A 69 49 GLY A 49 6.4717 0 1 1 1 9 9 0 +R 691 69 THR A 69 50 SER A 50 5.5332 1 1 0 0 0 60 0 +R 692 69 THR A 69 60 SER A 60 6.5717 1 1 1 0 -24 149 0 +R 693 69 THR A 69 61 ARG A 61 6.2823 1 1 0 0 -127 127 0 +R 694 69 THR A 69 66 ASP A 66 6.6481 1 1 1 1 128 149 0 +R 695 69 THR A 69 67 GLY A 67 6.0387 1 0 0 0 0 0 0 +R 696 69 THR A 69 68 ARG A 68 3.8098 1 1 1 0 -11 357 0 +R 697 69 THR A 69 70 PRO A 70 3.8378 1 1 0 0 -10 323 0 +R 698 69 THR A 69 71 GLY A 71 6.1353 1 1 1 1 1 1 0 +R 699 69 THR A 69 72 SER A 72 5.4835 1 1 1 1 166 196 0 +R 700 70 PRO A 70 49 GLY A 49 8.6350 0 1 0 0 -12 17 0 +R 701 70 PRO A 70 61 ARG A 61 8.0292 1 1 1 1 74 96 0 +R 702 70 PRO A 70 68 ARG A 68 6.1627 1 1 0 0 -40 50 0 +R 703 70 PRO A 70 69 THR A 69 3.8378 1 1 1 0 -8 416 0 +R 704 70 PRO A 70 71 GLY A 71 3.7037 1 1 1 0 -7 364 0 +R 705 70 PRO A 70 72 SER A 72 5.5397 1 0 0 0 0 0 0 +R 706 71 GLY A 71 61 ARG A 61 7.0231 0 1 1 0 -8 65 0 +R 707 71 GLY A 71 69 THR A 69 6.1353 1 1 1 1 1 1 0 +R 708 71 GLY A 71 70 PRO A 70 3.7037 1 1 0 0 -62 367 0 +R 709 71 GLY A 71 72 SER A 72 3.7913 1 1 1 1 16 371 0 +R 710 71 GLY A 71 73 ARG A 73 6.3954 1 1 1 0 -31 70 0 +R 711 72 SER A 72 60 SER A 60 6.4249 1 1 1 1 96 125 0 +R 712 72 SER A 72 61 ARG A 61 4.5693 1 1 0 0 0 31 0 +R 713 72 SER A 72 64 CYS A 64 7.6034 1 1 1 1 90 93 0 +R 714 72 SER A 72 65 ASN A 65 6.7196 0 1 0 0 0 44 0 +R 715 72 SER A 72 69 THR A 69 5.4835 1 1 1 1 6 95 0 +R 716 72 SER A 72 70 PRO A 70 5.5397 1 0 0 0 0 0 0 +R 717 72 SER A 72 71 GLY A 71 3.7913 1 1 1 0 -18 376 0 +R 718 72 SER A 72 73 ARG A 73 3.8449 1 1 1 1 35 355 0 +R 719 72 SER A 72 74 ASN A 74 5.9277 1 1 1 1 7 24 0 +R 720 73 ARG A 73 61 ARG A 61 6.4875 1 1 1 1 13 13 0 +R 721 73 ARG A 73 62 TRP A 62 4.7823 1 1 1 0 -114 187 0 +R 722 73 ARG A 73 71 GLY A 71 6.3954 1 1 0 0 -41 43 0 +R 723 73 ARG A 73 72 SER A 72 3.8449 1 1 0 0 -4 357 0 +R 724 73 ARG A 73 74 ASN A 74 3.8190 1 1 1 0 -20 388 0 +R 725 73 ARG A 73 75 LEU A 75 5.6080 1 1 1 0 -44 102 0 +R 726 74 ASN A 74 62 TRP A 62 5.5079 1 1 1 1 13 21 0 +R 727 74 ASN A 74 63 TRP A 63 4.6495 1 1 0 0 0 12 0 +R 728 74 ASN A 74 64 CYS A 64 4.3585 1 1 0 0 0 15 0 +R 729 74 ASN A 74 65 ASN A 65 5.3596 1 1 1 0 -112 159 0 +R 730 74 ASN A 74 72 SER A 72 5.9277 1 1 1 0 -2 24 0 +R 731 74 ASN A 74 73 ARG A 73 3.8190 1 1 0 0 -48 374 0 +R 732 74 ASN A 74 75 LEU A 75 3.7831 1 1 1 1 15 371 0 +R 733 74 ASN A 74 76 CYS A 76 5.6175 1 0 0 0 0 0 0 +R 734 74 ASN A 74 77 ASN A 77 5.1976 1 1 1 1 25 156 0 +R 735 74 ASN A 74 78 ILE A 78 6.8599 1 1 1 1 14 235 0 +R 736 74 ASN A 74 79 PRO A 79 8.2352 0 1 0 0 -2 3 0 +R 737 75 LEU A 75 62 TRP A 62 5.9402 1 1 1 0 0 128 0 +R 738 75 LEU A 75 63 TRP A 63 4.5592 1 1 1 1 134 134 0 +R 739 75 LEU A 75 73 ARG A 73 5.6080 1 1 1 0 -23 144 0 +R 740 75 LEU A 75 74 ASN A 74 3.7831 1 1 0 0 -13 349 0 +R 741 75 LEU A 75 76 CYS A 76 3.8164 1 1 1 1 18 338 0 +R 742 75 LEU A 75 77 ASN A 77 5.4213 1 1 1 0 -15 21 0 +R 743 75 LEU A 75 97 LYS A 97 8.3701 0 1 1 0 -39 65 0 +R 744 75 LEU A 75 101 ASP A 101 10.9431 0 1 0 0 -36 36 0 +R 745 76 CYS A 76 63 TRP A 63 5.1313 1 1 1 0 -12 99 0 +R 746 76 CYS A 76 74 ASN A 74 5.6175 1 0 0 0 0 0 0 +R 747 76 CYS A 76 75 LEU A 75 3.8164 1 1 0 0 -15 369 0 +R 748 76 CYS A 76 77 ASN A 77 3.7920 1 1 1 0 -31 391 0 +R 749 76 CYS A 76 78 ILE A 78 5.6591 1 1 1 0 -13 45 0 +R 750 76 CYS A 76 94 CYS A 94 5.4641 1 1 1 1 31 297 0 +R 751 76 CYS A 76 97 LYS A 97 7.3462 1 1 1 1 1 27 0 +R 752 77 ASN A 77 74 ASN A 74 5.1976 1 1 1 0 -37 102 0 +R 753 77 ASN A 77 75 LEU A 75 5.4213 1 1 0 0 -13 13 0 +R 754 77 ASN A 77 76 CYS A 76 3.7920 1 1 0 0 -63 407 0 +R 755 77 ASN A 77 78 ILE A 78 3.7096 1 1 1 0 -12 368 0 +R 756 77 ASN A 77 79 PRO A 79 7.0593 0 1 0 0 -8 8 0 +R 757 78 ILE A 78 63 TRP A 63 7.9100 1 0 0 0 0 0 0 +R 758 78 ILE A 78 64 CYS A 64 5.2721 1 1 1 1 22 22 0 +R 759 78 ILE A 78 65 ASN A 65 6.2178 1 1 1 1 125 126 0 +R 760 78 ILE A 78 74 ASN A 74 6.8599 1 1 1 0 0 12 0 +R 761 78 ILE A 78 76 CYS A 76 5.6591 1 1 1 1 40 132 0 +R 762 78 ILE A 78 77 ASN A 77 3.7096 1 1 0 0 -33 394 0 +R 763 78 ILE A 78 79 PRO A 79 3.7780 1 1 1 0 -15 412 0 +R 764 78 ILE A 78 80 CYS A 80 6.2029 1 0 0 0 0 0 0 +R 765 78 ILE A 78 82 ALA A 82 6.8387 1 1 1 1 55 55 0 +R 766 78 ILE A 78 83 LEU A 83 8.3786 1 1 1 1 191 191 0 +R 767 78 ILE A 78 90 ALA A 90 8.2888 0 1 1 1 46 47 0 +R 768 78 ILE A 78 94 CYS A 94 8.8596 1 1 1 1 5 5 0 +R 769 79 PRO A 79 64 CYS A 64 5.5062 1 0 0 0 0 0 0 +R 770 79 PRO A 79 65 ASN A 65 4.7112 1 1 1 0 -57 79 0 +R 771 79 PRO A 79 66 ASP A 66 5.9021 0 1 0 0 0 2 0 +R 772 79 PRO A 79 74 ASN A 74 8.2352 0 1 0 0 -5 5 0 +R 773 79 PRO A 79 77 ASN A 77 7.0593 0 1 0 0 -8 8 0 +R 774 79 PRO A 79 78 ILE A 78 3.7780 1 1 1 1 24 426 0 +R 775 79 PRO A 79 80 CYS A 80 3.8413 1 1 1 0 -13 376 0 +R 776 79 PRO A 79 81 SER A 81 5.4310 1 1 0 0 -74 74 0 +R 777 79 PRO A 79 82 ALA A 82 5.6534 1 1 1 1 81 143 0 +R 778 80 CYS A 80 53 TYR A 53 6.5643 1 1 1 1 74 104 0 +R 779 80 CYS A 80 60 SER A 60 6.8143 1 1 0 0 0 16 0 +R 780 80 CYS A 80 64 CYS A 64 4.9610 1 1 0 0 0 284 0 +R 781 80 CYS A 80 65 ASN A 65 5.3811 1 1 1 1 23 52 0 +R 782 80 CYS A 80 66 ASP A 66 5.2749 1 1 1 1 11 49 0 +R 783 80 CYS A 80 78 ILE A 78 6.2029 1 0 0 0 0 0 0 +R 784 80 CYS A 80 79 PRO A 79 3.8413 1 1 0 0 -57 340 0 +R 785 80 CYS A 80 81 SER A 81 3.8305 1 1 1 1 7 326 0 +R 786 80 CYS A 80 82 ALA A 82 5.3155 1 0 0 0 0 0 0 +R 787 80 CYS A 80 83 LEU A 83 5.4505 1 1 1 1 57 153 0 +R 788 81 SER A 81 53 TYR A 53 7.5160 0 1 0 0 0 9 0 +R 789 81 SER A 81 79 PRO A 79 5.4310 1 1 0 0 -86 87 0 +R 790 81 SER A 81 80 CYS A 80 3.8305 1 1 0 0 -25 371 0 +R 791 81 SER A 81 82 ALA A 82 3.8111 1 1 1 1 44 373 0 +R 792 81 SER A 81 83 LEU A 83 5.1899 1 0 0 0 0 0 0 +R 793 81 SER A 81 84 LEU A 84 5.4183 1 1 1 1 42 165 0 +R 794 81 SER A 81 85 SER A 85 7.5229 0 1 1 1 10 14 0 +R 795 82 ALA A 82 78 ILE A 78 6.8387 1 1 1 1 107 107 0 +R 796 82 ALA A 82 79 PRO A 79 5.6534 1 1 1 0 -24 101 0 +R 797 82 ALA A 82 80 CYS A 80 5.3155 1 0 0 0 0 0 0 +R 798 82 ALA A 82 81 SER A 81 3.8111 1 1 1 0 -1 378 0 +R 799 82 ALA A 82 83 LEU A 83 3.7944 1 1 1 1 8 341 0 +R 800 82 ALA A 82 84 LEU A 84 5.4609 1 1 1 1 13 13 0 +R 801 82 ALA A 82 85 SER A 85 5.9325 1 1 0 0 0 115 0 +R 802 82 ALA A 82 90 ALA A 90 6.7558 1 1 1 0 -10 50 0 +R 803 83 LEU A 83 40 THR A 40 7.4963 0 1 0 0 -2 3 0 +R 804 83 LEU A 83 53 TYR A 53 6.1854 1 1 1 1 30 30 0 +R 805 83 LEU A 83 54 GLY A 54 5.3232 1 1 0 0 0 93 0 +R 806 83 LEU A 83 55 ILE A 55 7.8149 0 1 1 1 1 1 0 +R 807 83 LEU A 83 58 ILE A 58 7.8716 1 1 1 1 103 103 0 +R 808 83 LEU A 83 64 CYS A 64 8.6424 1 1 1 1 7 170 0 +R 809 83 LEU A 83 78 ILE A 78 8.3786 1 1 1 1 102 102 0 +R 810 83 LEU A 83 80 CYS A 80 5.4505 1 1 0 0 -36 36 0 +R 811 83 LEU A 83 81 SER A 81 5.1899 1 0 0 0 0 0 0 +R 812 83 LEU A 83 82 ALA A 82 3.7944 1 1 0 0 -15 371 0 +R 813 83 LEU A 83 84 LEU A 84 3.8682 1 1 1 1 25 309 0 +R 814 83 LEU A 83 85 SER A 85 5.7541 1 1 1 1 2 4 0 +R 815 83 LEU A 83 90 ALA A 90 6.0317 1 1 0 0 -1 2 0 +R 816 83 LEU A 83 91 SER A 91 5.2891 1 1 1 0 -36 193 0 +R 817 83 LEU A 83 94 CYS A 94 8.8633 1 1 1 1 3 3 0 +R 818 84 LEU A 84 40 THR A 40 5.0346 1 1 1 1 15 152 0 +R 819 84 LEU A 84 41 GLN A 41 4.8606 1 1 1 0 -53 101 0 +R 820 84 LEU A 84 42 ALA A 42 7.3563 1 1 0 0 -30 30 0 +R 821 84 LEU A 84 43 THR A 43 8.5599 1 1 1 1 95 95 0 +R 822 84 LEU A 84 53 TYR A 53 6.6054 1 1 1 1 40 40 0 +R 823 84 LEU A 84 54 GLY A 54 4.8428 1 1 0 0 -115 115 0 +R 824 84 LEU A 84 80 CYS A 80 7.5698 0 1 0 0 -15 15 0 +R 825 84 LEU A 84 81 SER A 81 5.4183 1 1 0 0 -39 91 0 +R 826 84 LEU A 84 82 ALA A 82 5.4609 1 0 0 0 0 0 0 +R 827 84 LEU A 84 83 LEU A 83 3.8682 1 1 0 0 -13 366 0 +R 828 84 LEU A 84 85 SER A 85 3.7737 1 1 1 1 10 356 0 +R 829 84 LEU A 84 86 SER A 86 6.7769 0 1 1 1 3 3 0 +R 830 85 SER A 85 40 THR A 40 6.2303 1 1 0 0 -14 75 0 +R 831 85 SER A 85 81 SER A 81 7.5229 0 1 1 1 2 13 0 +R 832 85 SER A 85 82 ALA A 82 5.9325 1 1 0 0 0 73 0 +R 833 85 SER A 85 83 LEU A 83 5.7541 1 1 0 0 -1 1 0 +R 834 85 SER A 85 84 LEU A 84 3.7737 1 1 0 0 -16 376 0 +R 835 85 SER A 85 86 SER A 86 3.8390 1 1 1 1 59 381 0 +R 836 85 SER A 85 87 ASP A 87 5.2323 1 1 1 1 8 169 0 +R 837 86 SER A 86 1 LYS A 1 5.1894 1 1 1 0 -65 208 0 +R 838 86 SER A 86 3 PHE A 3 8.8941 1 1 0 0 -115 115 0 +R 839 86 SER A 86 40 THR A 40 6.2290 1 0 0 0 0 0 0 +R 840 86 SER A 86 84 LEU A 84 6.7769 0 1 1 1 2 2 0 +R 841 86 SER A 86 85 SER A 85 3.8390 1 1 1 1 5 348 0 +R 842 86 SER A 86 87 ASP A 87 3.8507 1 1 1 1 20 342 0 +R 843 86 SER A 86 88 ILE A 88 6.0595 1 1 1 1 25 25 0 +R 844 87 ASP A 87 3 PHE A 3 10.7648 0 1 0 0 0 1 0 +R 845 87 ASP A 87 15 HIS A 15 10.7991 0 1 1 1 6 22 0 +R 846 87 ASP A 87 85 SER A 85 5.2323 1 1 0 0 -45 134 0 +R 847 87 ASP A 87 86 SER A 86 3.8507 1 1 0 0 -16 361 0 +R 848 87 ASP A 87 88 ILE A 88 3.8129 1 1 1 1 35 371 0 +R 849 87 ASP A 87 89 THR A 89 5.6671 1 1 1 1 207 234 0 +R 850 87 ASP A 87 90 ALA A 90 7.7602 0 1 1 1 9 9 0 +R 851 88 ILE A 88 3 PHE A 3 10.4372 1 1 1 1 143 143 0 +R 852 88 ILE A 88 8 LEU A 8 9.1166 1 0 0 0 0 0 0 +R 853 88 ILE A 88 11 ALA A 11 7.9512 1 1 1 1 135 162 0 +R 854 88 ILE A 88 12 MET A 12 8.1191 1 1 1 1 11 35 0 +R 855 88 ILE A 88 15 HIS A 15 8.6713 1 1 1 0 -29 35 0 +R 856 88 ILE A 88 40 THR A 40 7.7607 1 1 1 1 47 47 0 +R 857 88 ILE A 88 55 ILE A 55 8.0660 1 1 1 1 35 35 0 +R 858 88 ILE A 88 86 SER A 86 6.0595 1 1 0 0 -4 4 0 +R 859 88 ILE A 88 87 ASP A 87 3.8129 1 1 1 1 1 353 0 +R 860 88 ILE A 88 89 THR A 89 3.7790 1 1 1 1 2 372 0 +R 861 88 ILE A 88 90 ALA A 90 5.7738 1 1 0 0 0 1 0 +R 862 88 ILE A 88 91 SER A 91 5.4216 1 1 1 1 4 23 0 +R 863 88 ILE A 88 92 VAL A 92 6.1853 1 1 1 1 212 212 0 +R 864 89 THR A 89 14 ARG A 14 10.0339 0 1 1 1 3 3 0 +R 865 89 THR A 89 15 HIS A 15 7.1554 1 1 1 1 55 149 0 +R 866 89 THR A 89 87 ASP A 87 5.6671 1 1 1 1 106 158 0 +R 867 89 THR A 89 88 ILE A 88 3.7790 1 1 0 0 -8 335 0 +R 868 89 THR A 89 90 ALA A 90 3.8512 1 1 1 1 13 372 0 +R 869 89 THR A 89 91 SER A 91 5.5409 1 0 0 0 0 0 0 +R 870 89 THR A 89 92 VAL A 92 5.2314 1 0 0 0 0 0 0 +R 871 89 THR A 89 93 ASN A 93 6.2336 1 1 1 1 47 199 0 +R 872 90 ALA A 90 78 ILE A 78 8.2888 0 1 1 1 45 45 0 +R 873 90 ALA A 90 82 ALA A 82 6.7558 1 1 1 0 -58 158 0 +R 874 90 ALA A 90 83 LEU A 83 6.0317 1 1 1 1 27 27 0 +R 875 90 ALA A 90 87 ASP A 87 7.7602 0 1 1 0 -2 4 0 +R 876 90 ALA A 90 88 ILE A 88 5.7738 1 0 0 0 0 0 0 +R 877 90 ALA A 90 89 THR A 89 3.8512 1 1 1 0 -8 373 0 +R 878 90 ALA A 90 91 SER A 91 3.8404 1 1 1 1 8 356 0 +R 879 90 ALA A 90 92 VAL A 92 5.4287 1 0 0 0 0 0 0 +R 880 90 ALA A 90 93 ASN A 93 5.1567 1 1 0 0 -1 28 0 +R 881 90 ALA A 90 94 CYS A 94 6.0715 1 1 1 1 85 133 0 +R 882 91 SER A 91 55 ILE A 55 7.4339 1 1 1 0 -16 119 0 +R 883 91 SER A 91 58 ILE A 58 7.7587 1 1 0 0 -3 14 0 +R 884 91 SER A 91 83 LEU A 83 5.2891 1 1 1 1 145 220 0 +R 885 91 SER A 91 88 ILE A 88 5.4216 1 1 0 0 0 37 0 +R 886 91 SER A 91 89 THR A 89 5.5409 1 0 0 0 0 0 0 +R 887 91 SER A 91 90 ALA A 90 3.8404 1 1 0 0 -14 349 0 +R 888 91 SER A 91 92 VAL A 92 3.7489 1 1 1 1 20 342 0 +R 889 91 SER A 91 93 ASN A 93 5.6148 1 0 0 0 0 0 0 +R 890 91 SER A 91 94 CYS A 94 5.2309 1 0 0 0 0 0 0 +R 891 91 SER A 91 95 ALA A 95 5.9715 1 1 1 1 115 161 0 +R 892 92 VAL A 92 12 MET A 12 7.4759 0 1 1 1 3 3 0 +R 893 92 VAL A 92 15 HIS A 15 7.1674 1 1 1 1 73 167 0 +R 894 92 VAL A 92 17 LEU A 17 7.6268 1 1 1 1 98 98 0 +R 895 92 VAL A 92 56 LEU A 56 8.3697 0 1 1 1 3 3 0 +R 896 92 VAL A 92 88 ILE A 88 6.1853 1 1 1 1 57 201 0 +R 897 92 VAL A 92 89 THR A 89 5.2314 1 1 0 0 -8 9 0 +R 898 92 VAL A 92 90 ALA A 90 5.4287 1 0 0 0 0 0 0 +R 899 92 VAL A 92 91 SER A 91 3.7489 1 1 0 0 -15 368 0 +R 900 92 VAL A 92 93 ASN A 93 3.8908 1 1 1 0 0 322 0 +R 901 92 VAL A 92 94 CYS A 94 5.4376 1 0 0 0 0 0 0 +R 902 92 VAL A 92 95 ALA A 95 4.9484 1 1 0 0 0 11 0 +R 903 92 VAL A 92 96 LYS A 96 6.2030 1 1 1 1 105 187 0 +R 904 93 ASN A 93 15 HIS A 15 8.5240 0 1 1 0 -2 4 0 +R 905 93 ASN A 93 89 THR A 89 6.2336 1 1 1 0 -125 178 0 +R 906 93 ASN A 93 90 ALA A 90 5.1567 1 1 1 0 -12 29 0 +R 907 93 ASN A 93 91 SER A 91 5.6148 1 0 0 0 0 0 0 +R 908 93 ASN A 93 92 VAL A 92 3.8908 1 1 0 0 -18 349 0 +R 909 93 ASN A 93 94 CYS A 94 3.7884 1 1 1 0 -4 357 0 +R 910 93 ASN A 93 95 ALA A 95 5.4444 1 0 0 0 0 0 0 +R 911 93 ASN A 93 96 LYS A 96 5.2091 1 1 1 0 -70 183 0 +R 912 93 ASN A 93 97 LYS A 97 6.7656 1 1 1 1 21 82 0 +R 913 94 CYS A 94 58 ILE A 58 8.1513 1 1 1 1 12 144 0 +R 914 94 CYS A 94 63 TRP A 63 7.4243 1 1 0 0 0 1 0 +R 915 94 CYS A 94 76 CYS A 76 5.4641 1 1 1 1 17 234 0 +R 916 94 CYS A 94 78 ILE A 78 8.8596 1 1 1 1 8 9 0 +R 917 94 CYS A 94 83 LEU A 83 8.8633 1 0 0 0 0 0 0 +R 918 94 CYS A 94 90 ALA A 90 6.0715 1 1 1 0 -62 76 0 +R 919 94 CYS A 94 91 SER A 91 5.2309 1 1 0 0 -11 11 0 +R 920 94 CYS A 94 92 VAL A 92 5.4376 1 0 0 0 0 0 0 +R 921 94 CYS A 94 93 ASN A 93 3.7884 1 1 0 0 -18 346 0 +R 922 94 CYS A 94 95 ALA A 95 3.8019 1 1 1 1 14 349 0 +R 923 94 CYS A 94 96 LYS A 96 5.3813 1 0 0 0 0 0 0 +R 924 94 CYS A 94 97 LYS A 97 5.2610 1 1 1 1 58 70 0 +R 925 94 CYS A 94 98 ILE A 98 6.4204 1 1 1 1 41 63 0 +R 926 95 ALA A 95 28 TRP A 28 9.8227 1 1 1 1 23 23 0 +R 927 95 ALA A 95 56 LEU A 56 7.7189 1 1 1 1 73 73 0 +R 928 95 ALA A 95 58 ILE A 58 7.7436 1 0 0 0 0 0 0 +R 929 95 ALA A 95 91 SER A 91 5.9715 1 1 1 0 -55 81 0 +R 930 95 ALA A 95 92 VAL A 92 4.9484 1 1 0 0 -18 18 0 +R 931 95 ALA A 95 93 ASN A 93 5.4444 1 0 0 0 0 0 0 +R 932 95 ALA A 95 94 CYS A 94 3.8019 1 1 0 0 -25 362 0 +R 933 95 ALA A 95 96 LYS A 96 3.7722 1 1 1 1 15 324 0 +R 934 95 ALA A 95 97 LYS A 97 5.3622 1 0 0 0 0 0 0 +R 935 95 ALA A 95 98 ILE A 98 4.9201 1 1 0 0 0 11 0 +R 936 95 ALA A 95 99 VAL A 99 6.0948 1 1 1 1 142 164 0 +R 937 95 ALA A 95 108 TRP A 108 10.0572 1 1 1 1 87 115 0 +R 938 96 LYS A 96 15 HIS A 15 10.3010 1 1 1 1 121 172 0 +R 939 96 LYS A 96 16 GLY A 16 9.2491 1 1 0 0 0 33 0 +R 940 96 LYS A 96 17 LEU A 17 7.9140 1 1 1 1 21 25 0 +R 941 96 LYS A 96 20 TYR A 20 7.7283 1 1 1 1 24 198 0 +R 942 96 LYS A 96 92 VAL A 92 6.2030 1 1 1 0 -37 54 0 +R 943 96 LYS A 96 93 ASN A 93 5.2091 1 1 0 0 -108 108 0 +R 944 96 LYS A 96 94 CYS A 94 5.3813 1 0 0 0 0 0 0 +R 945 96 LYS A 96 95 ALA A 95 3.7722 1 1 0 0 -8 346 0 +R 946 96 LYS A 96 97 LYS A 97 3.8989 1 1 1 1 13 346 0 +R 947 96 LYS A 96 98 ILE A 98 5.4629 1 0 0 0 0 0 0 +R 948 96 LYS A 96 99 VAL A 99 5.3592 1 1 0 0 0 2 0 +R 949 96 LYS A 96 100 SER A 100 6.2176 1 1 1 1 160 160 0 +R 950 97 LYS A 97 63 TRP A 63 9.0609 1 1 1 1 19 21 0 +R 951 97 LYS A 97 75 LEU A 75 8.3701 0 1 0 0 -14 51 0 +R 952 97 LYS A 97 76 CYS A 76 7.3462 1 1 1 1 4 83 0 +R 953 97 LYS A 97 93 ASN A 93 6.7656 1 1 0 0 -41 44 0 +R 954 97 LYS A 97 94 CYS A 94 5.2610 1 1 0 0 -30 31 0 +R 955 97 LYS A 97 95 ALA A 95 5.3622 1 0 0 0 0 0 0 +R 956 97 LYS A 97 96 LYS A 96 3.8989 1 1 0 0 -9 339 0 +R 957 97 LYS A 97 98 ILE A 98 3.7983 1 1 1 0 -7 374 0 +R 958 97 LYS A 97 99 VAL A 99 5.7111 1 0 0 0 0 0 0 +R 959 97 LYS A 97 100 SER A 100 5.2541 1 1 1 1 55 84 0 +R 960 97 LYS A 97 101 ASP A 101 6.4431 1 1 1 1 20 69 0 +R 961 98 ILE A 98 58 ILE A 58 8.9872 1 1 1 1 183 184 0 +R 962 98 ILE A 98 63 TRP A 63 8.1327 1 1 1 1 140 169 0 +R 963 98 ILE A 98 94 CYS A 94 6.4204 1 1 0 0 -44 44 0 +R 964 98 ILE A 98 95 ALA A 95 4.9201 1 1 0 0 -12 12 0 +R 965 98 ILE A 98 96 LYS A 96 5.4629 1 0 0 0 0 0 0 +R 966 98 ILE A 98 97 LYS A 97 3.7983 1 1 0 0 -16 354 0 +R 967 98 ILE A 98 99 VAL A 99 3.8242 1 1 1 1 2 332 0 +R 968 98 ILE A 98 100 SER A 100 5.4112 1 0 0 0 0 0 0 +R 969 98 ILE A 98 101 ASP A 101 5.2299 1 1 0 0 -140 143 0 +R 970 98 ILE A 98 104 GLY A 104 7.3510 0 1 0 0 -10 10 0 +R 971 98 ILE A 98 107 ALA A 107 7.4522 1 1 1 1 145 145 0 +R 972 98 ILE A 98 108 TRP A 108 9.5294 1 1 1 1 25 25 0 +R 973 99 VAL A 99 20 TYR A 20 8.7657 1 1 1 1 115 115 0 +R 974 99 VAL A 99 21 ARG A 21 7.5366 1 1 1 0 -13 25 0 +R 975 99 VAL A 99 23 TYR A 23 9.4052 1 1 1 1 105 105 0 +R 976 99 VAL A 99 28 TRP A 28 10.7709 1 1 1 1 28 28 0 +R 977 99 VAL A 99 95 ALA A 95 6.0948 1 1 1 0 -50 86 0 +R 978 99 VAL A 99 96 LYS A 96 5.3592 1 1 0 0 -29 29 0 +R 979 99 VAL A 99 97 LYS A 97 5.7111 1 0 0 0 0 0 0 +R 980 99 VAL A 99 98 ILE A 98 3.8242 1 1 0 0 -4 345 0 +R 981 99 VAL A 99 100 SER A 100 3.8421 1 1 1 0 -7 356 0 +R 982 99 VAL A 99 101 ASP A 101 5.3917 1 0 0 0 0 0 0 +R 983 99 VAL A 99 102 GLY A 102 7.0039 0 1 1 1 1 1 0 +R 984 99 VAL A 99 104 GLY A 104 4.3408 1 1 0 0 0 177 0 +R 985 99 VAL A 99 105 MET A 105 5.6156 1 1 1 1 46 46 0 +R 986 99 VAL A 99 108 TRP A 108 9.1731 1 1 1 1 5 5 0 +R 987 100 SER A 100 20 TYR A 20 9.2326 1 1 1 1 32 33 0 +R 988 100 SER A 100 21 ARG A 21 7.2028 1 1 1 1 183 249 0 +R 989 100 SER A 100 96 LYS A 96 6.2176 1 1 1 1 89 119 0 +R 990 100 SER A 100 97 LYS A 97 5.2541 1 1 0 0 0 48 0 +R 991 100 SER A 100 98 ILE A 98 5.4112 1 0 0 0 0 0 0 +R 992 100 SER A 100 99 VAL A 99 3.8421 1 1 0 0 -13 357 0 +R 993 100 SER A 100 101 ASP A 101 3.8203 1 1 1 1 13 316 0 +R 994 100 SER A 100 102 GLY A 102 5.9600 1 1 1 1 44 50 0 +R 995 101 ASP A 101 63 TRP A 63 11.5849 1 1 0 0 -131 140 0 +R 996 101 ASP A 101 75 LEU A 75 10.9431 0 1 0 0 -44 44 0 +R 997 101 ASP A 101 97 LYS A 97 6.4431 1 1 0 0 -35 37 0 +R 998 101 ASP A 101 98 ILE A 98 5.2299 1 1 0 0 -86 92 0 +R 999 101 ASP A 101 99 VAL A 99 5.3917 1 0 0 0 0 0 0 +R 1000 101 ASP A 101 100 SER A 100 3.8203 1 1 0 0 -8 347 0 +R 1001 101 ASP A 101 102 GLY A 102 3.7587 1 1 1 1 27 326 0 +R 1002 101 ASP A 101 103 ASN A 103 6.3794 1 1 1 1 17 20 0 +R 1003 102 GLY A 102 99 VAL A 99 7.0039 0 1 0 0 0 1 0 +R 1004 102 GLY A 102 100 SER A 100 5.9600 1 1 1 1 29 43 0 +R 1005 102 GLY A 102 101 ASP A 101 3.7587 1 1 0 0 -28 409 0 +R 1006 102 GLY A 102 103 ASN A 103 3.8452 1 1 1 1 49 380 0 +R 1007 102 GLY A 102 104 GLY A 104 5.4960 1 1 1 1 2 18 0 +R 1008 103 ASN A 103 23 TYR A 23 12.4992 0 1 0 0 0 1 0 +R 1009 103 ASN A 103 101 ASP A 101 6.3794 1 1 1 0 -1 11 0 +R 1010 103 ASN A 103 102 GLY A 102 3.8452 1 1 1 1 10 398 0 +R 1011 103 ASN A 103 104 GLY A 104 3.8263 1 1 1 1 18 340 0 +R 1012 103 ASN A 103 105 MET A 105 6.4440 1 0 0 0 0 0 0 +R 1013 103 ASN A 103 106 ASN A 106 5.4867 1 1 1 1 228 242 0 +R 1014 103 ASN A 103 107 ALA A 107 6.1089 0 1 1 0 -27 32 0 +R 1015 104 GLY A 104 23 TYR A 23 8.8920 1 1 0 0 0 56 0 +R 1016 104 GLY A 104 99 VAL A 99 4.3408 1 1 1 1 6 132 0 +R 1017 104 GLY A 104 102 GLY A 102 5.4960 1 1 1 1 2 26 0 +R 1018 104 GLY A 104 103 ASN A 103 3.8263 1 1 0 0 -32 376 0 +R 1019 104 GLY A 104 105 MET A 105 3.8395 1 1 1 1 27 367 0 +R 1020 104 GLY A 104 106 ASN A 106 5.3817 1 1 1 1 5 5 0 +R 1021 104 GLY A 104 107 ALA A 107 6.2555 1 1 1 0 -10 94 0 +R 1022 105 MET A 105 23 TYR A 23 8.1535 1 1 1 1 72 178 0 +R 1023 105 MET A 105 27 ASN A 27 8.5492 1 1 0 0 -13 66 0 +R 1024 105 MET A 105 28 TRP A 28 8.7636 1 1 1 1 53 65 0 +R 1025 105 MET A 105 31 ALA A 31 8.7729 1 1 1 1 99 99 0 +R 1026 105 MET A 105 99 VAL A 99 5.6156 1 1 1 1 57 57 0 +R 1027 105 MET A 105 103 ASN A 103 6.4440 1 0 0 0 0 0 0 +R 1028 105 MET A 105 104 GLY A 104 3.8395 1 1 0 0 0 343 0 +R 1029 105 MET A 105 106 ASN A 106 3.7700 1 1 1 1 18 321 0 +R 1030 105 MET A 105 107 ALA A 107 5.0282 1 1 0 0 0 4 0 +R 1031 105 MET A 105 108 TRP A 108 5.6343 1 1 1 1 127 148 0 +R 1032 105 MET A 105 111 TRP A 111 6.7413 1 1 1 1 127 195 0 +R 1033 106 ASN A 106 23 TYR A 23 11.3626 0 1 1 1 22 22 0 +R 1034 106 ASN A 106 103 ASN A 103 5.4867 1 1 1 1 84 175 0 +R 1035 106 ASN A 106 104 GLY A 104 5.3817 1 0 0 0 0 0 0 +R 1036 106 ASN A 106 105 MET A 105 3.7700 1 1 0 0 -17 357 0 +R 1037 106 ASN A 106 107 ALA A 107 3.8144 1 1 1 1 11 348 0 +R 1038 106 ASN A 106 108 TRP A 108 5.0992 1 1 1 1 12 12 0 +R 1039 106 ASN A 106 111 TRP A 111 6.6687 1 1 0 0 -47 56 0 +R 1040 106 ASN A 106 112 ARG A 112 5.3634 1 1 1 1 52 179 0 +R 1041 106 ASN A 106 116 LYS A 116 8.4376 1 1 1 1 81 209 0 +R 1042 107 ALA A 107 63 TRP A 63 11.8922 0 1 1 1 15 15 0 +R 1043 107 ALA A 107 98 ILE A 98 7.4522 1 1 1 1 134 144 0 +R 1044 107 ALA A 107 103 ASN A 103 6.1089 0 1 1 1 17 34 0 +R 1045 107 ALA A 107 104 GLY A 104 6.2555 1 1 1 0 -68 78 0 +R 1046 107 ALA A 107 105 MET A 105 5.0282 1 0 0 0 0 0 0 +R 1047 107 ALA A 107 106 ASN A 106 3.8144 1 1 0 0 -31 366 0 +R 1048 107 ALA A 107 108 TRP A 108 3.8323 1 1 1 1 1 344 0 +R 1049 107 ALA A 107 109 VAL A 109 6.1899 1 1 1 1 11 40 0 +R 1050 107 ALA A 107 112 ARG A 112 7.9613 0 1 1 1 4 4 0 +R 1051 108 TRP A 108 28 TRP A 28 10.2074 1 1 1 1 79 79 0 +R 1052 108 TRP A 108 31 ALA A 31 7.3841 0 1 1 1 1 1 0 +R 1053 108 TRP A 108 35 GLU A 35 8.1006 1 1 1 0 -56 82 0 +R 1054 108 TRP A 108 56 LEU A 56 8.2153 1 1 1 1 43 175 0 +R 1055 108 TRP A 108 57 GLN A 57 8.2910 0 1 1 1 8 22 0 +R 1056 108 TRP A 108 58 ILE A 58 8.7782 0 1 0 0 -2 2 0 +R 1057 108 TRP A 108 95 ALA A 95 10.0572 1 1 1 1 155 217 0 +R 1058 108 TRP A 108 98 ILE A 98 9.5294 1 1 1 1 106 112 0 +R 1059 108 TRP A 108 99 VAL A 99 9.1731 1 1 1 1 4 4 0 +R 1060 108 TRP A 108 105 MET A 105 5.6343 1 1 1 0 -53 139 0 +R 1061 108 TRP A 108 106 ASN A 106 5.0992 1 0 0 0 0 0 0 +R 1062 108 TRP A 108 107 ALA A 107 3.8323 1 1 0 0 -33 366 0 +R 1063 108 TRP A 108 109 VAL A 109 3.7513 1 1 1 1 24 373 0 +R 1064 108 TRP A 108 110 ALA A 110 5.5900 1 0 0 0 0 0 0 +R 1065 108 TRP A 108 111 TRP A 111 5.1466 1 1 1 1 47 47 0 +R 1066 108 TRP A 108 112 ARG A 112 6.3103 1 1 1 1 120 126 0 +R 1067 109 VAL A 109 35 GLU A 35 8.4267 0 1 0 0 -59 59 0 +R 1068 109 VAL A 109 107 ALA A 107 6.1899 1 1 1 0 -7 19 0 +R 1069 109 VAL A 109 108 TRP A 108 3.7513 1 1 0 0 -3 339 0 +R 1070 109 VAL A 109 110 ALA A 110 3.8699 1 1 1 0 -4 348 0 +R 1071 109 VAL A 109 111 TRP A 111 5.3384 1 0 0 0 0 0 0 +R 1072 109 VAL A 109 112 ARG A 112 5.1089 1 1 0 0 -73 99 0 +R 1073 109 VAL A 109 113 ASN A 113 6.1028 1 1 1 1 44 250 0 +R 1074 110 ALA A 110 34 PHE A 34 5.8542 1 1 1 1 122 157 0 +R 1075 110 ALA A 110 35 GLU A 35 6.0785 1 1 0 0 -66 82 0 +R 1076 110 ALA A 110 108 TRP A 108 5.5900 1 0 0 0 0 0 0 +R 1077 110 ALA A 110 109 VAL A 109 3.8699 1 1 1 0 -23 376 0 +R 1078 110 ALA A 110 111 TRP A 111 3.7781 1 1 1 1 1 300 0 +R 1079 110 ALA A 110 112 ARG A 112 5.4225 1 0 0 0 0 0 0 +R 1080 110 ALA A 110 113 ASN A 113 5.0166 1 1 0 0 0 2 0 +R 1081 110 ALA A 110 114 ARG A 114 5.4505 1 1 1 1 153 261 0 +R 1082 110 ALA A 110 115 CYS A 115 7.0432 1 0 0 0 0 0 0 +R 1083 111 TRP A 111 23 TYR A 23 11.4919 1 1 1 1 99 99 0 +R 1084 111 TRP A 111 27 ASN A 27 7.6026 1 1 1 1 11 193 0 +R 1085 111 TRP A 111 31 ALA A 31 4.9166 1 1 1 1 14 14 0 +R 1086 111 TRP A 111 105 MET A 105 6.7413 1 1 1 1 2 178 0 +R 1087 111 TRP A 111 106 ASN A 106 6.6687 1 1 0 0 -113 113 0 +R 1088 111 TRP A 111 108 TRP A 108 5.1466 1 1 1 1 38 95 0 +R 1089 111 TRP A 111 109 VAL A 109 5.3384 1 0 0 0 0 0 0 +R 1090 111 TRP A 111 110 ALA A 110 3.7781 1 1 0 0 -34 370 0 +R 1091 111 TRP A 111 112 ARG A 112 3.7781 1 1 1 0 -31 326 0 +R 1092 111 TRP A 111 113 ASN A 113 5.5291 1 0 0 0 0 0 0 +R 1093 111 TRP A 111 114 ARG A 114 5.3790 1 0 0 0 0 0 0 +R 1094 111 TRP A 111 115 CYS A 115 4.7065 1 1 1 1 79 128 0 +R 1095 111 TRP A 111 116 LYS A 116 5.8402 1 1 1 1 317 340 0 +R 1096 111 TRP A 111 117 GLY A 117 9.5925 0 1 0 0 -2 2 0 +R 1097 112 ARG A 112 106 ASN A 106 5.3634 1 1 1 1 43 215 0 +R 1098 112 ARG A 112 107 ALA A 107 7.9613 0 1 1 1 6 6 0 +R 1099 112 ARG A 112 108 TRP A 108 6.3103 1 1 1 0 -6 24 0 +R 1100 112 ARG A 112 109 VAL A 109 5.1089 1 1 0 0 -58 149 0 +R 1101 112 ARG A 112 110 ALA A 110 5.4225 1 0 0 0 0 0 0 +R 1102 112 ARG A 112 111 TRP A 111 3.7781 1 1 0 0 -46 402 0 +R 1103 112 ARG A 112 113 ASN A 113 3.8018 1 1 1 1 50 413 0 +R 1104 112 ARG A 112 114 ARG A 114 5.8854 1 0 0 0 0 0 0 +R 1105 112 ARG A 112 116 LYS A 116 5.0012 1 1 1 0 -56 117 0 +R 1106 113 ASN A 113 109 VAL A 109 6.1028 1 1 0 0 -184 184 0 +R 1107 113 ASN A 113 110 ALA A 110 5.0166 1 1 0 0 0 1 0 +R 1108 113 ASN A 113 111 TRP A 111 5.5291 1 0 0 0 0 0 0 +R 1109 113 ASN A 113 112 ARG A 112 3.8018 1 1 1 1 12 483 0 +R 1110 113 ASN A 113 114 ARG A 114 3.7971 1 1 1 1 50 378 0 +R 1111 113 ASN A 113 115 CYS A 115 6.1707 1 0 0 0 0 0 0 +R 1112 114 ARG A 114 30 CYS A 30 8.0485 0 1 0 0 0 14 0 +R 1113 114 ARG A 114 34 PHE A 34 7.4511 1 1 1 0 -135 302 0 +R 1114 114 ARG A 114 110 ALA A 110 5.4505 1 1 1 0 -36 105 0 +R 1115 114 ARG A 114 111 TRP A 111 5.3790 1 0 0 0 0 0 0 +R 1116 114 ARG A 114 112 ARG A 112 5.8854 1 0 0 0 0 0 0 +R 1117 114 ARG A 114 113 ASN A 113 3.7971 1 1 1 1 11 420 0 +R 1118 114 ARG A 114 115 CYS A 115 3.7433 1 1 1 1 15 327 0 +R 1119 114 ARG A 114 116 LYS A 116 6.0770 1 0 0 0 0 0 0 +R 1120 114 ARG A 114 118 THR A 118 7.6414 1 1 1 0 -71 93 0 +R 1121 115 CYS A 115 30 CYS A 30 6.0621 1 1 1 1 1 281 0 +R 1122 115 CYS A 115 31 ALA A 31 6.6938 1 1 0 0 0 11 0 +R 1123 115 CYS A 115 34 PHE A 34 8.4896 1 1 0 0 0 16 0 +R 1124 115 CYS A 115 110 ALA A 110 7.0432 1 0 0 0 0 0 0 +R 1125 115 CYS A 115 111 TRP A 111 4.7065 1 1 1 1 89 123 0 +R 1126 115 CYS A 115 113 ASN A 113 6.1707 1 0 0 0 0 0 0 +R 1127 115 CYS A 115 114 ARG A 114 3.7433 1 1 0 0 -25 384 0 +R 1128 115 CYS A 115 116 LYS A 116 3.7040 1 1 1 0 -10 351 0 +R 1129 115 CYS A 115 117 GLY A 117 6.2355 1 1 1 1 2 2 0 +R 1130 115 CYS A 115 118 THR A 118 5.5424 1 1 1 1 145 145 0 +R 1131 115 CYS A 115 120 VAL A 120 6.5881 1 1 0 0 -19 19 0 +R 1132 116 LYS A 116 106 ASN A 106 8.4376 1 1 1 1 80 167 0 +R 1133 116 LYS A 116 111 TRP A 111 5.8402 1 1 1 1 35 186 0 +R 1134 116 LYS A 116 112 ARG A 112 5.0012 1 1 1 0 -34 104 0 +R 1135 116 LYS A 116 113 ASN A 113 6.5212 0 1 0 0 0 1 0 +R 1136 116 LYS A 116 114 ARG A 114 6.0770 1 1 1 1 1 1 0 +R 1137 116 LYS A 116 115 CYS A 115 3.7040 1 1 0 0 -6 350 0 +R 1138 116 LYS A 116 117 GLY A 117 3.8305 1 1 1 0 -5 378 0 +R 1139 116 LYS A 116 118 THR A 118 5.6274 1 1 1 0 -36 42 0 +R 1140 117 GLY A 117 111 TRP A 111 9.5925 0 1 0 0 -11 11 0 +R 1141 117 GLY A 117 115 CYS A 115 6.2355 1 1 1 1 2 2 0 +R 1142 117 GLY A 117 116 LYS A 116 3.8305 1 1 0 0 -24 389 0 +R 1143 117 GLY A 117 118 THR A 118 3.8121 1 1 1 1 5 362 0 +R 1144 117 GLY A 117 119 ASP A 119 6.8454 0 1 1 1 3 3 0 +R 1145 117 GLY A 117 120 VAL A 120 7.8645 0 1 0 0 -1 1 0 +R 1146 118 THR A 118 30 CYS A 30 9.7068 0 1 0 0 0 8 0 +R 1147 118 THR A 118 114 ARG A 114 7.6414 1 1 1 0 -66 98 0 +R 1148 118 THR A 118 115 CYS A 115 5.5424 1 1 1 1 38 121 0 +R 1149 118 THR A 118 116 LYS A 116 5.6274 1 1 0 0 -51 51 0 +R 1150 118 THR A 118 117 GLY A 117 3.8121 1 1 0 0 -20 397 0 +R 1151 118 THR A 118 119 ASP A 119 3.8550 1 1 1 1 39 360 0 +R 1152 118 THR A 118 120 VAL A 120 5.5102 1 1 1 0 -26 145 0 +R 1153 118 THR A 118 123 TRP A 123 10.4382 0 1 1 1 4 4 0 +R 1154 119 ASP A 119 117 GLY A 117 6.8454 0 1 1 1 2 2 0 +R 1155 119 ASP A 119 118 THR A 118 3.8550 1 1 1 1 2 342 0 +R 1156 119 ASP A 119 120 VAL A 120 3.7995 1 1 1 1 24 333 0 +R 1157 119 ASP A 119 121 GLN A 121 5.3570 1 1 1 0 -131 165 0 +R 1158 119 ASP A 119 122 ALA A 122 5.9464 1 1 1 0 -52 178 0 +R 1159 119 ASP A 119 123 TRP A 123 8.2961 0 1 1 0 -5 7 0 +R 1160 120 VAL A 120 24 SER A 24 8.3132 1 1 0 0 -27 27 0 +R 1161 120 VAL A 120 26 GLY A 26 4.8514 1 1 0 0 -2 84 0 +R 1162 120 VAL A 120 27 ASN A 27 5.7252 1 1 0 0 -182 182 0 +R 1163 120 VAL A 120 30 CYS A 30 6.6406 1 1 1 1 5 5 0 +R 1164 120 VAL A 120 115 CYS A 115 6.5881 1 1 1 0 -114 184 0 +R 1165 120 VAL A 120 118 THR A 118 5.5102 1 1 1 0 -21 53 0 +R 1166 120 VAL A 120 119 ASP A 119 3.7995 1 1 0 0 0 339 0 +R 1167 120 VAL A 120 121 GLN A 121 3.7722 1 1 1 1 5 364 0 +R 1168 120 VAL A 120 122 ALA A 122 5.1321 1 1 0 0 0 4 0 +R 1169 120 VAL A 120 123 TRP A 123 5.6692 1 1 1 1 75 93 0 +R 1170 121 GLN A 121 24 SER A 24 8.0270 0 1 0 0 -27 39 0 +R 1171 121 GLN A 121 119 ASP A 119 5.3570 1 1 1 0 -40 78 0 +R 1172 121 GLN A 121 120 VAL A 120 3.7722 1 1 1 1 14 385 0 +R 1173 121 GLN A 121 122 ALA A 122 3.7981 1 1 1 1 20 347 0 +R 1174 121 GLN A 121 123 TRP A 123 5.2614 1 0 0 0 0 0 0 +R 1175 121 GLN A 121 124 ILE A 124 5.7666 1 1 1 0 -5 212 0 +R 1176 121 GLN A 121 125 ARG A 125 6.5900 1 1 1 1 15 31 0 +R 1177 122 ALA A 122 5 ARG A 5 10.7979 1 1 1 1 28 33 0 +R 1178 122 ALA A 122 119 ASP A 119 5.9464 1 1 1 0 -111 132 0 +R 1179 122 ALA A 122 120 VAL A 120 5.1321 1 0 0 0 0 0 0 +R 1180 122 ALA A 122 121 GLN A 121 3.7981 1 1 0 0 -25 367 0 +R 1181 122 ALA A 122 123 TRP A 123 3.8012 1 1 1 1 22 381 0 +R 1182 122 ALA A 122 124 ILE A 124 5.5575 1 1 1 1 12 12 0 +R 1183 122 ALA A 122 125 ARG A 125 5.1332 1 1 1 0 -27 197 0 +R 1184 123 TRP A 123 5 ARG A 5 7.4230 1 1 1 1 60 235 0 +R 1185 123 TRP A 123 26 GLY A 26 5.1305 1 1 0 0 -12 12 0 +R 1186 123 TRP A 123 29 VAL A 29 6.3580 1 1 1 1 87 87 0 +R 1187 123 TRP A 123 30 CYS A 30 6.2969 1 1 1 1 63 137 0 +R 1188 123 TRP A 123 33 LYS A 33 9.2780 1 1 1 1 169 181 0 +R 1189 123 TRP A 123 34 PHE A 34 11.6342 1 1 1 1 115 121 0 +R 1190 123 TRP A 123 118 THR A 118 10.4382 0 1 1 1 12 12 0 +R 1191 123 TRP A 123 119 ASP A 119 8.2961 0 1 1 1 14 14 0 +R 1192 123 TRP A 123 120 VAL A 120 5.6692 1 1 0 0 -65 95 0 +R 1193 123 TRP A 123 121 GLN A 121 5.2614 1 0 0 0 0 0 0 +R 1194 123 TRP A 123 122 ALA A 122 3.8012 1 1 0 0 -32 379 0 +R 1195 123 TRP A 123 124 ILE A 124 3.7623 1 1 1 1 15 327 0 +R 1196 123 TRP A 123 125 ARG A 125 5.6814 1 0 0 0 0 0 0 +R 1197 124 ILE A 124 5 ARG A 5 7.5648 1 1 0 0 0 6 0 +R 1198 124 ILE A 124 9 ALA A 9 6.6308 1 1 1 1 111 111 0 +R 1199 124 ILE A 124 25 LEU A 25 7.3355 1 1 1 1 109 113 0 +R 1200 124 ILE A 124 26 GLY A 26 5.7057 1 1 0 0 -36 41 0 +R 1201 124 ILE A 124 29 VAL A 29 7.6402 1 1 1 1 2 2 0 +R 1202 124 ILE A 124 121 GLN A 121 5.7666 1 1 1 0 -135 159 0 +R 1203 124 ILE A 124 122 ALA A 122 5.5575 1 0 0 0 0 0 0 +R 1204 124 ILE A 124 123 TRP A 123 3.7623 1 1 0 0 -12 388 0 +R 1205 124 ILE A 124 125 ARG A 125 3.8072 1 1 1 1 13 344 0 +R 1206 124 ILE A 124 126 GLY A 126 6.3927 1 1 1 1 1 1 0 +R 1207 124 ILE A 124 127 CYS A 127 5.6869 1 1 1 1 82 107 0 +R 1208 124 ILE A 124 129 LEU A 129 8.6327 1 1 1 1 73 73 0 +R 1209 125 ARG A 125 5 ARG A 5 9.6347 1 1 1 1 174 208 0 +R 1210 125 ARG A 125 121 GLN A 121 6.5900 1 1 1 0 -20 38 0 +R 1211 125 ARG A 125 122 ALA A 122 5.1332 1 1 1 1 2 181 0 +R 1212 125 ARG A 125 123 TRP A 123 5.6814 1 0 0 0 0 0 0 +R 1213 125 ARG A 125 124 ILE A 124 3.8072 1 1 0 0 -21 350 0 +R 1214 125 ARG A 125 126 GLY A 126 3.8134 1 1 1 0 -8 370 0 +R 1215 125 ARG A 125 127 CYS A 127 5.5076 1 0 0 0 0 0 0 +R 1216 126 GLY A 126 5 ARG A 5 10.0418 0 1 1 1 2 13 0 +R 1217 126 GLY A 126 6 CYS A 6 7.9731 0 1 0 0 0 25 0 +R 1218 126 GLY A 126 124 ILE A 124 6.3927 1 1 1 1 1 1 0 +R 1219 126 GLY A 126 125 ARG A 125 3.8134 1 1 0 0 -21 405 0 +R 1220 126 GLY A 126 127 CYS A 127 3.7148 1 1 1 1 21 351 0 +R 1221 126 GLY A 126 128 ARG A 128 6.5352 1 1 1 1 10 24 0 +R 1222 127 CYS A 127 5 ARG A 5 8.4264 1 1 0 0 0 42 0 +R 1223 127 CYS A 127 6 CYS A 6 5.3179 1 1 1 1 22 251 0 +R 1224 127 CYS A 127 124 ILE A 124 5.6869 1 1 1 0 -32 103 0 +R 1225 127 CYS A 127 125 ARG A 125 5.5076 1 0 0 0 0 0 0 +R 1226 127 CYS A 127 126 GLY A 126 3.7148 1 1 1 0 -24 391 0 +R 1227 127 CYS A 127 128 ARG A 128 3.7185 1 1 1 1 10 344 0 +R 1228 127 CYS A 127 129 LEU A 129 5.8167 1 1 1 1 102 126 0 +R 1229 128 ARG A 128 6 CYS A 6 7.4354 0 1 0 0 -5 11 0 +R 1230 128 ARG A 128 10 ALA A 10 7.8262 0 1 0 0 -52 52 0 +R 1231 128 ARG A 128 126 GLY A 126 6.5352 1 1 1 0 -1 17 0 +R 1232 128 ARG A 128 127 CYS A 127 3.7185 1 1 0 0 -5 354 0 +R 1233 128 ARG A 128 129 LEU A 129 3.7614 1 1 1 0 -47 416 0 +R 1234 129 LEU A 129 9 ALA A 9 7.9700 1 1 1 0 -1 20 0 +R 1235 129 LEU A 129 10 ALA A 10 6.1221 1 1 1 0 -12 221 0 +R 1236 129 LEU A 129 13 LYS A 13 8.0834 1 1 1 0 -26 153 0 +R 1237 129 LEU A 129 25 LEU A 25 10.5318 1 1 1 1 101 101 0 +R 1238 129 LEU A 129 124 ILE A 124 8.6327 1 1 1 1 138 138 0 +R 1239 129 LEU A 129 127 CYS A 127 5.8167 1 1 1 1 31 53 0 +R 1240 129 LEU A 129 128 ARG A 128 3.7614 1 1 0 0 -27 412 0 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb new file mode 100644 index 00000000..33477ad5 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/cg.pdb @@ -0,0 +1,616 @@ +ATOM 1 BB LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 2 SC1 LYS A 1 -0.175 10.268 8.951 1.00 0.00 +ATOM 3 SC2 LYS A 1 -3.127 10.593 7.836 1.00 0.00 +ATOM 4 BB VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 5 SC1 VAL A 2 3.923 14.682 6.344 1.00 0.00 +ATOM 6 BB PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 7 SC1 PHE A 3 -2.271 14.922 9.060 1.00 0.00 +ATOM 8 SC2 PHE A 3 -2.225 13.320 10.859 1.00 0.00 +ATOM 9 SC3 PHE A 3 -3.911 13.493 10.120 1.00 0.00 +ATOM 10 BB GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 11 BB ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 12 SC1 ARG A 5 -4.291 23.082 5.095 1.00 0.00 +ATOM 13 SC2 ARG A 5 -6.292 24.514 3.025 1.00 0.00 +ATOM 14 BB CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 15 SC1 CYS A 6 -8.652 20.827 3.310 1.00 0.00 +ATOM 16 BB GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 17 SC1 GLU A 7 -5.177 13.208 6.001 1.00 0.00 +ATOM 18 BB LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 19 SC1 LEU A 8 -4.062 18.230 11.133 1.00 0.00 +ATOM 20 BB ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 21 SC1 ALA A 9 -9.039 21.012 8.954 1.00 0.00 +ATOM 22 BB ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 23 SC1 ALA A 10 -11.457 16.297 8.313 1.00 0.00 +ATOM 24 BB ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 25 SC1 ALA A 11 -8.153 14.250 12.041 1.00 0.00 +ATOM 26 BB MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 27 SC1 MET A 12 -6.277 19.726 14.570 1.00 0.00 +ATOM 28 BB LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 29 SC1 LYS A 13 -14.633 19.476 12.605 1.00 0.00 +ATOM 30 SC2 LYS A 13 -17.419 20.478 11.394 1.00 0.00 +ATOM 31 BB ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 32 SC1 ARG A 14 -13.808 12.618 13.693 1.00 0.00 +ATOM 33 SC2 ARG A 14 -12.388 9.675 14.151 1.00 0.00 +ATOM 34 BB HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 35 SC1 HIS A 15 -10.087 14.082 17.707 1.00 0.00 +ATOM 36 SC2 HIS A 15 -9.556 11.718 17.990 1.00 0.00 +ATOM 37 SC3 HIS A 15 -9.583 12.289 16.299 1.00 0.00 +ATOM 38 BB GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 39 BB LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 40 SC1 LEU A 17 -8.675 20.110 19.004 1.00 0.00 +ATOM 41 BB ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 42 SC1 ASP A 18 -14.750 24.262 14.952 1.00 0.00 +ATOM 43 BB ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 44 SC1 ASN A 19 -15.703 27.056 17.780 1.00 0.00 +ATOM 45 BB TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 46 SC1 TYR A 20 -11.624 22.480 22.680 1.00 0.00 +ATOM 47 SC2 TYR A 20 -12.378 20.931 24.472 1.00 0.00 +ATOM 48 SC3 TYR A 20 -10.403 22.290 24.823 1.00 0.00 +ATOM 49 SC4 TYR A 20 -11.170 20.782 26.643 1.00 0.00 +ATOM 50 BB ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 51 SC1 ARG A 21 -11.039 25.993 26.476 1.00 0.00 +ATOM 52 SC2 ARG A 21 -11.248 25.333 29.887 1.00 0.00 +ATOM 53 BB GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 54 BB TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 55 SC1 TYR A 23 -8.709 28.306 20.758 1.00 0.00 +ATOM 56 SC2 TYR A 23 -7.220 30.161 21.378 1.00 0.00 +ATOM 57 SC3 TYR A 23 -8.220 28.823 23.132 1.00 0.00 +ATOM 58 SC4 TYR A 23 -6.690 30.729 23.724 1.00 0.00 +ATOM 59 BB SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 60 SC1 SER A 24 -11.357 29.505 15.047 1.00 0.00 +ATOM 61 BB LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 62 SC1 LEU A 25 -11.124 23.037 12.733 1.00 0.00 +ATOM 63 BB GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 64 BB ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 65 SC1 ASN A 27 -7.130 30.091 16.604 1.00 0.00 +ATOM 66 BB TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 67 SC1 TRP A 28 -6.816 23.669 16.888 1.00 0.00 +ATOM 68 SC2 TRP A 28 -8.472 24.497 18.485 1.00 0.00 +ATOM 69 SC3 TRP A 28 -7.007 23.915 19.324 1.00 0.00 +ATOM 70 SC4 TRP A 28 -5.190 23.090 19.929 1.00 0.00 +ATOM 71 SC5 TRP A 28 -6.586 23.809 21.385 1.00 0.00 +ATOM 72 BB VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 73 SC1 VAL A 29 -5.534 23.426 10.637 1.00 0.00 +ATOM 74 BB CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 75 SC1 CYS A 30 -1.819 29.329 12.180 1.00 0.00 +ATOM 76 BB ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 77 SC1 ALA A 31 -1.089 25.781 16.704 1.00 0.00 +ATOM 78 BB ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 79 SC1 ALA A 32 -0.823 21.268 13.540 1.00 0.00 +ATOM 80 BB LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 81 SC1 LYS A 33 1.528 24.936 8.648 1.00 0.00 +ATOM 82 SC2 LYS A 33 3.181 24.241 6.023 1.00 0.00 +ATOM 83 BB PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 84 SC1 PHE A 34 3.533 28.017 11.764 1.00 0.00 +ATOM 85 SC2 PHE A 34 3.676 28.811 9.478 1.00 0.00 +ATOM 86 SC3 PHE A 34 2.119 29.392 10.320 1.00 0.00 +ATOM 87 BB GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 88 SC1 GLU A 35 4.384 24.445 17.868 1.00 0.00 +ATOM 89 BB SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 90 SC1 SER A 36 3.910 19.302 13.526 1.00 0.00 +ATOM 91 BB ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 92 SC1 ASN A 37 5.825 21.444 7.332 1.00 0.00 +ATOM 93 BB PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 94 SC1 PHE A 38 0.483 19.631 8.557 1.00 0.00 +ATOM 95 SC2 PHE A 38 -0.946 21.473 9.190 1.00 0.00 +ATOM 96 SC3 PHE A 38 -0.576 21.466 7.384 1.00 0.00 +ATOM 97 BB ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 98 SC1 ASN A 39 6.545 14.631 10.411 1.00 0.00 +ATOM 99 BB THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 100 SC1 THR A 40 2.081 11.990 13.217 1.00 0.00 +ATOM 101 BB GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 102 SC1 GLN A 41 7.443 9.446 12.260 1.00 0.00 +ATOM 103 BB ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 104 SC1 ALA A 42 7.744 17.108 14.349 1.00 0.00 +ATOM 105 BB THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 106 SC1 THR A 43 11.479 14.266 18.039 1.00 0.00 +ATOM 107 BB ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 108 SC1 ASN A 44 11.937 20.259 16.961 1.00 0.00 +ATOM 109 BB ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 110 SC1 ARG A 45 16.691 18.207 23.144 1.00 0.00 +ATOM 111 SC2 ARG A 45 18.247 15.570 23.629 1.00 0.00 +ATOM 112 BB ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 113 SC1 ASN A 46 12.650 22.425 24.012 1.00 0.00 +ATOM 114 BB THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 115 SC1 THR A 47 18.237 25.668 25.594 1.00 0.00 +ATOM 116 BB ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 117 SC1 ASP A 48 14.075 22.841 29.287 1.00 0.00 +ATOM 118 BB GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 119 BB SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 120 SC1 SER A 50 12.091 20.191 27.770 1.00 0.00 +ATOM 121 BB THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 122 SC1 THR A 51 12.864 16.026 23.443 1.00 0.00 +ATOM 123 BB ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 124 SC1 ASP A 52 9.031 21.088 22.419 1.00 0.00 +ATOM 125 BB TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 126 SC1 TYR A 53 7.247 14.330 21.880 1.00 0.00 +ATOM 127 SC2 TYR A 53 8.942 14.562 23.703 1.00 0.00 +ATOM 128 SC3 TYR A 53 9.232 12.836 22.050 1.00 0.00 +ATOM 129 SC4 TYR A 53 10.883 13.050 23.887 1.00 0.00 +ATOM 130 BB GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 131 BB ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 132 SC1 ILE A 55 0.153 16.813 14.439 1.00 0.00 +ATOM 133 BB LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 134 SC1 LEU A 56 -1.026 20.379 18.593 1.00 0.00 +ATOM 135 BB GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 136 SC1 GLN A 57 7.224 19.970 18.175 1.00 0.00 +ATOM 137 BB ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 138 SC1 ILE A 58 1.868 17.963 23.794 1.00 0.00 +ATOM 139 BB ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 140 SC1 ASN A 59 8.436 20.830 27.190 1.00 0.00 +ATOM 141 BB SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 142 SC1 SER A 60 10.130 16.060 27.751 1.00 0.00 +ATOM 143 BB ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 144 SC1 ARG A 61 9.759 21.040 32.156 1.00 0.00 +ATOM 145 SC2 ARG A 61 12.735 20.588 32.524 1.00 0.00 +ATOM 146 BB TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 147 SC1 TRP A 62 4.900 20.805 31.898 1.00 0.00 +ATOM 148 SC2 TRP A 62 6.376 22.506 31.097 1.00 0.00 +ATOM 149 SC3 TRP A 62 6.294 22.487 32.881 1.00 0.00 +ATOM 150 SC4 TRP A 62 5.936 22.198 34.895 1.00 0.00 +ATOM 151 SC5 TRP A 62 7.247 23.716 34.252 1.00 0.00 +ATOM 152 BB TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 153 SC1 TRP A 63 2.540 18.368 28.720 1.00 0.00 +ATOM 154 SC2 TRP A 63 2.928 20.769 28.863 1.00 0.00 +ATOM 155 SC3 TRP A 63 1.466 20.330 29.738 1.00 0.00 +ATOM 156 SC4 TRP A 63 -0.224 19.473 30.655 1.00 0.00 +ATOM 157 SC5 TRP A 63 0.131 21.566 30.772 1.00 0.00 +ATOM 158 BB CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 159 SC1 CYS A 64 5.333 13.856 26.701 1.00 0.00 +ATOM 160 BB ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 161 SC1 ASN A 65 8.140 9.329 31.687 1.00 0.00 +ATOM 162 BB ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 163 SC1 ASP A 66 11.494 12.585 27.497 1.00 0.00 +ATOM 164 BB GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 165 BB ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 166 SC1 ARG A 68 15.780 11.749 27.753 1.00 0.00 +ATOM 167 SC2 ARG A 68 16.274 12.982 24.249 1.00 0.00 +ATOM 168 BB THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 169 SC1 THR A 69 12.492 15.745 30.301 1.00 0.00 +ATOM 170 BB PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 171 SC1 PRO A 70 16.140 15.248 34.269 1.00 0.00 +ATOM 172 BB GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 173 BB SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 174 SC1 SER A 72 8.557 14.615 32.981 1.00 0.00 +ATOM 175 BB ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 176 SC1 ARG A 73 5.100 18.319 36.883 1.00 0.00 +ATOM 177 SC2 ARG A 73 4.230 20.855 39.417 1.00 0.00 +ATOM 178 BB ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 179 SC1 ASN A 74 3.473 11.411 32.304 1.00 0.00 +ATOM 180 BB LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 181 SC1 LEU A 75 0.573 17.947 34.719 1.00 0.00 +ATOM 182 BB CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 183 SC1 CYS A 76 -1.265 15.571 28.787 1.00 0.00 +ATOM 184 BB ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 185 SC1 ASN A 77 -1.365 8.776 33.204 1.00 0.00 +ATOM 186 BB ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 187 SC1 ILE A 78 0.451 10.630 27.183 1.00 0.00 +ATOM 188 BB PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 189 SC1 PRO A 79 3.738 6.626 27.089 1.00 0.00 +ATOM 190 BB CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 191 SC1 CYS A 80 7.217 12.587 26.174 1.00 0.00 +ATOM 192 BB SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 193 SC1 SER A 81 6.595 6.616 22.740 1.00 0.00 +ATOM 194 BB ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 195 SC1 ALA A 82 1.481 8.009 23.384 1.00 0.00 +ATOM 196 BB LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 197 SC1 LEU A 83 2.319 13.242 22.880 1.00 0.00 +ATOM 198 BB LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 199 SC1 LEU A 84 6.667 10.906 18.168 1.00 0.00 +ATOM 200 BB SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 201 SC1 SER A 85 -0.052 7.196 16.978 1.00 0.00 +ATOM 202 BB SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 203 SC1 SER A 86 0.142 7.237 11.707 1.00 0.00 +ATOM 204 BB ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 205 SC1 ASP A 87 -5.391 7.382 16.677 1.00 0.00 +ATOM 206 BB ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 207 SC1 ILE A 88 -4.687 13.702 15.370 1.00 0.00 +ATOM 208 BB THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 209 SC1 THR A 89 -7.305 9.653 19.626 1.00 0.00 +ATOM 210 BB ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 211 SC1 ALA A 90 -2.331 10.290 22.751 1.00 0.00 +ATOM 212 BB SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 213 SC1 SER A 91 -0.683 14.603 19.718 1.00 0.00 +ATOM 214 BB VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 215 SC1 VAL A 92 -6.856 15.900 19.617 1.00 0.00 +ATOM 216 BB ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 217 SC1 ASN A 93 -7.766 12.659 24.393 1.00 0.00 +ATOM 218 BB CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 219 SC1 CYS A 94 -0.957 16.123 26.475 1.00 0.00 +ATOM 220 BB ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 221 SC1 ALA A 95 -3.774 19.698 22.627 1.00 0.00 +ATOM 222 BB LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 223 SC1 LYS A 96 -9.033 18.462 24.585 1.00 0.00 +ATOM 224 SC2 LYS A 96 -11.333 17.085 22.831 1.00 0.00 +ATOM 225 BB LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 226 SC1 LYS A 97 -5.546 17.841 30.375 1.00 0.00 +ATOM 227 SC2 LYS A 97 -7.854 16.295 31.743 1.00 0.00 +ATOM 228 BB ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 229 SC1 ILE A 98 -0.911 21.639 26.782 1.00 0.00 +ATOM 230 BB VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 231 SC1 VAL A 99 -6.389 24.959 25.034 1.00 0.00 +ATOM 232 BB SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 233 SC1 SER A 100 -8.629 23.014 29.561 1.00 0.00 +ATOM 234 BB ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 235 SC1 ASP A 101 -2.145 24.522 32.746 1.00 0.00 +ATOM 236 BB GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 237 BB ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 238 SC1 ASN A 103 -0.657 31.446 30.604 1.00 0.00 +ATOM 239 BB GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 240 BB MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 241 SC1 MET A 105 -4.583 27.642 20.426 1.00 0.00 +ATOM 242 BB ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 243 SC1 ASN A 106 -1.234 33.304 24.677 1.00 0.00 +ATOM 244 BB ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 245 SC1 ALA A 107 0.585 26.599 26.143 1.00 0.00 +ATOM 246 BB TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 247 SC1 TRP A 108 1.201 25.872 21.084 1.00 0.00 +ATOM 248 SC2 TRP A 108 1.421 23.478 21.263 1.00 0.00 +ATOM 249 SC3 TRP A 108 -0.097 24.022 21.986 1.00 0.00 +ATOM 250 SC4 TRP A 108 -1.738 24.948 22.755 1.00 0.00 +ATOM 251 SC5 TRP A 108 -1.597 22.821 22.864 1.00 0.00 +ATOM 252 BB VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 253 SC1 VAL A 109 6.981 29.495 20.948 1.00 0.00 +ATOM 254 BB ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 255 SC1 ALA A 110 4.783 28.117 16.262 1.00 0.00 +ATOM 256 BB TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 257 SC1 TRP A 111 -0.914 29.450 18.540 1.00 0.00 +ATOM 258 SC2 TRP A 111 -3.120 29.950 17.528 1.00 0.00 +ATOM 259 SC3 TRP A 111 -2.831 30.936 19.012 1.00 0.00 +ATOM 260 SC4 TRP A 111 -2.231 31.907 20.786 1.00 0.00 +ATOM 261 SC5 TRP A 111 -4.106 32.361 19.902 1.00 0.00 +ATOM 262 BB ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 263 SC1 ARG A 112 2.360 34.094 21.939 1.00 0.00 +ATOM 264 SC2 ARG A 112 4.788 33.235 23.642 1.00 0.00 +ATOM 265 BB ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 266 SC1 ASN A 113 6.187 34.311 18.635 1.00 0.00 +ATOM 267 BB ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 268 SC1 ARG A 114 4.636 31.613 13.473 1.00 0.00 +ATOM 269 SC2 ARG A 114 6.636 30.401 10.985 1.00 0.00 +ATOM 270 BB CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 271 SC1 CYS A 115 -0.808 30.194 14.254 1.00 0.00 +ATOM 272 BB LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 273 SC1 LYS A 116 -2.027 35.559 19.418 1.00 0.00 +ATOM 274 SC2 LYS A 116 -2.220 36.558 22.473 1.00 0.00 +ATOM 275 BB GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 276 BB THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 277 SC1 THR A 118 -2.485 35.254 11.745 1.00 0.00 +ATOM 278 BB ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 279 SC1 ASP A 119 -8.345 35.153 7.571 1.00 0.00 +ATOM 280 BB VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 281 SC1 VAL A 120 -6.503 31.706 12.841 1.00 0.00 +ATOM 282 BB GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 283 SC1 GLN A 121 -12.840 31.907 8.761 1.00 0.00 +ATOM 284 BB ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 285 SC1 ALA A 122 -6.378 31.657 5.724 1.00 0.00 +ATOM 286 BB TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 287 SC1 TRP A 123 -4.923 27.686 8.656 1.00 0.00 +ATOM 288 SC2 TRP A 123 -3.421 29.540 9.108 1.00 0.00 +ATOM 289 SC3 TRP A 123 -2.625 28.266 8.146 1.00 0.00 +ATOM 290 SC4 TRP A 123 -2.046 26.596 7.064 1.00 0.00 +ATOM 291 SC5 TRP A 123 -0.697 28.183 7.392 1.00 0.00 +ATOM 292 BB ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 293 SC1 ILE A 124 -10.902 25.947 8.637 1.00 0.00 +ATOM 294 BB ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 295 SC1 ARG A 125 -10.343 29.456 2.036 1.00 0.00 +ATOM 296 SC2 ARG A 125 -7.917 30.428 0.891 1.00 0.00 +ATOM 297 BB GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 298 BB CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 299 SC1 CYS A 127 -10.025 22.210 4.507 1.00 0.00 +ATOM 300 BB ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 301 SC1 ARG A 128 -16.241 17.914 2.040 1.00 0.00 +ATOM 302 SC2 ARG A 128 -15.487 16.199 -0.582 1.00 0.00 +ATOM 303 BB LEU A 129 -17.104 19.979 6.793 1.00 0.00 +ATOM 304 SC1 LEU A 129 -13.806 20.960 8.017 1.00 0.00 +ATOM 305 CA LYS A 1 2.639 11.475 9.582 1.00 0.00 +ATOM 306 CA VAL A 2 1.690 13.537 6.781 1.00 0.00 +ATOM 307 CA PHE A 3 -0.462 15.938 6.712 1.00 0.00 +ATOM 308 CA GLY A 4 -3.140 17.400 5.451 1.00 0.00 +ATOM 309 CA ARG A 5 -4.795 20.126 6.006 1.00 0.00 +ATOM 310 CA CYS A 6 -7.808 18.930 5.720 1.00 0.00 +ATOM 311 CA GLU A 7 -7.382 16.259 7.180 1.00 0.00 +ATOM 312 CA LEU A 8 -6.702 17.550 9.915 1.00 0.00 +ATOM 313 CA ALA A 9 -9.165 19.238 10.352 1.00 0.00 +ATOM 314 CA ALA A 10 -11.115 16.799 10.385 1.00 0.00 +ATOM 315 CA ALA A 11 -9.799 15.341 12.828 1.00 0.00 +ATOM 316 CA MET A 12 -10.001 17.627 14.914 1.00 0.00 +ATOM 317 CA LYS A 13 -13.057 17.914 14.703 1.00 0.00 +ATOM 318 CA ARG A 14 -13.733 15.012 15.508 1.00 0.00 +ATOM 319 CA HIS A 15 -11.988 15.613 18.357 1.00 0.00 +ATOM 320 CA GLY A 16 -13.198 18.589 19.528 1.00 0.00 +ATOM 321 CA LEU A 17 -11.512 21.352 18.621 1.00 0.00 +ATOM 322 CA ASP A 18 -13.779 23.076 17.745 1.00 0.00 +ATOM 323 CA ASN A 19 -14.017 25.660 19.997 1.00 0.00 +ATOM 324 CA TYR A 20 -12.098 24.907 22.104 1.00 0.00 +ATOM 325 CA ARG A 21 -12.138 27.347 24.261 1.00 0.00 +ATOM 326 CA GLY A 22 -12.733 29.396 21.691 1.00 0.00 +ATOM 327 CA TYR A 23 -10.999 27.802 19.437 1.00 0.00 +ATOM 328 CA SER A 24 -10.710 27.715 16.317 1.00 0.00 +ATOM 329 CA LEU A 25 -9.704 25.486 13.971 1.00 0.00 +ATOM 330 CA GLY A 26 -7.516 27.367 12.601 1.00 0.00 +ATOM 331 CA ASN A 27 -5.621 27.444 15.114 1.00 0.00 +ATOM 332 CA TRP A 28 -4.823 24.437 15.216 1.00 0.00 +ATOM 333 CA VAL A 29 -3.693 24.286 12.296 1.00 0.00 +ATOM 334 CA CYS A 30 -1.621 26.525 12.561 1.00 0.00 +ATOM 335 CA ALA A 31 -0.017 25.310 14.844 1.00 0.00 +ATOM 336 CA ALA A 32 0.803 22.643 13.335 1.00 0.00 +ATOM 337 CA LYS A 33 2.315 23.856 11.063 1.00 0.00 +ATOM 338 CA PHE A 34 4.489 25.452 12.866 1.00 0.00 +ATOM 339 CA GLU A 35 5.438 23.062 14.808 1.00 0.00 +ATOM 340 CA SER A 36 5.460 20.261 12.481 1.00 0.00 +ATOM 341 CA ASN A 37 4.373 20.311 9.536 1.00 0.00 +ATOM 342 CA PHE A 38 2.210 17.893 10.035 1.00 0.00 +ATOM 343 CA ASN A 39 4.173 16.002 11.723 1.00 0.00 +ATOM 344 CA THR A 40 3.958 13.345 14.027 1.00 0.00 +ATOM 345 CA GLN A 41 7.384 12.897 14.242 1.00 0.00 +ATOM 346 CA ALA A 42 8.128 15.397 15.663 1.00 0.00 +ATOM 347 CA THR A 43 11.243 16.628 17.077 1.00 0.00 +ATOM 348 CA ASN A 44 12.562 18.715 19.852 1.00 0.00 +ATOM 349 CA ARG A 45 15.129 20.096 21.456 1.00 0.00 +ATOM 350 CA ASN A 46 16.041 21.551 24.473 1.00 0.00 +ATOM 351 CA THR A 47 18.023 23.297 26.635 1.00 0.00 +ATOM 352 CA ASP A 48 16.675 21.999 29.253 1.00 0.00 +ATOM 353 CA GLY A 49 16.204 18.860 28.035 1.00 0.00 +ATOM 354 CA SER A 50 13.844 18.923 26.736 1.00 0.00 +ATOM 355 CA THR A 51 11.005 17.685 24.693 1.00 0.00 +ATOM 356 CA ASP A 52 9.219 17.821 21.592 1.00 0.00 +ATOM 357 CA TYR A 53 6.010 16.280 20.504 1.00 0.00 +ATOM 358 CA GLY A 54 4.646 16.325 17.560 1.00 0.00 +ATOM 359 CA ILE A 55 2.163 18.176 16.074 1.00 0.00 +ATOM 360 CA LEU A 56 2.206 19.986 18.993 1.00 0.00 +ATOM 361 CA GLN A 57 4.751 20.064 20.691 1.00 0.00 +ATOM 362 CA ILE A 58 4.983 18.397 23.441 1.00 0.00 +ATOM 363 CA ASN A 59 6.232 18.680 26.587 1.00 0.00 +ATOM 364 CA SER A 60 8.395 16.813 28.976 1.00 0.00 +ATOM 365 CA ARG A 61 8.281 18.584 31.532 1.00 0.00 +ATOM 366 CA TRP A 62 4.865 18.317 31.928 1.00 0.00 +ATOM 367 CA TRP A 63 3.099 16.093 29.851 1.00 0.00 +ATOM 368 CA CYS A 64 5.378 13.811 29.460 1.00 0.00 +ATOM 369 CA ASN A 65 7.125 10.685 29.302 1.00 0.00 +ATOM 370 CA ASP A 66 10.804 10.101 28.348 1.00 0.00 +ATOM 371 CA GLY A 67 13.137 9.353 30.627 1.00 0.00 +ATOM 372 CA ARG A 68 15.010 12.302 30.311 1.00 0.00 +ATOM 373 CA THR A 69 13.256 14.339 32.420 1.00 0.00 +ATOM 374 CA PRO A 70 14.071 15.853 35.155 1.00 0.00 +ATOM 375 CA GLY A 71 11.144 16.674 36.571 1.00 0.00 +ATOM 376 CA SER A 72 8.817 15.450 35.411 1.00 0.00 +ATOM 377 CA ARG A 73 5.096 15.473 35.500 1.00 0.00 +ATOM 378 CA ASN A 74 2.925 13.984 33.620 1.00 0.00 +ATOM 379 CA LEU A 75 -0.018 15.290 33.079 1.00 0.00 +ATOM 380 CA CYS A 76 -1.120 13.150 30.669 1.00 0.00 +ATOM 381 CA ASN A 77 -0.240 10.215 31.165 1.00 0.00 +ATOM 382 CA ILE A 78 2.290 9.735 29.023 1.00 0.00 +ATOM 383 CA PRO A 79 4.082 8.766 26.632 1.00 0.00 +ATOM 384 CA CYS A 80 5.658 10.589 24.229 1.00 0.00 +ATOM 385 CA SER A 81 5.429 8.481 21.897 1.00 0.00 +ATOM 386 CA ALA A 82 2.295 8.651 21.623 1.00 0.00 +ATOM 387 CA LEU A 83 2.615 11.581 20.063 1.00 0.00 +ATOM 388 CA LEU A 84 3.681 10.054 17.106 1.00 0.00 +ATOM 389 CA SER A 85 1.264 9.077 15.966 1.00 0.00 +ATOM 390 CA SER A 86 -1.140 8.821 13.379 1.00 0.00 +ATOM 391 CA ASP A 87 -2.939 9.008 15.828 1.00 0.00 +ATOM 392 CA ILE A 88 -4.179 12.019 17.409 1.00 0.00 +ATOM 393 CA THR A 89 -5.604 11.572 20.168 1.00 0.00 +ATOM 394 CA ALA A 90 -3.403 12.099 22.406 1.00 0.00 +ATOM 395 CA SER A 91 -2.701 15.008 21.510 1.00 0.00 +ATOM 396 CA VAL A 92 -5.495 16.211 21.888 1.00 0.00 +ATOM 397 CA ASN A 93 -6.052 15.518 24.908 1.00 0.00 +ATOM 398 CA CYS A 94 -3.559 17.000 25.910 1.00 0.00 +ATOM 399 CA ALA A 95 -4.255 19.812 24.686 1.00 0.00 +ATOM 400 CA LYS A 96 -6.784 20.236 26.367 1.00 0.00 +ATOM 401 CA LYS A 97 -5.235 20.566 29.058 1.00 0.00 +ATOM 402 CA ILE A 98 -3.395 22.896 28.310 1.00 0.00 +ATOM 403 CA VAL A 99 -5.623 25.068 27.332 1.00 0.00 +ATOM 404 CA SER A 100 -7.076 25.024 30.315 1.00 0.00 +ATOM 405 CA ASP A 101 -4.377 26.175 32.122 1.00 0.00 +ATOM 406 CA GLY A 102 -4.573 29.668 31.411 1.00 0.00 +ATOM 407 CA ASN A 103 -2.911 30.608 28.504 1.00 0.00 +ATOM 408 CA GLY A 104 -3.754 28.780 26.490 1.00 0.00 +ATOM 409 CA MET A 105 -2.262 29.047 23.290 1.00 0.00 +ATOM 410 CA ASN A 106 0.330 30.437 24.437 1.00 0.00 +ATOM 411 CA ALA A 107 1.799 27.756 24.924 1.00 0.00 +ATOM 412 CA TRP A 108 2.266 28.283 21.836 1.00 0.00 +ATOM 413 CA VAL A 109 4.676 29.905 20.293 1.00 0.00 +ATOM 414 CA ALA A 110 3.789 29.741 17.230 1.00 0.00 +ATOM 415 CA TRP A 111 1.005 30.817 17.760 1.00 0.00 +ATOM 416 CA ARG A 112 1.738 33.540 18.922 1.00 0.00 +ATOM 417 CA ASN A 113 3.756 34.374 16.423 1.00 0.00 +ATOM 418 CA ARG A 114 1.852 33.135 13.724 1.00 0.00 +ATOM 419 CA CYS A 115 -1.437 33.238 14.504 1.00 0.00 +ATOM 420 CA LYS A 116 -1.988 35.329 16.238 1.00 0.00 +ATOM 421 CA GLY A 117 -4.045 37.726 14.692 1.00 0.00 +ATOM 422 CA THR A 118 -4.893 36.143 12.264 1.00 0.00 +ATOM 423 CA ASP A 119 -6.359 34.587 9.404 1.00 0.00 +ATOM 424 CA VAL A 120 -7.168 31.420 10.401 1.00 0.00 +ATOM 425 CA GLN A 121 -9.427 30.636 8.355 1.00 0.00 +ATOM 426 CA ALA A 122 -7.518 29.912 5.982 1.00 0.00 +ATOM 427 CA TRP A 123 -6.857 26.906 7.032 1.00 0.00 +ATOM 428 CA ILE A 124 -9.996 25.855 6.127 1.00 0.00 +ATOM 429 CA ARG A 125 -10.025 26.520 3.346 1.00 0.00 +ATOM 430 CA GLY A 126 -11.809 24.221 1.156 1.00 0.00 +ATOM 431 CA CYS A 127 -13.006 22.378 3.220 1.00 0.00 +ATOM 432 CA ARG A 128 -14.539 19.397 4.032 1.00 0.00 +ATOM 433 CA LEU A 129 -17.104 19.979 6.793 1.00 0.00 +TER 434 LEU A 129 +CONECT 1 2 4 +CONECT 2 3 +CONECT 4 5 6 +CONECT 6 7 10 +CONECT 7 8 9 +CONECT 8 9 +CONECT 10 11 +CONECT 11 12 14 +CONECT 12 13 +CONECT 14 15 16 +CONECT 16 17 18 +CONECT 18 19 20 +CONECT 20 21 22 +CONECT 22 23 24 +CONECT 24 25 26 +CONECT 26 27 28 +CONECT 28 29 31 +CONECT 29 30 +CONECT 31 32 34 +CONECT 32 33 +CONECT 34 35 38 +CONECT 35 36 37 +CONECT 36 37 +CONECT 38 39 +CONECT 39 40 41 +CONECT 41 42 43 +CONECT 43 44 45 +CONECT 45 46 50 +CONECT 46 47 48 +CONECT 47 48 49 +CONECT 48 49 +CONECT 50 51 53 +CONECT 51 52 +CONECT 53 54 +CONECT 54 55 59 +CONECT 55 56 57 +CONECT 56 57 58 +CONECT 57 58 +CONECT 59 60 61 +CONECT 61 62 63 +CONECT 63 64 +CONECT 64 65 66 +CONECT 66 67 72 +CONECT 67 68 70 +CONECT 68 70 71 +CONECT 70 71 +CONECT 72 73 74 +CONECT 74 75 76 +CONECT 76 77 78 +CONECT 78 79 80 +CONECT 80 81 83 +CONECT 81 82 +CONECT 83 84 87 +CONECT 84 85 86 +CONECT 85 86 +CONECT 87 88 89 +CONECT 89 90 91 +CONECT 91 92 93 +CONECT 93 94 97 +CONECT 94 95 96 +CONECT 95 96 +CONECT 97 98 99 +CONECT 99 100 101 +CONECT 101 102 103 +CONECT 103 104 105 +CONECT 105 106 107 +CONECT 107 108 109 +CONECT 109 110 112 +CONECT 110 111 +CONECT 112 113 114 +CONECT 114 115 116 +CONECT 116 117 118 +CONECT 118 119 +CONECT 119 120 121 +CONECT 121 122 123 +CONECT 123 124 125 +CONECT 125 126 130 +CONECT 126 127 128 +CONECT 127 128 129 +CONECT 128 129 +CONECT 130 131 +CONECT 131 132 133 +CONECT 133 134 135 +CONECT 135 136 137 +CONECT 137 138 139 +CONECT 139 140 141 +CONECT 141 142 143 +CONECT 143 144 146 +CONECT 144 145 +CONECT 146 147 152 +CONECT 147 148 150 +CONECT 148 150 151 +CONECT 150 151 +CONECT 152 153 158 +CONECT 153 154 156 +CONECT 154 156 157 +CONECT 156 157 +CONECT 158 159 160 +CONECT 160 161 162 +CONECT 162 163 164 +CONECT 164 165 +CONECT 165 166 168 +CONECT 166 167 +CONECT 168 169 170 +CONECT 170 171 172 +CONECT 172 173 +CONECT 173 174 175 +CONECT 175 176 178 +CONECT 176 177 +CONECT 178 179 180 +CONECT 180 181 182 +CONECT 182 183 184 +CONECT 184 185 186 +CONECT 186 187 188 +CONECT 188 189 190 +CONECT 190 191 192 +CONECT 192 193 194 +CONECT 194 195 196 +CONECT 196 197 198 +CONECT 198 199 200 +CONECT 200 201 202 +CONECT 202 203 204 +CONECT 204 205 206 +CONECT 206 207 208 +CONECT 208 209 210 +CONECT 210 211 212 +CONECT 212 213 214 +CONECT 214 215 216 +CONECT 216 217 218 +CONECT 218 219 220 +CONECT 220 221 222 +CONECT 222 223 225 +CONECT 223 224 +CONECT 225 226 228 +CONECT 226 227 +CONECT 228 229 230 +CONECT 230 231 232 +CONECT 232 233 234 +CONECT 234 235 236 +CONECT 236 237 +CONECT 237 238 239 +CONECT 239 240 +CONECT 240 241 242 +CONECT 242 243 244 +CONECT 244 245 246 +CONECT 246 247 252 +CONECT 247 248 250 +CONECT 248 250 251 +CONECT 250 251 +CONECT 252 253 254 +CONECT 254 255 256 +CONECT 256 257 262 +CONECT 257 258 260 +CONECT 258 260 261 +CONECT 260 261 +CONECT 262 263 265 +CONECT 263 264 +CONECT 265 266 267 +CONECT 267 268 270 +CONECT 268 269 +CONECT 270 271 272 +CONECT 272 273 275 +CONECT 273 274 +CONECT 275 276 +CONECT 276 277 278 +CONECT 278 279 280 +CONECT 280 281 282 +CONECT 282 283 284 +CONECT 284 285 286 +CONECT 286 287 292 +CONECT 287 288 290 +CONECT 288 290 291 +CONECT 290 291 +CONECT 292 293 294 +CONECT 294 295 297 +CONECT 295 296 +CONECT 297 298 +CONECT 298 299 300 +CONECT 300 301 303 +CONECT 301 302 +CONECT 303 304 +END \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation new file mode 100644 index 00000000..6209c13b --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation @@ -0,0 +1 @@ +Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command new file mode 100755 index 00000000..36791420 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command @@ -0,0 +1,11 @@ +martinize2 +-f ../aa.pdb +-ff martini3001 +-x cg.pdb +-o topol.top +-ignore HOH +-ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC +-go +-go-map ../map.map +-water-bias +-water-bias-eps E:-.5 C:1.0 H:-1.0 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp new file mode 100644 index 00000000..bcbcf614 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_atomtypes.itp @@ -0,0 +1,130 @@ +[ atomtypes ] +molecule_0_1 0.0 0 A 0.00000000 0.00000000 +molecule_0_2 0.0 0 A 0.00000000 0.00000000 +molecule_0_3 0.0 0 A 0.00000000 0.00000000 +molecule_0_4 0.0 0 A 0.00000000 0.00000000 +molecule_0_5 0.0 0 A 0.00000000 0.00000000 +molecule_0_6 0.0 0 A 0.00000000 0.00000000 +molecule_0_7 0.0 0 A 0.00000000 0.00000000 +molecule_0_8 0.0 0 A 0.00000000 0.00000000 +molecule_0_9 0.0 0 A 0.00000000 0.00000000 +molecule_0_10 0.0 0 A 0.00000000 0.00000000 +molecule_0_11 0.0 0 A 0.00000000 0.00000000 +molecule_0_12 0.0 0 A 0.00000000 0.00000000 +molecule_0_13 0.0 0 A 0.00000000 0.00000000 +molecule_0_14 0.0 0 A 0.00000000 0.00000000 +molecule_0_15 0.0 0 A 0.00000000 0.00000000 +molecule_0_16 0.0 0 A 0.00000000 0.00000000 +molecule_0_17 0.0 0 A 0.00000000 0.00000000 +molecule_0_18 0.0 0 A 0.00000000 0.00000000 +molecule_0_19 0.0 0 A 0.00000000 0.00000000 +molecule_0_20 0.0 0 A 0.00000000 0.00000000 +molecule_0_21 0.0 0 A 0.00000000 0.00000000 +molecule_0_22 0.0 0 A 0.00000000 0.00000000 +molecule_0_23 0.0 0 A 0.00000000 0.00000000 +molecule_0_24 0.0 0 A 0.00000000 0.00000000 +molecule_0_25 0.0 0 A 0.00000000 0.00000000 +molecule_0_26 0.0 0 A 0.00000000 0.00000000 +molecule_0_27 0.0 0 A 0.00000000 0.00000000 +molecule_0_28 0.0 0 A 0.00000000 0.00000000 +molecule_0_29 0.0 0 A 0.00000000 0.00000000 +molecule_0_30 0.0 0 A 0.00000000 0.00000000 +molecule_0_31 0.0 0 A 0.00000000 0.00000000 +molecule_0_32 0.0 0 A 0.00000000 0.00000000 +molecule_0_33 0.0 0 A 0.00000000 0.00000000 +molecule_0_34 0.0 0 A 0.00000000 0.00000000 +molecule_0_35 0.0 0 A 0.00000000 0.00000000 +molecule_0_36 0.0 0 A 0.00000000 0.00000000 +molecule_0_37 0.0 0 A 0.00000000 0.00000000 +molecule_0_38 0.0 0 A 0.00000000 0.00000000 +molecule_0_39 0.0 0 A 0.00000000 0.00000000 +molecule_0_40 0.0 0 A 0.00000000 0.00000000 +molecule_0_41 0.0 0 A 0.00000000 0.00000000 +molecule_0_42 0.0 0 A 0.00000000 0.00000000 +molecule_0_43 0.0 0 A 0.00000000 0.00000000 +molecule_0_44 0.0 0 A 0.00000000 0.00000000 +molecule_0_45 0.0 0 A 0.00000000 0.00000000 +molecule_0_46 0.0 0 A 0.00000000 0.00000000 +molecule_0_47 0.0 0 A 0.00000000 0.00000000 +molecule_0_48 0.0 0 A 0.00000000 0.00000000 +molecule_0_49 0.0 0 A 0.00000000 0.00000000 +molecule_0_50 0.0 0 A 0.00000000 0.00000000 +molecule_0_51 0.0 0 A 0.00000000 0.00000000 +molecule_0_52 0.0 0 A 0.00000000 0.00000000 +molecule_0_53 0.0 0 A 0.00000000 0.00000000 +molecule_0_54 0.0 0 A 0.00000000 0.00000000 +molecule_0_55 0.0 0 A 0.00000000 0.00000000 +molecule_0_56 0.0 0 A 0.00000000 0.00000000 +molecule_0_57 0.0 0 A 0.00000000 0.00000000 +molecule_0_58 0.0 0 A 0.00000000 0.00000000 +molecule_0_59 0.0 0 A 0.00000000 0.00000000 +molecule_0_60 0.0 0 A 0.00000000 0.00000000 +molecule_0_61 0.0 0 A 0.00000000 0.00000000 +molecule_0_62 0.0 0 A 0.00000000 0.00000000 +molecule_0_63 0.0 0 A 0.00000000 0.00000000 +molecule_0_64 0.0 0 A 0.00000000 0.00000000 +molecule_0_65 0.0 0 A 0.00000000 0.00000000 +molecule_0_66 0.0 0 A 0.00000000 0.00000000 +molecule_0_67 0.0 0 A 0.00000000 0.00000000 +molecule_0_68 0.0 0 A 0.00000000 0.00000000 +molecule_0_69 0.0 0 A 0.00000000 0.00000000 +molecule_0_70 0.0 0 A 0.00000000 0.00000000 +molecule_0_71 0.0 0 A 0.00000000 0.00000000 +molecule_0_72 0.0 0 A 0.00000000 0.00000000 +molecule_0_73 0.0 0 A 0.00000000 0.00000000 +molecule_0_74 0.0 0 A 0.00000000 0.00000000 +molecule_0_75 0.0 0 A 0.00000000 0.00000000 +molecule_0_76 0.0 0 A 0.00000000 0.00000000 +molecule_0_77 0.0 0 A 0.00000000 0.00000000 +molecule_0_78 0.0 0 A 0.00000000 0.00000000 +molecule_0_79 0.0 0 A 0.00000000 0.00000000 +molecule_0_80 0.0 0 A 0.00000000 0.00000000 +molecule_0_81 0.0 0 A 0.00000000 0.00000000 +molecule_0_82 0.0 0 A 0.00000000 0.00000000 +molecule_0_83 0.0 0 A 0.00000000 0.00000000 +molecule_0_84 0.0 0 A 0.00000000 0.00000000 +molecule_0_85 0.0 0 A 0.00000000 0.00000000 +molecule_0_86 0.0 0 A 0.00000000 0.00000000 +molecule_0_87 0.0 0 A 0.00000000 0.00000000 +molecule_0_88 0.0 0 A 0.00000000 0.00000000 +molecule_0_89 0.0 0 A 0.00000000 0.00000000 +molecule_0_90 0.0 0 A 0.00000000 0.00000000 +molecule_0_91 0.0 0 A 0.00000000 0.00000000 +molecule_0_92 0.0 0 A 0.00000000 0.00000000 +molecule_0_93 0.0 0 A 0.00000000 0.00000000 +molecule_0_94 0.0 0 A 0.00000000 0.00000000 +molecule_0_95 0.0 0 A 0.00000000 0.00000000 +molecule_0_96 0.0 0 A 0.00000000 0.00000000 +molecule_0_97 0.0 0 A 0.00000000 0.00000000 +molecule_0_98 0.0 0 A 0.00000000 0.00000000 +molecule_0_99 0.0 0 A 0.00000000 0.00000000 +molecule_0_100 0.0 0 A 0.00000000 0.00000000 +molecule_0_101 0.0 0 A 0.00000000 0.00000000 +molecule_0_102 0.0 0 A 0.00000000 0.00000000 +molecule_0_103 0.0 0 A 0.00000000 0.00000000 +molecule_0_104 0.0 0 A 0.00000000 0.00000000 +molecule_0_105 0.0 0 A 0.00000000 0.00000000 +molecule_0_106 0.0 0 A 0.00000000 0.00000000 +molecule_0_107 0.0 0 A 0.00000000 0.00000000 +molecule_0_108 0.0 0 A 0.00000000 0.00000000 +molecule_0_109 0.0 0 A 0.00000000 0.00000000 +molecule_0_110 0.0 0 A 0.00000000 0.00000000 +molecule_0_111 0.0 0 A 0.00000000 0.00000000 +molecule_0_112 0.0 0 A 0.00000000 0.00000000 +molecule_0_113 0.0 0 A 0.00000000 0.00000000 +molecule_0_114 0.0 0 A 0.00000000 0.00000000 +molecule_0_115 0.0 0 A 0.00000000 0.00000000 +molecule_0_116 0.0 0 A 0.00000000 0.00000000 +molecule_0_117 0.0 0 A 0.00000000 0.00000000 +molecule_0_118 0.0 0 A 0.00000000 0.00000000 +molecule_0_119 0.0 0 A 0.00000000 0.00000000 +molecule_0_120 0.0 0 A 0.00000000 0.00000000 +molecule_0_121 0.0 0 A 0.00000000 0.00000000 +molecule_0_122 0.0 0 A 0.00000000 0.00000000 +molecule_0_123 0.0 0 A 0.00000000 0.00000000 +molecule_0_124 0.0 0 A 0.00000000 0.00000000 +molecule_0_125 0.0 0 A 0.00000000 0.00000000 +molecule_0_126 0.0 0 A 0.00000000 0.00000000 +molecule_0_127 0.0 0 A 0.00000000 0.00000000 +molecule_0_128 0.0 0 A 0.00000000 0.00000000 +molecule_0_129 0.0 0 A 0.00000000 0.00000000 diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp new file mode 100644 index 00000000..1d80a41d --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/go_nbparams.itp @@ -0,0 +1,305 @@ +[ nonbond_params ] +molecule_0_7 molecule_0_3 1 0.61856233 9.41400000 ;go bond 0.6943127420198613 +molecule_0_8 molecule_0_3 1 0.64124177 9.41400000 ;go bond 0.7197695451276599 +molecule_0_8 molecule_0_4 1 0.50903643 9.41400000 ;go bond 0.5713740769670111 +molecule_0_9 molecule_0_5 1 0.55472986 9.41400000 ;go bond 0.6226632146695402 +molecule_0_10 molecule_0_6 1 0.54368812 9.41400000 ;go bond 0.6102692815201157 +molecule_0_11 molecule_0_7 1 0.55342129 9.41400000 ;go bond 0.6211943930892219 +molecule_0_12 molecule_0_8 1 0.53361672 9.41400000 ;go bond 0.5989645139498613 +molecule_0_13 molecule_0_9 1 0.53327864 9.41400000 ;go bond 0.5985850372139335 +molecule_0_14 molecule_0_10 1 0.53671899 9.41400000 ;go bond 0.6024467010331567 +molecule_0_15 molecule_0_11 1 0.53037897 9.41400000 ;go bond 0.595330266318212 +molecule_0_16 molecule_0_12 1 0.50737179 9.41400000 ;go bond 0.5695055830955082 +molecule_0_17 molecule_0_12 1 0.48713361 9.41400000 ;go bond 0.5467889885980936 +molecule_0_18 molecule_0_13 1 0.53766042 9.41400000 ;go bond 0.6035034151508717 +molecule_0_20 molecule_0_16 1 0.61569519 9.41400000 ;go bond 0.69109448834759 +molecule_0_23 molecule_0_19 1 0.33345408 9.41400000 ;go bond 0.37428954456239344 +molecule_0_24 molecule_0_18 1 0.51159570 9.41400000 ;go bond 0.5742467616612773 +molecule_0_24 molecule_0_19 1 0.47724942 9.41400000 ;go bond 0.5356943617696797 +molecule_0_25 molecule_0_9 1 0.64504569 9.41400000 ;go bond 0.7240393024330681 +molecule_0_25 molecule_0_12 1 0.70562045 9.41400000 ;go bond 0.7920321742591826 +molecule_0_25 molecule_0_13 1 0.74064090 9.41400000 ;go bond 0.8313413048383407 +molecule_0_25 molecule_0_18 1 0.53932816 9.41400000 ;go bond 0.6053753887831144 +molecule_0_27 molecule_0_22 1 0.88032159 9.41400000 ;go bond 0.9881275776497356 +molecule_0_27 molecule_0_23 1 0.61550377 9.41400000 ;go bond 0.6908796205335538 +molecule_0_28 molecule_0_12 1 0.76259122 9.41400000 ;go bond 0.8559796975673322 +molecule_0_28 molecule_0_17 1 0.72301913 9.41400000 ;go bond 0.8115615324462473 +molecule_0_28 molecule_0_23 1 0.73074896 9.41400000 ;go bond 0.820237971332657 +molecule_0_28 molecule_0_24 1 0.60820755 9.41400000 ;go bond 0.6826898970154524 +molecule_0_29 molecule_0_5 1 0.67893755 9.41400000 ;go bond 0.7620816384409441 +molecule_0_29 molecule_0_9 1 0.68543008 9.41400000 ;go bond 0.7693692478654458 +molecule_0_29 molecule_0_12 1 0.84972238 9.41400000 ;go bond 0.9537811278820617 +molecule_0_29 molecule_0_25 1 0.56612103 9.41400000 ;go bond 0.6354493737814462 +molecule_0_30 molecule_0_26 1 0.53052057 9.41400000 ;go bond 0.5954892061460799 +molecule_0_31 molecule_0_27 1 0.53475952 9.41400000 ;go bond 0.6002472707440369 +molecule_0_32 molecule_0_8 1 0.86357891 9.41400000 ;go bond 0.9693345501899973 +molecule_0_32 molecule_0_28 1 0.55212353 9.41400000 ;go bond 0.6197377072510204 +molecule_0_33 molecule_0_29 1 0.54779556 9.41400000 ;go bond 0.6148797210161288 +molecule_0_34 molecule_0_30 1 0.55336548 9.41400000 ;go bond 0.6211317466812124 +molecule_0_35 molecule_0_31 1 0.52569919 9.41400000 ;go bond 0.590077387289496 +molecule_0_36 molecule_0_32 1 0.47223535 9.41400000 ;go bond 0.5300662608889427 +molecule_0_37 molecule_0_32 1 0.50881207 9.41400000 ;go bond 0.5711222438387489 +molecule_0_37 molecule_0_33 1 0.38969170 9.41400000 ;go bond 0.4374141472808427 +molecule_0_38 molecule_0_1 1 0.57448609 9.41400000 ;go bond 0.6448388341942877 +molecule_0_38 molecule_0_2 1 0.48657983 9.41400000 ;go bond 0.546167392701615 +molecule_0_38 molecule_0_3 1 0.41787399 9.41400000 ;go bond 0.4690476911327112 +molecule_0_38 molecule_0_5 1 0.74691290 9.41400000 ;go bond 0.8383813795148045 +molecule_0_38 molecule_0_8 1 0.79461448 9.41400000 ;go bond 0.8919245972085443 +molecule_0_38 molecule_0_29 1 0.80094100 9.41400000 ;go bond 0.8990258716681456 +molecule_0_38 molecule_0_32 1 0.53035146 9.41400000 ;go bond 0.5952993899396771 +molecule_0_38 molecule_0_33 1 0.53919231 9.41400000 ;go bond 0.6052229058691948 +molecule_0_39 molecule_0_1 1 0.46661085 9.41400000 ;go bond 0.5237529677441939 +molecule_0_39 molecule_0_2 1 0.53945286 9.41400000 ;go bond 0.6055153634186972 +molecule_0_40 molecule_0_1 1 0.44540084 9.41400000 ;go bond 0.4999455361832126 +molecule_0_40 molecule_0_3 1 0.79571603 9.41400000 ;go bond 0.893161039670135 +molecule_0_41 molecule_0_1 1 0.60586911 9.41400000 ;go bond 0.6800650807838239 +molecule_0_42 molecule_0_36 1 0.56978667 9.41400000 ;go bond 0.6395639081914954 +molecule_0_44 molecule_0_35 1 0.86874460 9.41400000 ;go bond 0.9751328464876157 +molecule_0_49 molecule_0_45 1 0.60399410 9.41400000 ;go bond 0.6779604545260989 +molecule_0_50 molecule_0_45 1 0.49525002 9.41400000 ;go bond 0.5558993511673289 +molecule_0_50 molecule_0_46 1 0.36572449 9.41400000 ;go bond 0.41051185789603073 +molecule_0_51 molecule_0_43 1 0.68530935 9.41400000 ;go bond 0.7692337357434095 +molecule_0_51 molecule_0_44 1 0.46223041 9.41400000 ;go bond 0.5188360959211756 +molecule_0_51 molecule_0_45 1 0.51412646 9.41400000 ;go bond 0.5770874427896645 +molecule_0_51 molecule_0_46 1 0.56601354 9.41400000 ;go bond 0.6353287162096511 +molecule_0_52 molecule_0_43 1 0.45347572 9.41400000 ;go bond 0.5090092826613196 +molecule_0_52 molecule_0_44 1 0.34512972 9.41400000 ;go bond 0.38739501690404493 +molecule_0_52 molecule_0_46 1 0.73874223 9.41400000 ;go bond 0.8292101153618309 +molecule_0_53 molecule_0_42 1 0.47723542 9.41400000 ;go bond 0.5356786434419246 +molecule_0_53 molecule_0_43 1 0.55815954 9.41400000 ;go bond 0.6265129049059701 +molecule_0_54 molecule_0_36 1 0.57709969 9.41400000 ;go bond 0.6477724993432106 +molecule_0_54 molecule_0_40 1 0.41626389 9.41400000 ;go bond 0.46724041889962603 +molecule_0_54 molecule_0_42 1 0.36281320 9.41400000 ;go bond 0.40724404485680404 +molecule_0_55 molecule_0_3 1 0.88888031 9.41400000 ;go bond 0.9977344141571017 +molecule_0_55 molecule_0_8 1 0.96327627 9.41400000 ;go bond 1.0812410554289593 +molecule_0_55 molecule_0_32 1 0.48229461 9.41400000 ;go bond 0.5413573920108359 +molecule_0_55 molecule_0_35 1 0.53603357 9.41400000 ;go bond 0.6016773437033557 +molecule_0_55 molecule_0_36 1 0.47250951 9.41400000 ;go bond 0.5303739892670865 +molecule_0_55 molecule_0_38 1 0.53863592 9.41400000 ;go bond 0.6045983765957093 +molecule_0_55 molecule_0_39 1 0.46884965 9.41400000 ;go bond 0.5262659343028784 +molecule_0_55 molecule_0_40 1 0.49397051 9.41400000 ;go bond 0.5544631488965023 +molecule_0_56 molecule_0_31 1 0.63305577 9.41400000 ;go bond 0.7105810801311345 +molecule_0_56 molecule_0_32 1 0.57070473 9.41400000 ;go bond 0.6405943964432239 +molecule_0_56 molecule_0_35 1 0.54499611 9.41400000 ;go bond 0.6117374504966917 +molecule_0_57 molecule_0_35 1 0.59142457 9.41400000 ;go bond 0.6638516326030536 +molecule_0_57 molecule_0_36 1 0.73443635 9.41400000 ;go bond 0.8243769340599911 +molecule_0_57 molecule_0_42 1 0.68123116 9.41400000 ;go bond 0.7646561231921536 +molecule_0_57 molecule_0_43 1 0.72932038 9.41400000 ;go bond 0.8186344517277264 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molecule_0_48 1 0.83253174 9.41400000 ;go bond 0.9344852838875899 +molecule_0_61 molecule_0_50 1 0.65515556 9.41400000 ;go bond 0.7353872567523113 +molecule_0_63 molecule_0_58 1 0.62967119 9.41400000 ;go bond 0.7067820082223201 +molecule_0_63 molecule_0_59 1 0.46427561 9.41400000 ;go bond 0.521131754230626 +molecule_0_64 molecule_0_53 1 0.82959737 9.41400000 ;go bond 0.9311915604701376 +molecule_0_64 molecule_0_60 1 0.38156281 9.41400000 ;go bond 0.4282897748904594 +molecule_0_66 molecule_0_51 1 0.75019821 9.41400000 ;go bond 0.8420690218004665 +molecule_0_66 molecule_0_60 1 0.63773507 9.41400000 ;go bond 0.7158334088350374 +molecule_0_68 molecule_0_51 1 0.77962271 9.41400000 ;go bond 0.8750968992083761 +molecule_0_69 molecule_0_49 1 0.61957584 9.41400000 ;go bond 0.6954503691813763 +molecule_0_69 molecule_0_50 1 0.65269177 9.41400000 ;go bond 0.732621739205985 +molecule_0_69 molecule_0_60 1 0.57472088 9.41400000 ;go bond 0.6451023780044498 +molecule_0_69 molecule_0_61 1 0.58802307 9.41400000 ;go bond 0.6600335825309095 +molecule_0_70 molecule_0_61 1 0.65533893 9.41400000 ;go bond 0.7355930799704493 +molecule_0_72 molecule_0_60 1 0.58726083 9.41400000 ;go bond 0.6591779944295714 +molecule_0_72 molecule_0_61 1 0.44682674 9.41400000 ;go bond 0.5015460538054222 +molecule_0_72 molecule_0_64 1 0.62949829 9.41400000 ;go bond 0.7065879353028186 +molecule_0_73 molecule_0_61 1 0.53130673 9.41400000 ;go bond 0.5963716385459682 +molecule_0_73 molecule_0_62 1 0.40729971 9.41400000 ;go bond 0.4571784705977002 +molecule_0_74 molecule_0_62 1 0.44897571 9.41400000 ;go bond 0.5039581950921611 +molecule_0_74 molecule_0_63 1 0.38506256 9.41400000 ;go bond 0.43221810950469636 +molecule_0_74 molecule_0_64 1 0.43052761 9.41400000 ;go bond 0.4832509069633833 +molecule_0_74 molecule_0_65 1 0.61184241 9.41400000 ;go bond 0.6867698876930867 +molecule_0_75 molecule_0_62 1 0.52199782 9.41400000 ;go bond 0.5859227452973559 +molecule_0_75 molecule_0_63 1 0.40610455 9.41400000 ;go bond 0.45583694740556885 +molecule_0_76 molecule_0_63 1 0.46409225 9.41400000 ;go bond 0.5209259369461889 +molecule_0_78 molecule_0_63 1 0.57576077 9.41400000 ;go bond 0.6462696105707938 +molecule_0_78 molecule_0_64 1 0.45724502 9.41400000 ;go bond 0.5132401787770625 +molecule_0_78 molecule_0_65 1 0.43974215 9.41400000 ;go bond 0.4935938729629976 +molecule_0_78 molecule_0_74 1 0.56052614 9.41400000 ;go bond 0.6291693208239874 +molecule_0_79 molecule_0_64 1 0.52803406 9.41400000 ;go bond 0.5926981930678074 +molecule_0_79 molecule_0_65 1 0.39916015 9.41400000 ;go bond 0.44804212253596193 +molecule_0_80 molecule_0_53 1 0.60673469 9.41400000 ;go bond 0.6810366626079589 +molecule_0_80 molecule_0_60 1 0.73868742 9.41400000 ;go bond 0.8291485950674535 +molecule_0_80 molecule_0_64 1 0.54789421 9.41400000 ;go bond 0.6149904606975389 +molecule_0_80 molecule_0_65 1 0.47057069 9.41400000 ;go bond 0.5281977457102484 +molecule_0_80 molecule_0_66 1 0.58883652 9.41400000 ;go bond 0.6609466408239479 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1 0.48170210 9.41400000 ;go bond 0.5406923273735796 +molecule_0_85 molecule_0_81 1 0.64785523 9.41400000 ;go bond 0.7271929039256984 +molecule_0_86 molecule_0_1 1 0.53262408 9.41400000 ;go bond 0.5978503129841565 +molecule_0_86 molecule_0_3 1 0.87090844 9.41400000 ;go bond 0.9775616735724965 +molecule_0_86 molecule_0_40 1 0.60999120 9.41400000 ;go bond 0.6846919673680466 +molecule_0_88 molecule_0_8 1 0.85969619 9.41400000 ;go bond 0.9649763505137079 +molecule_0_88 molecule_0_11 1 0.71056849 9.41400000 ;go bond 0.7975861593614438 +molecule_0_88 molecule_0_12 1 0.75368061 9.41400000 ;go bond 0.8459778840905773 +molecule_0_88 molecule_0_15 1 0.77050258 9.41400000 ;go bond 0.864859899514801 +molecule_0_88 molecule_0_40 1 0.79388724 9.41400000 ;go bond 0.8911082942214028 +molecule_0_88 molecule_0_55 1 0.79641633 9.41400000 ;go bond 0.8939471074581451 +molecule_0_89 molecule_0_14 1 0.88919389 9.41400000 ;go bond 0.998086397883772 +molecule_0_89 molecule_0_15 1 0.69215886 9.41400000 ;go bond 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1 0.54860993 9.41400000 ;go bond 0.6157938252917854 +molecule_0_97 molecule_0_63 1 0.84557275 9.41400000 ;go bond 0.9491233248865086 +molecule_0_97 molecule_0_76 1 0.76910096 9.41400000 ;go bond 0.8632866370341634 +molecule_0_97 molecule_0_93 1 0.58672221 9.41400000 ;go bond 0.6585734126705566 +molecule_0_98 molecule_0_58 1 0.95186722 9.41400000 ;go bond 1.0684348259540144 +molecule_0_98 molecule_0_63 1 0.84907243 9.41400000 ;go bond 0.9530515735530009 +molecule_0_98 molecule_0_94 1 0.56734136 9.41400000 ;go bond 0.6368191395430418 +molecule_0_99 molecule_0_20 1 0.74154421 9.41400000 ;go bond 0.832355228430924 +molecule_0_99 molecule_0_21 1 0.67304644 9.41400000 ;go bond 0.7554690813350494 +molecule_0_99 molecule_0_23 1 0.88512807 9.41400000 ;go bond 0.9935226692398884 +molecule_0_99 molecule_0_95 1 0.53820962 9.41400000 ;go bond 0.604119869395205 +molecule_0_100 molecule_0_20 1 0.85755666 9.41400000 ;go bond 0.9625748060503135 +molecule_0_100 molecule_0_21 1 0.73290562 9.41400000 ;go bond 0.8226587489947874 +molecule_0_100 molecule_0_96 1 0.55353826 9.41400000 ;go bond 0.6213256912734973 +molecule_0_101 molecule_0_97 1 0.57454537 9.41400000 ;go bond 0.6449053740097164 +molecule_0_104 molecule_0_23 1 0.90496194 9.41400000 ;go bond 1.0157854279713863 +molecule_0_104 molecule_0_99 1 0.37779975 9.41400000 ;go bond 0.42406587714866395 +molecule_0_105 molecule_0_23 1 0.85792539 9.41400000 ;go bond 0.9629886926477136 +molecule_0_105 molecule_0_27 1 0.80028132 9.41400000 ;go bond 0.8982854095190085 +molecule_0_105 molecule_0_28 1 0.85914649 9.41400000 ;go bond 0.9643593287596212 +molecule_0_105 molecule_0_31 1 0.84674626 9.41400000 ;go bond 0.950440544780807 +molecule_0_105 molecule_0_99 1 0.58741430 9.41400000 ;go bond 0.6593502594081683 +molecule_0_107 molecule_0_98 1 0.70183885 9.41400000 ;go bond 0.7877874714268905 +molecule_0_108 molecule_0_28 1 0.92956079 9.41400000 ;go bond 1.0433967044744268 +molecule_0_108 molecule_0_35 1 0.82960839 9.41400000 ;go bond 0.9312039368635526 +molecule_0_108 molecule_0_56 1 0.78133210 9.41400000 ;go bond 0.8770156294387439 +molecule_0_108 molecule_0_57 1 0.77168204 9.41400000 ;go bond 0.8661838041857776 +molecule_0_108 molecule_0_98 1 0.90403083 9.41400000 ;go bond 1.014740292066367 +molecule_0_108 molecule_0_99 1 0.90315750 9.41400000 ;go bond 1.0137600206889819 +molecule_0_110 molecule_0_34 1 0.54869664 9.41400000 ;go bond 0.6158911542488904 +molecule_0_110 molecule_0_35 1 0.64980269 9.41400000 ;go bond 0.7293788607697123 +molecule_0_111 molecule_0_27 1 0.70311941 9.41400000 ;go bond 0.7892248529963473 +molecule_0_111 molecule_0_31 1 0.56259884 9.41400000 ;go bond 0.6314958500157425 +molecule_0_111 molecule_0_105 1 0.59346888 9.41400000 ;go bond 0.6661462995266982 +molecule_0_111 molecule_0_106 1 0.59882239 9.41400000 ;go bond 0.6721554100763635 +molecule_0_112 molecule_0_106 1 0.57753815 9.41400000 ;go bond 0.6482646568405853 +molecule_0_112 molecule_0_107 1 0.74260248 9.41400000 ;go bond 0.833543103918769 +molecule_0_112 molecule_0_108 1 0.53753958 9.41400000 ;go bond 0.603367775987529 +molecule_0_113 molecule_0_109 1 0.53306219 9.41400000 ;go bond 0.5983420831461288 +molecule_0_114 molecule_0_34 1 0.72771145 9.41400000 ;go bond 0.8168284821715603 +molecule_0_114 molecule_0_110 1 0.46768238 9.41400000 ;go bond 0.5249557267503717 +molecule_0_115 molecule_0_30 1 0.62277169 9.41400000 ;go bond 0.6990375917289473 +molecule_0_115 molecule_0_31 1 0.71820218 9.41400000 ;go bond 0.8061546928175227 +molecule_0_115 molecule_0_34 1 0.88387345 9.41400000 ;go bond 0.9921144054413411 +molecule_0_115 molecule_0_110 1 0.61061778 9.41400000 ;go bond 0.6853952887981661 +molecule_0_115 molecule_0_111 1 0.42196703 9.41400000 ;go bond 0.47364198031256005 +molecule_0_116 molecule_0_106 1 0.87532705 9.41400000 ;go bond 0.9825213984552684 +molecule_0_116 molecule_0_111 1 0.50113645 9.41400000 ;go bond 0.5625066449356023 +molecule_0_116 molecule_0_112 1 0.43911399 9.41400000 ;go bond 0.49288878427344174 +molecule_0_118 molecule_0_114 1 0.67078608 9.41400000 ;go bond 0.7529319131070445 +molecule_0_120 molecule_0_24 1 0.69733857 9.41400000 ;go bond 0.782736084608438 +molecule_0_120 molecule_0_26 1 0.41196240 9.41400000 ;go bond 0.46241216001948066 +molecule_0_120 molecule_0_27 1 0.56639954 9.41400000 ;go bond 0.635761991521061 +molecule_0_120 molecule_0_30 1 0.68659111 9.41400000 ;go bond 0.7706724627863119 +molecule_0_120 molecule_0_115 1 0.64848013 9.41400000 ;go bond 0.7278943320955625 +molecule_0_122 molecule_0_5 1 0.90496806 9.41400000 ;go bond 1.0157923048257507 +molecule_0_123 molecule_0_5 1 0.63785927 9.41400000 ;go bond 0.7159728234146279 +molecule_0_123 molecule_0_26 1 0.50129185 9.41400000 ;go bond 0.5626810823295224 +molecule_0_123 molecule_0_29 1 0.59480241 9.41400000 ;go bond 0.6676431279994454 +molecule_0_123 molecule_0_30 1 0.67921805 9.41400000 ;go bond 0.7623964880604177 +molecule_0_123 molecule_0_33 1 0.93299536 9.41400000 ;go bond 1.0472518822731016 +molecule_0_123 molecule_0_118 1 0.96185327 9.41400000 ;go bond 1.0796437933509648 +molecule_0_124 molecule_0_5 1 0.68943443 9.41400000 ;go bond 0.7738639843643694 +molecule_0_124 molecule_0_9 1 0.70339384 9.41400000 ;go bond 0.7895328862371291 +molecule_0_124 molecule_0_25 1 0.70011179 9.41400000 ;go bond 0.7858489085818863 +molecule_0_124 molecule_0_26 1 0.63220546 9.41400000 ;go bond 0.7096266311407308 +molecule_0_124 molecule_0_29 1 0.79807070 9.41400000 ;go bond 0.8958040736345152 +molecule_0_125 molecule_0_5 1 0.77312403 9.41400000 ;go bond 0.867802386232067 +molecule_0_125 molecule_0_121 1 0.58002816 9.41400000 ;go bond 0.6510595975914277 +molecule_0_127 molecule_0_5 1 0.79805432 9.41400000 ;go bond 0.8957856911439042 +molecule_0_127 molecule_0_6 1 0.59870073 9.41400000 ;go bond 0.6720188457372778 +molecule_0_129 molecule_0_9 1 0.77796857 9.41400000 ;go bond 0.8732401925194813 +molecule_0_129 molecule_0_10 1 0.68369587 9.41400000 ;go bond 0.7674226629042717 +molecule_0_129 molecule_0_13 1 0.81265668 9.41400000 ;go bond 0.912176279663995 +molecule_0_129 molecule_0_124 1 0.82375149 9.41400000 ;go bond 0.9246297801730708 +W molecule_0_1 1 0.47000000 1.00000000 ;water bias C +W molecule_0_2 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_3 1 0.47000000 1.00000000 ;water bias C +W molecule_0_4 1 0.41000000 1.00000000 ;water bias C +W molecule_0_9 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_10 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_17 1 0.47000000 1.00000000 ;water bias C +W molecule_0_20 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_23 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_24 1 0.47000000 1.00000000 ;water bias C +W molecule_0_29 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_30 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_31 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_32 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_39 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_42 1 0.41000000 1.00000000 ;water bias C +W molecule_0_43 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_44 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_45 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_46 1 0.47000000 1.00000000 ;water bias C +W molecule_0_50 1 0.47000000 1.00000000 ;water bias C +W molecule_0_51 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_52 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_53 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_58 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_59 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_64 1 0.47000000 1.00000000 ;water bias C +W molecule_0_65 1 0.47000000 -0.50000000 ;water bias E +W molecule_0_66 1 0.47000000 1.00000000 ;water bias C +W molecule_0_68 1 0.47000000 1.00000000 ;water bias C +W molecule_0_69 1 0.47000000 1.00000000 ;water bias C +W molecule_0_72 1 0.47000000 1.00000000 ;water bias C +W molecule_0_73 1 0.47000000 1.00000000 ;water bias C +W molecule_0_74 1 0.47000000 1.00000000 ;water bias C +W molecule_0_77 1 0.47000000 1.00000000 ;water bias C +W molecule_0_79 1 0.41000000 -0.50000000 ;water bias E +W molecule_0_88 1 0.47000000 1.00000000 ;water bias C +W molecule_0_93 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_94 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_95 1 0.41000000 -1.00000000 ;water bias H +W molecule_0_96 1 0.47000000 -1.00000000 ;water bias H +W molecule_0_119 1 0.47000000 1.00000000 ;water bias C +W molecule_0_127 1 0.47000000 1.00000000 ;water bias C +W molecule_0_128 1 0.47000000 1.00000000 ;water bias C +W molecule_0_129 1 0.47000000 1.00000000 ;water bias C diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp new file mode 100644 index 00000000..bfc214c6 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/molecule_0.itp @@ -0,0 +1,1669 @@ +; This file was generated using the following command: +; /local/lborge01/martinize_stuff/dev_go/devmartinize/bin/martinize2 -f ../aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go -go-map ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 +; martinize with vermouth 0.9.7.dev79 +; The following sequence of secondary structure +; was used for the full system: +; CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC + +; Pleas cite the following papers: +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 LYS BB 1 1 + 2 SC3 1 LYS SC1 2 0.0 + 3 SQ4p 1 LYS SC2 3 1.0 + 4 SP2 2 VAL BB 4 0.0 + 5 SC3 2 VAL SC1 5 0.0 + 6 P2 3 PHE BB 6 0.0 + 7 SC4 3 PHE SC1 7 0.0 + 8 TC5 3 PHE SC2 8 0.0 + 9 TC5 3 PHE SC3 9 0.0 + 10 SP1 4 GLY BB 10 0.0 + 11 P2 5 ARG BB 11 0.0 + 12 SC3 5 ARG SC1 12 0.0 + 13 SQ3p 5 ARG SC2 13 1.0 + 14 P2 6 CYS BB 14 0.0 + 15 TC6 6 CYS SC1 15 0.0 + 16 P2 7 GLU BB 16 0.0 + 17 Q5n 7 GLU SC1 17 -1.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 SP2 9 ALA BB 20 0.0 + 21 TC3 9 ALA SC1 21 0.0 + 22 SP2 10 ALA BB 22 0.0 + 23 TC3 10 ALA SC1 23 0.0 + 24 SP2 11 ALA BB 24 0.0 + 25 TC3 11 ALA SC1 25 0.0 + 26 P2 12 MET BB 26 0.0 + 27 C6 12 MET SC1 27 0.0 + 28 P2 13 LYS BB 28 0.0 + 29 SC3 13 LYS SC1 29 0.0 + 30 SQ4p 13 LYS SC2 30 1.0 + 31 P2 14 ARG BB 31 0.0 + 32 SC3 14 ARG SC1 32 0.0 + 33 SQ3p 14 ARG SC2 33 1.0 + 34 P2 15 HIS BB 34 0.0 + 35 TC4 15 HIS SC1 35 0.0 + 36 TN6d 15 HIS SC2 36 0.0 + 37 TN5a 15 HIS SC3 37 0.0 + 38 SP1 16 GLY BB 38 0.0 + 39 P2 17 LEU BB 39 0.0 + 40 SC2 17 LEU SC1 40 0.0 + 41 P2 18 ASP BB 41 0.0 + 42 SQ5n 18 ASP SC1 42 -1.0 + 43 P2 19 ASN BB 43 0.0 + 44 SP5 19 ASN SC1 44 0.0 + 45 P2 20 TYR BB 45 0.0 + 46 TC4 20 TYR SC1 46 0.0 + 47 TC5 20 TYR SC2 47 0.0 + 48 TC5 20 TYR SC3 48 0.0 + 49 TN6 20 TYR SC4 49 0.0 + 50 P2 21 ARG BB 50 0.0 + 51 SC3 21 ARG SC1 51 0.0 + 52 SQ3p 21 ARG SC2 52 1.0 + 53 SP1 22 GLY BB 53 0.0 + 54 P2 23 TYR BB 54 0.0 + 55 TC4 23 TYR SC1 55 0.0 + 56 TC5 23 TYR SC2 56 0.0 + 57 TC5 23 TYR SC3 57 0.0 + 58 TN6 23 TYR SC4 58 0.0 + 59 P2 24 SER BB 59 0.0 + 60 TP1 24 SER SC1 60 0.0 + 61 P2 25 LEU BB 61 0.0 + 62 SC2 25 LEU SC1 62 0.0 + 63 SP1 26 GLY BB 63 0.0 + 64 P2 27 ASN BB 64 0.0 + 65 SP5 27 ASN SC1 65 0.0 + 66 P2 28 TRP BB 66 0.0 + 67 TC4 28 TRP SC1 67 0.0 36.0 + 68 TN6d 28 TRP SC2 68 0.0 36.0 + 69 TC5 28 TRP SC3 69 0.0 0.0 + 70 TC5 28 TRP SC4 70 0.0 36.0 + 71 TC5 28 TRP SC5 71 0.0 36.0 + 72 SP2 29 VAL BB 72 0.0 + 73 SC3 29 VAL SC1 73 0.0 + 74 P2 30 CYS BB 74 0.0 + 75 TC6 30 CYS SC1 75 0.0 + 76 SP2 31 ALA BB 76 0.0 + 77 TC3 31 ALA SC1 77 0.0 + 78 SP2 32 ALA BB 78 0.0 + 79 TC3 32 ALA SC1 79 0.0 + 80 P2 33 LYS BB 80 0.0 + 81 SC3 33 LYS SC1 81 0.0 + 82 SQ4p 33 LYS SC2 82 1.0 + 83 P2 34 PHE BB 83 0.0 + 84 SC4 34 PHE SC1 84 0.0 + 85 TC5 34 PHE SC2 85 0.0 + 86 TC5 34 PHE SC3 86 0.0 + 87 P2 35 GLU BB 87 0.0 + 88 Q5n 35 GLU SC1 88 -1.0 + 89 P2 36 SER BB 89 0.0 + 90 TP1 36 SER SC1 90 0.0 + 91 P2 37 ASN BB 91 0.0 + 92 SP5 37 ASN SC1 92 0.0 + 93 P2 38 PHE BB 93 0.0 + 94 SC4 38 PHE SC1 94 0.0 + 95 TC5 38 PHE SC2 95 0.0 + 96 TC5 38 PHE SC3 96 0.0 + 97 P2 39 ASN BB 97 0.0 + 98 SP5 39 ASN SC1 98 0.0 + 99 P2 40 THR BB 99 0.0 +100 SP1 40 THR SC1 100 0.0 +101 P2 41 GLN BB 101 0.0 +102 P5 41 GLN SC1 102 0.0 +103 SP2 42 ALA BB 103 0.0 +104 TC3 42 ALA SC1 104 0.0 +105 P2 43 THR BB 105 0.0 +106 SP1 43 THR SC1 106 0.0 +107 P2 44 ASN BB 107 0.0 +108 SP5 44 ASN SC1 108 0.0 +109 P2 45 ARG BB 109 0.0 +110 SC3 45 ARG SC1 110 0.0 +111 SQ3p 45 ARG SC2 111 1.0 +112 P2 46 ASN BB 112 0.0 +113 SP5 46 ASN SC1 113 0.0 +114 P2 47 THR BB 114 0.0 +115 SP1 47 THR SC1 115 0.0 +116 P2 48 ASP BB 116 0.0 +117 SQ5n 48 ASP SC1 117 -1.0 +118 SP1 49 GLY BB 118 0.0 +119 P2 50 SER BB 119 0.0 +120 TP1 50 SER SC1 120 0.0 +121 P2 51 THR BB 121 0.0 +122 SP1 51 THR SC1 122 0.0 +123 P2 52 ASP BB 123 0.0 +124 SQ5n 52 ASP SC1 124 -1.0 +125 P2 53 TYR BB 125 0.0 +126 TC4 53 TYR SC1 126 0.0 +127 TC5 53 TYR SC2 127 0.0 +128 TC5 53 TYR SC3 128 0.0 +129 TN6 53 TYR SC4 129 0.0 +130 SP1 54 GLY BB 130 0.0 +131 P2 55 ILE BB 131 0.0 +132 SC2 55 ILE SC1 132 0.0 +133 P2 56 LEU BB 133 0.0 +134 SC2 56 LEU SC1 134 0.0 +135 P2 57 GLN BB 135 0.0 +136 P5 57 GLN SC1 136 0.0 +137 P2 58 ILE BB 137 0.0 +138 SC2 58 ILE SC1 138 0.0 +139 P2 59 ASN BB 139 0.0 +140 SP5 59 ASN SC1 140 0.0 +141 P2 60 SER BB 141 0.0 +142 TP1 60 SER SC1 142 0.0 +143 P2 61 ARG BB 143 0.0 +144 SC3 61 ARG SC1 144 0.0 +145 SQ3p 61 ARG SC2 145 1.0 +146 P2 62 TRP BB 146 0.0 +147 TC4 62 TRP SC1 147 0.0 36.0 +148 TN6d 62 TRP SC2 148 0.0 36.0 +149 TC5 62 TRP SC3 149 0.0 0.0 +150 TC5 62 TRP SC4 150 0.0 36.0 +151 TC5 62 TRP SC5 151 0.0 36.0 +152 P2 63 TRP BB 152 0.0 +153 TC4 63 TRP SC1 153 0.0 36.0 +154 TN6d 63 TRP SC2 154 0.0 36.0 +155 TC5 63 TRP SC3 155 0.0 0.0 +156 TC5 63 TRP SC4 156 0.0 36.0 +157 TC5 63 TRP SC5 157 0.0 36.0 +158 P2 64 CYS BB 158 0.0 +159 TC6 64 CYS SC1 159 0.0 +160 P2 65 ASN BB 160 0.0 +161 SP5 65 ASN SC1 161 0.0 +162 P2 66 ASP BB 162 0.0 +163 SQ5n 66 ASP SC1 163 -1.0 +164 SP1 67 GLY BB 164 0.0 +165 P2 68 ARG BB 165 0.0 +166 SC3 68 ARG SC1 166 0.0 +167 SQ3p 68 ARG SC2 167 1.0 +168 P2 69 THR BB 168 0.0 +169 SP1 69 THR SC1 169 0.0 +170 SP2a 70 PRO BB 170 0.0 +171 SC3 70 PRO SC1 171 0.0 +172 SP1 71 GLY BB 172 0.0 +173 P2 72 SER BB 173 0.0 +174 TP1 72 SER SC1 174 0.0 +175 P2 73 ARG BB 175 0.0 +176 SC3 73 ARG SC1 176 0.0 +177 SQ3p 73 ARG SC2 177 1.0 +178 P2 74 ASN BB 178 0.0 +179 SP5 74 ASN SC1 179 0.0 +180 P2 75 LEU BB 180 0.0 +181 SC2 75 LEU SC1 181 0.0 +182 P2 76 CYS BB 182 0.0 +183 TC6 76 CYS SC1 183 0.0 +184 P2 77 ASN BB 184 0.0 +185 SP5 77 ASN SC1 185 0.0 +186 P2 78 ILE BB 186 0.0 +187 SC2 78 ILE SC1 187 0.0 +188 SP2a 79 PRO BB 188 0.0 +189 SC3 79 PRO SC1 189 0.0 +190 P2 80 CYS BB 190 0.0 +191 TC6 80 CYS SC1 191 0.0 +192 P2 81 SER BB 192 0.0 +193 TP1 81 SER SC1 193 0.0 +194 SP2 82 ALA BB 194 0.0 +195 TC3 82 ALA SC1 195 0.0 +196 P2 83 LEU BB 196 0.0 +197 SC2 83 LEU SC1 197 0.0 +198 P2 84 LEU BB 198 0.0 +199 SC2 84 LEU SC1 199 0.0 +200 P2 85 SER BB 200 0.0 +201 TP1 85 SER SC1 201 0.0 +202 P2 86 SER BB 202 0.0 +203 TP1 86 SER SC1 203 0.0 +204 P2 87 ASP BB 204 0.0 +205 SQ5n 87 ASP SC1 205 -1.0 +206 P2 88 ILE BB 206 0.0 +207 SC2 88 ILE SC1 207 0.0 +208 P2 89 THR BB 208 0.0 +209 SP1 89 THR SC1 209 0.0 +210 SP2 90 ALA BB 210 0.0 +211 TC3 90 ALA SC1 211 0.0 +212 P2 91 SER BB 212 0.0 +213 TP1 91 SER SC1 213 0.0 +214 SP2 92 VAL BB 214 0.0 +215 SC3 92 VAL SC1 215 0.0 +216 P2 93 ASN BB 216 0.0 +217 SP5 93 ASN SC1 217 0.0 +218 P2 94 CYS BB 218 0.0 +219 TC6 94 CYS SC1 219 0.0 +220 SP2 95 ALA BB 220 0.0 +221 TC3 95 ALA SC1 221 0.0 +222 P2 96 LYS BB 222 0.0 +223 SC3 96 LYS SC1 223 0.0 +224 SQ4p 96 LYS SC2 224 1.0 +225 P2 97 LYS BB 225 0.0 +226 SC3 97 LYS SC1 226 0.0 +227 SQ4p 97 LYS SC2 227 1.0 +228 P2 98 ILE BB 228 0.0 +229 SC2 98 ILE SC1 229 0.0 +230 SP2 99 VAL BB 230 0.0 +231 SC3 99 VAL SC1 231 0.0 +232 P2 100 SER BB 232 0.0 +233 TP1 100 SER SC1 233 0.0 +234 P2 101 ASP BB 234 0.0 +235 SQ5n 101 ASP SC1 235 -1.0 +236 SP1 102 GLY BB 236 0.0 +237 P2 103 ASN BB 237 0.0 +238 SP5 103 ASN SC1 238 0.0 +239 SP1 104 GLY BB 239 0.0 +240 P2 105 MET BB 240 0.0 +241 C6 105 MET SC1 241 0.0 +242 P2 106 ASN BB 242 0.0 +243 SP5 106 ASN SC1 243 0.0 +244 SP2 107 ALA BB 244 0.0 +245 TC3 107 ALA SC1 245 0.0 +246 P2 108 TRP BB 246 0.0 +247 TC4 108 TRP SC1 247 0.0 36.0 +248 TN6d 108 TRP SC2 248 0.0 36.0 +249 TC5 108 TRP SC3 249 0.0 0.0 +250 TC5 108 TRP SC4 250 0.0 36.0 +251 TC5 108 TRP SC5 251 0.0 36.0 +252 SP2 109 VAL BB 252 0.0 +253 SC3 109 VAL SC1 253 0.0 +254 SP2 110 ALA BB 254 0.0 +255 TC3 110 ALA SC1 255 0.0 +256 P2 111 TRP BB 256 0.0 +257 TC4 111 TRP SC1 257 0.0 36.0 +258 TN6d 111 TRP SC2 258 0.0 36.0 +259 TC5 111 TRP SC3 259 0.0 0.0 +260 TC5 111 TRP SC4 260 0.0 36.0 +261 TC5 111 TRP SC5 261 0.0 36.0 +262 P2 112 ARG BB 262 0.0 +263 SC3 112 ARG SC1 263 0.0 +264 SQ3p 112 ARG SC2 264 1.0 +265 P2 113 ASN BB 265 0.0 +266 SP5 113 ASN SC1 266 0.0 +267 P2 114 ARG BB 267 0.0 +268 SC3 114 ARG SC1 268 0.0 +269 SQ3p 114 ARG SC2 269 1.0 +270 P2 115 CYS BB 270 0.0 +271 TC6 115 CYS SC1 271 0.0 +272 P2 116 LYS BB 272 0.0 +273 SC3 116 LYS SC1 273 0.0 +274 SQ4p 116 LYS SC2 274 1.0 +275 SP1 117 GLY BB 275 0.0 +276 P2 118 THR BB 276 0.0 +277 SP1 118 THR SC1 277 0.0 +278 P2 119 ASP BB 278 0.0 +279 SQ5n 119 ASP SC1 279 -1.0 +280 SP2 120 VAL BB 280 0.0 +281 SC3 120 VAL SC1 281 0.0 +282 P2 121 GLN BB 282 0.0 +283 P5 121 GLN SC1 283 0.0 +284 SP2 122 ALA BB 284 0.0 +285 TC3 122 ALA SC1 285 0.0 +286 P2 123 TRP BB 286 0.0 +287 TC4 123 TRP SC1 287 0.0 36.0 +288 TN6d 123 TRP SC2 288 0.0 36.0 +289 TC5 123 TRP SC3 289 0.0 0.0 +290 TC5 123 TRP SC4 290 0.0 36.0 +291 TC5 123 TRP SC5 291 0.0 36.0 +292 P2 124 ILE BB 292 0.0 +293 SC2 124 ILE SC1 293 0.0 +294 P2 125 ARG BB 294 0.0 +295 SC3 125 ARG SC1 295 0.0 +296 SQ3p 125 ARG SC2 296 1.0 +297 SP1 126 GLY BB 297 0.0 +298 P2 127 CYS BB 298 0.0 +299 TC6 127 CYS SC1 299 0.0 +300 P2 128 ARG BB 300 0.0 +301 SC3 128 ARG SC1 301 0.0 +302 SQ3p 128 ARG SC2 302 1.0 +303 Q5 129 LEU BB 303 -1 +304 SC2 129 LEU SC1 304 0.0 +305 molecule_0_1 1 LYS CA 305 0 0.0 +306 molecule_0_2 2 VAL CA 306 0 0.0 +307 molecule_0_3 3 PHE CA 307 0 0.0 +308 molecule_0_4 4 GLY CA 308 0 0.0 +309 molecule_0_5 5 ARG CA 309 0 0.0 +310 molecule_0_6 6 CYS CA 310 0 0.0 +311 molecule_0_7 7 GLU CA 311 0 0.0 +312 molecule_0_8 8 LEU CA 312 0 0.0 +313 molecule_0_9 9 ALA CA 313 0 0.0 +314 molecule_0_10 10 ALA CA 314 0 0.0 +315 molecule_0_11 11 ALA CA 315 0 0.0 +316 molecule_0_12 12 MET CA 316 0 0.0 +317 molecule_0_13 13 LYS CA 317 0 0.0 +318 molecule_0_14 14 ARG CA 318 0 0.0 +319 molecule_0_15 15 HIS CA 319 0 0.0 +320 molecule_0_16 16 GLY CA 320 0 0.0 +321 molecule_0_17 17 LEU CA 321 0 0.0 +322 molecule_0_18 18 ASP CA 322 0 0.0 +323 molecule_0_19 19 ASN CA 323 0 0.0 +324 molecule_0_20 20 TYR CA 324 0 0.0 +325 molecule_0_21 21 ARG CA 325 0 0.0 +326 molecule_0_22 22 GLY CA 326 0 0.0 +327 molecule_0_23 23 TYR CA 327 0 0.0 +328 molecule_0_24 24 SER CA 328 0 0.0 +329 molecule_0_25 25 LEU CA 329 0 0.0 +330 molecule_0_26 26 GLY CA 330 0 0.0 +331 molecule_0_27 27 ASN CA 331 0 0.0 +332 molecule_0_28 28 TRP CA 332 0 0.0 +333 molecule_0_29 29 VAL CA 333 0 0.0 +334 molecule_0_30 30 CYS CA 334 0 0.0 +335 molecule_0_31 31 ALA CA 335 0 0.0 +336 molecule_0_32 32 ALA CA 336 0 0.0 +337 molecule_0_33 33 LYS CA 337 0 0.0 +338 molecule_0_34 34 PHE CA 338 0 0.0 +339 molecule_0_35 35 GLU CA 339 0 0.0 +340 molecule_0_36 36 SER CA 340 0 0.0 +341 molecule_0_37 37 ASN CA 341 0 0.0 +342 molecule_0_38 38 PHE CA 342 0 0.0 +343 molecule_0_39 39 ASN CA 343 0 0.0 +344 molecule_0_40 40 THR CA 344 0 0.0 +345 molecule_0_41 41 GLN CA 345 0 0.0 +346 molecule_0_42 42 ALA CA 346 0 0.0 +347 molecule_0_43 43 THR CA 347 0 0.0 +348 molecule_0_44 44 ASN CA 348 0 0.0 +349 molecule_0_45 45 ARG CA 349 0 0.0 +350 molecule_0_46 46 ASN CA 350 0 0.0 +351 molecule_0_47 47 THR CA 351 0 0.0 +352 molecule_0_48 48 ASP CA 352 0 0.0 +353 molecule_0_49 49 GLY CA 353 0 0.0 +354 molecule_0_50 50 SER CA 354 0 0.0 +355 molecule_0_51 51 THR CA 355 0 0.0 +356 molecule_0_52 52 ASP CA 356 0 0.0 +357 molecule_0_53 53 TYR CA 357 0 0.0 +358 molecule_0_54 54 GLY CA 358 0 0.0 +359 molecule_0_55 55 ILE CA 359 0 0.0 +360 molecule_0_56 56 LEU CA 360 0 0.0 +361 molecule_0_57 57 GLN CA 361 0 0.0 +362 molecule_0_58 58 ILE CA 362 0 0.0 +363 molecule_0_59 59 ASN CA 363 0 0.0 +364 molecule_0_60 60 SER CA 364 0 0.0 +365 molecule_0_61 61 ARG CA 365 0 0.0 +366 molecule_0_62 62 TRP CA 366 0 0.0 +367 molecule_0_63 63 TRP CA 367 0 0.0 +368 molecule_0_64 64 CYS CA 368 0 0.0 +369 molecule_0_65 65 ASN CA 369 0 0.0 +370 molecule_0_66 66 ASP CA 370 0 0.0 +371 molecule_0_67 67 GLY CA 371 0 0.0 +372 molecule_0_68 68 ARG CA 372 0 0.0 +373 molecule_0_69 69 THR CA 373 0 0.0 +374 molecule_0_70 70 PRO CA 374 0 0.0 +375 molecule_0_71 71 GLY CA 375 0 0.0 +376 molecule_0_72 72 SER CA 376 0 0.0 +377 molecule_0_73 73 ARG CA 377 0 0.0 +378 molecule_0_74 74 ASN CA 378 0 0.0 +379 molecule_0_75 75 LEU CA 379 0 0.0 +380 molecule_0_76 76 CYS CA 380 0 0.0 +381 molecule_0_77 77 ASN CA 381 0 0.0 +382 molecule_0_78 78 ILE CA 382 0 0.0 +383 molecule_0_79 79 PRO CA 383 0 0.0 +384 molecule_0_80 80 CYS CA 384 0 0.0 +385 molecule_0_81 81 SER CA 385 0 0.0 +386 molecule_0_82 82 ALA CA 386 0 0.0 +387 molecule_0_83 83 LEU CA 387 0 0.0 +388 molecule_0_84 84 LEU CA 388 0 0.0 +389 molecule_0_85 85 SER CA 389 0 0.0 +390 molecule_0_86 86 SER CA 390 0 0.0 +391 molecule_0_87 87 ASP CA 391 0 0.0 +392 molecule_0_88 88 ILE CA 392 0 0.0 +393 molecule_0_89 89 THR CA 393 0 0.0 +394 molecule_0_90 90 ALA CA 394 0 0.0 +395 molecule_0_91 91 SER CA 395 0 0.0 +396 molecule_0_92 92 VAL CA 396 0 0.0 +397 molecule_0_93 93 ASN CA 397 0 0.0 +398 molecule_0_94 94 CYS CA 398 0 0.0 +399 molecule_0_95 95 ALA CA 399 0 0.0 +400 molecule_0_96 96 LYS CA 400 0 0.0 +401 molecule_0_97 97 LYS CA 401 0 0.0 +402 molecule_0_98 98 ILE CA 402 0 0.0 +403 molecule_0_99 99 VAL CA 403 0 0.0 +404 molecule_0_100 100 SER CA 404 0 0.0 +405 molecule_0_101 101 ASP CA 405 0 0.0 +406 molecule_0_102 102 GLY CA 406 0 0.0 +407 molecule_0_103 103 ASN CA 407 0 0.0 +408 molecule_0_104 104 GLY CA 408 0 0.0 +409 molecule_0_105 105 MET CA 409 0 0.0 +410 molecule_0_106 106 ASN CA 410 0 0.0 +411 molecule_0_107 107 ALA CA 411 0 0.0 +412 molecule_0_108 108 TRP CA 412 0 0.0 +413 molecule_0_109 109 VAL CA 413 0 0.0 +414 molecule_0_110 110 ALA CA 414 0 0.0 +415 molecule_0_111 111 TRP CA 415 0 0.0 +416 molecule_0_112 112 ARG CA 416 0 0.0 +417 molecule_0_113 113 ASN CA 417 0 0.0 +418 molecule_0_114 114 ARG CA 418 0 0.0 +419 molecule_0_115 115 CYS CA 419 0 0.0 +420 molecule_0_116 116 LYS CA 420 0 0.0 +421 molecule_0_117 117 GLY CA 421 0 0.0 +422 molecule_0_118 118 THR CA 422 0 0.0 +423 molecule_0_119 119 ASP CA 423 0 0.0 +424 molecule_0_120 120 VAL CA 424 0 0.0 +425 molecule_0_121 121 GLN CA 425 0 0.0 +426 molecule_0_122 122 ALA CA 426 0 0.0 +427 molecule_0_123 123 TRP CA 427 0 0.0 +428 molecule_0_124 124 ILE CA 428 0 0.0 +429 molecule_0_125 125 ARG CA 429 0 0.0 +430 molecule_0_126 126 GLY CA 430 0 0.0 +431 molecule_0_127 127 CYS CA 431 0 0.0 +432 molecule_0_128 128 ARG CA 432 0 0.0 +433 molecule_0_129 129 LEU CA 433 0 0.0 + +[ bonds ] +; Backbone bonds + 1 4 1 0.350 4000 + 4 6 1 0.350 4000 + 6 10 1 0.350 4000 + 34 38 1 0.350 4000 + 38 39 1 0.350 4000 + 39 41 1 0.350 4000 + 41 43 1 0.350 4000 + 43 45 1 0.350 4000 + 45 50 1 0.350 4000 + 50 53 1 0.350 4000 + 53 54 1 0.350 4000 + 54 59 1 0.350 4000 + 91 93 1 0.350 4000 + 93 97 1 0.350 4000 + 97 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 103 1 0.350 4000 +103 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 112 1 0.350 4000 +112 114 1 0.350 4000 +114 116 1 0.350 4000 +116 118 1 0.350 4000 +118 119 1 0.350 4000 +119 121 1 0.350 4000 +121 123 1 0.350 4000 +123 125 1 0.350 4000 +125 130 1 0.350 4000 +130 131 1 0.350 4000 +131 133 1 0.350 4000 +133 135 1 0.350 4000 +135 137 1 0.350 4000 +137 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 146 1 0.350 4000 +146 152 1 0.350 4000 +152 158 1 0.350 4000 +158 160 1 0.350 4000 +160 162 1 0.350 4000 +162 164 1 0.350 4000 +164 165 1 0.350 4000 +165 168 1 0.350 4000 +168 170 1 0.350 4000 +170 172 1 0.350 4000 +172 173 1 0.350 4000 +173 175 1 0.350 4000 +175 178 1 0.350 4000 +178 180 1 0.350 4000 +180 182 1 0.350 4000 +182 184 1 0.350 4000 +184 186 1 0.350 4000 +186 188 1 0.350 4000 +200 202 1 0.350 4000 +202 204 1 0.350 4000 +204 206 1 0.350 4000 +234 236 1 0.350 4000 +236 237 1 0.350 4000 +270 272 1 0.350 4000 +272 275 1 0.350 4000 +275 276 1 0.350 4000 +276 278 1 0.350 4000 +294 297 1 0.350 4000 +297 298 1 0.350 4000 +298 300 1 0.350 4000 +300 303 1 0.350 4000 + +; Side chain bonds + 1 2 1 0.330 5000 + 2 3 1 0.360 5000 + 6 7 1 0.325 7500 + 11 12 1 0.330 5000 + 12 13 1 0.380 5000 + 14 15 1 0.341 7500 + 16 17 1 0.400 5000 + 18 19 1 0.363 7500 + 26 27 1 0.40 2500 + 28 29 1 0.330 5000 + 29 30 1 0.360 5000 + 31 32 1 0.330 5000 + 32 33 1 0.380 5000 + 34 35 1 0.336 7500 + 39 40 1 0.363 7500 + 41 42 1 0.352 7500 + 43 44 1 0.352 5000 + 45 46 1 0.325 5000 + 50 51 1 0.330 5000 + 51 52 1 0.380 5000 + 54 55 1 0.325 5000 + 59 60 1 0.287 7500 + 61 62 1 0.363 7500 + 64 65 1 0.352 5000 + 66 67 1 0.315 5000 + 74 75 1 0.341 7500 + 80 81 1 0.330 5000 + 81 82 1 0.360 5000 + 83 84 1 0.325 7500 + 87 88 1 0.400 5000 + 89 90 1 0.287 7500 + 91 92 1 0.352 5000 + 93 94 1 0.325 7500 + 97 98 1 0.352 5000 +101 102 1 0.400 5000 +107 108 1 0.352 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238 1 0.352 5000 +240 241 1 0.40 2500 +242 243 1 0.352 5000 +246 247 1 0.315 5000 +256 257 1 0.315 5000 +262 263 1 0.330 5000 +263 264 1 0.380 5000 +265 266 1 0.352 5000 +267 268 1 0.330 5000 +268 269 1 0.380 5000 +270 271 1 0.341 7500 +272 273 1 0.330 5000 +273 274 1 0.360 5000 +278 279 1 0.352 7500 +282 283 1 0.400 5000 +286 287 1 0.315 5000 +294 295 1 0.330 5000 +295 296 1 0.380 5000 +298 299 1 0.341 7500 +300 301 1 0.330 5000 +301 302 1 0.380 5000 +303 304 1 0.363 7500 + +#ifdef FLEXIBLE +; Side chain bonds + 4 5 1 0.292 1000000 + 7 8 1 0.340 1000000 + 7 9 1 0.340 1000000 + 8 9 1 0.290 1000000 + 20 21 1 0.270 1000000 + 22 23 1 0.270 1000000 + 24 25 1 0.270 1000000 + 35 36 1 0.320 1000000 + 35 37 1 0.300 1000000 + 36 37 1 0.270 1000000 + 46 47 1 0.300 1000000 + 46 48 1 0.300 1000000 + 47 49 1 0.285 1000000 + 48 49 1 0.285 1000000 + 47 48 1 0.300 1000000 + 55 56 1 0.300 1000000 + 55 57 1 0.300 1000000 + 56 58 1 0.285 1000000 + 57 58 1 0.285 1000000 + 56 57 1 0.300 1000000 + 67 68 1 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100 20 +143 146 152 10 100 20 +270 272 275 10 100 20 + +; BBS angles regular martini + 1 4 5 2 100 25 + 4 6 7 2 100 25 + 10 11 12 2 100 25 + 11 14 15 2 100 25 + 14 16 17 2 100 25 + 16 18 19 2 100 25 + 18 20 21 2 100 25 + 20 22 23 2 100 25 + 22 24 25 2 100 25 + 24 26 27 2 100 25 + 26 28 29 2 100 25 + 28 31 32 2 100 25 + 31 34 35 2 100 25 + 38 39 40 2 100 25 + 39 41 42 2 100 25 + 41 43 44 2 100 25 + 43 45 46 2 100 25 + 45 50 51 2 100 25 + 53 54 55 2 100 25 + 54 59 60 2 100 25 + 59 61 62 2 100 25 + 63 64 65 2 100 25 + 64 66 67 2 100 25 + 66 72 73 2 100 25 + 72 74 75 2 100 25 + 74 76 77 2 100 25 + 76 78 79 2 100 25 + 78 80 81 2 100 25 + 80 83 84 2 100 25 + 83 87 88 2 100 25 + 87 89 90 2 100 25 + 89 91 92 2 100 25 + 91 93 94 2 100 25 + 93 97 98 2 100 25 + 97 99 100 2 100 25 + 99 101 102 2 100 25 +101 103 104 2 100 25 +103 105 106 2 100 25 +105 107 108 2 100 25 +107 109 110 2 100 25 +109 112 113 2 100 25 +112 114 115 2 100 25 +114 116 117 2 100 25 +118 119 120 2 100 25 +119 121 122 2 100 25 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180.0 100.0 +291 290 288 287 2 180.0 100.0 + +[ virtual_sitesn ] + 69 2 71 70 68 67 +149 2 151 150 148 147 +155 2 157 156 154 153 +249 2 251 250 248 247 +259 2 261 260 258 257 +289 2 291 290 288 287 + +; Virtual go site +305 1 1 +306 1 4 +307 1 6 +308 1 10 +309 1 11 +310 1 14 +311 1 16 +312 1 18 +313 1 20 +314 1 22 +315 1 24 +316 1 26 +317 1 28 +318 1 31 +319 1 34 +320 1 38 +321 1 39 +322 1 41 +323 1 43 +324 1 45 +325 1 50 +326 1 53 +327 1 54 +328 1 59 +329 1 61 +330 1 63 +331 1 64 +332 1 66 +333 1 72 +334 1 74 +335 1 76 +336 1 78 +337 1 80 +338 1 83 +339 1 87 +340 1 89 +341 1 91 +342 1 93 +343 1 97 +344 1 99 +345 1 101 +346 1 103 +347 1 105 +348 1 107 +349 1 109 +350 1 112 +351 1 114 +352 1 116 +353 1 118 +354 1 119 +355 1 121 +356 1 123 +357 1 125 +358 1 130 +359 1 131 +360 1 133 +361 1 135 +362 1 137 +363 1 139 +364 1 141 +365 1 143 +366 1 146 +367 1 152 +368 1 158 +369 1 160 +370 1 162 +371 1 164 +372 1 165 +373 1 168 +374 1 170 +375 1 172 +376 1 173 +377 1 175 +378 1 178 +379 1 180 +380 1 182 +381 1 184 +382 1 186 +383 1 188 +384 1 190 +385 1 192 +386 1 194 +387 1 196 +388 1 198 +389 1 200 +390 1 202 +391 1 204 +392 1 206 +393 1 208 +394 1 210 +395 1 212 +396 1 214 +397 1 216 +398 1 218 +399 1 220 +400 1 222 +401 1 225 +402 1 228 +403 1 230 +404 1 232 +405 1 234 +406 1 236 +407 1 237 +408 1 239 +409 1 240 +410 1 242 +411 1 244 +412 1 246 +413 1 252 +414 1 254 +415 1 256 +416 1 262 +417 1 265 +418 1 267 +419 1 270 +420 1 272 +421 1 275 +422 1 276 +423 1 278 +424 1 280 +425 1 282 +426 1 284 +427 1 286 +428 1 292 +429 1 294 +430 1 297 +431 1 298 +432 1 300 +433 1 303 + diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top new file mode 100644 index 00000000..a8528540 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top @@ -0,0 +1,12 @@ +#define GO_VIRT +#include "martini.itp" + + #include "go_atomtypes.itp" + #include "go_nbparams.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index bd632662..74588260 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -137,7 +137,9 @@ def compare_goatomtypes(fileref, filecomp): assert(ref[key] == compare[key]) ##assert correct atom definition string GOCOMPARERS = {'go_nbparams.itp': compare_nbparams, - 'go_atomtypes.itp': compare_goatomtypes} + 'virtual_sites_nonbond_params.itp': compare_nbparams, + 'go_atomtypes.itp': compare_goatomtypes, + 'virtual_sites_atomtypes.itp': compare_goatomtypes} def _interaction_equal(interaction1, interaction2): """ @@ -152,21 +154,23 @@ def _interaction_equal(interaction1, interaction2): @pytest.mark.parametrize("tier, protein", [ - # ['tier-0', 'mini-protein1_betasheet'], - # ['tier-0', 'mini-protein2_helix'], - # ['tier-0', 'mini-protein3_trp-cage'], - # ['tier-0', 'dipro-termini'], - # ['tier-1', 'bpti'], - # ['tier-1', 'lysozyme'], - # ['tier-1', 'lysozyme_prot'], + ['tier-0', 'mini-protein1_betasheet'], + ['tier-0', 'mini-protein2_helix'], + ['tier-0', 'mini-protein3_trp-cage'], + ['tier-0', 'dipro-termini'], + ['tier-1', 'bpti'], + ['tier-1', 'lysozyme'], + ['tier-1', 'lysozyme_prot'], ['tier-1', 'lysozyme_GO'], - # ['tier-1', 'villin'], - # ['tier-1', '3i40'], - # ['tier-1', '6LFO_gap'], - # ['tier-1', '1mj5'], - # ['tier-1', '1mj5-charmm'], - # ['tier-1', 'EN_chain'], - # ['tier-1', 'EN_region'], + ['tier-1', 'lysozyme_GObias'], + ['tier-1', 'lysozyme_ENbias'], + ['tier-1', 'villin'], + ['tier-1', '3i40'], + ['tier-1', '6LFO_gap'], + ['tier-1', '1mj5'], + ['tier-1', '1mj5-charmm'], + ['tier-1', 'EN_chain'], + ['tier-1', 'EN_region'], # ['tier-2', 'barnase_barstar'], # ['tier-2', 'dna'], # ['tier-2', 'gpa_dimer'], @@ -232,7 +236,9 @@ def test_integration_protein(tmp_path, monkeypatch, tier, protein): filename = new_file.name reference_file = data_path/filename assert reference_file.is_file() - if filename in ['go_nbparams.itp','go_atomtypes.itp']: + if filename in ['go_nbparams.itp','go_atomtypes.itp', + 'virtual_sites_nonbond_params.itp','virtual_sites_atomtypes.itp']: + ## compare the extra go/vs model files GOCOMPARERS[filename](str(reference_file), str(new_file)) else: ext = new_file.suffix.lower() From 9f4cb1795053427581822653ee0f59f6e5ced4c4 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 30 Nov 2023 17:07:24 +0100 Subject: [PATCH 69/95] use -go for map parsing --- bin/martinize2 | 12 +++--------- .../tier-1/lysozyme_GO/martinize2/command | 3 +-- .../tier-1/lysozyme_GObias/martinize2/command | 7 +++---- 3 files changed, 7 insertions(+), 15 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 0c8cfd6b..15835387 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -532,16 +532,10 @@ def entry(): go_group = parser.add_argument_group("Virtual site based GoMartini") go_group.add_argument( "-go", - action="store_true", - default=False, - help="Apply the Martini Go model as structural bias and/or water bias.", - ) - go_group.add_argument( - "-go-map", - dest="go_map", + dest="go", required=False, type=Path, - default=False, + default=None, help="Contact map to be used for the Martini Go model." "Currently, only one format is supported. See docs.", ) @@ -951,7 +945,7 @@ def entry(): # Generate the Go model if required if args.go: LOGGER.info("Reading Go model contact map.", type="step") - go_map = read_go_map(args.go_map) + go_map = read_go_map(args.go) LOGGER.info("Generating the Go model.", type="step") GoPipeline.run_system(system, moltype=args.govs_moltype, diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command index 92de3c34..31dd6a43 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command @@ -5,5 +5,4 @@ martinize2 -o topol.top -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC --go --go-map ../map.map +-go ../map.map diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command index 36791420..17b5b458 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command @@ -4,8 +4,7 @@ martinize2 -x cg.pdb -o topol.top -ignore HOH --ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC --go --go-map ../map.map +-ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC +-go ../map.map -water-bias --water-bias-eps E:-.5 C:1.0 H:-1.0 \ No newline at end of file +-water-bias-eps E:-.5 C:1.0 H:-1.0 From 911b3a67ec03e62d2b8c17a93d6f87fd1adfd200 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 30 Nov 2023 17:08:25 +0100 Subject: [PATCH 70/95] fix docs --- vermouth/processors/water_bias.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index a412845c..32d4bb27 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -75,9 +75,9 @@ def assign_residue_water_bias(self, molecule, res_graph): Parameters ---------- - molecule: :class:vermouth.Molecule + molecule: :class:vermouth.molecule.Molecule the molecule - res_graph: :class:vermouth.Molecule + res_graph: :class:vermouth.molecule.Molecule the residue graph of the molecule """ for res_node in res_graph.nodes: From 23138d6f908d9e8a1a458cbb0f848e1821b7d13f Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:04:22 +0100 Subject: [PATCH 71/95] Update vermouth/processors/water_bias.py Co-authored-by: Peter C Kroon --- vermouth/processors/water_bias.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 32d4bb27..7982b837 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -75,9 +75,9 @@ def assign_residue_water_bias(self, molecule, res_graph): Parameters ---------- - molecule: :class:vermouth.molecule.Molecule + molecule: :class:`vermouth.molecule.Molecule` the molecule - res_graph: :class:vermouth.molecule.Molecule + res_graph: :class:`vermouth.molecule.Molecule` the residue graph of the molecule """ for res_node in res_graph.nodes: From f31201b9630ffcf8be519ceeee60fbfa366e8901 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:04:35 +0100 Subject: [PATCH 72/95] Update vermouth/processors/water_bias.py Co-authored-by: Peter C Kroon --- vermouth/processors/water_bias.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 7982b837..80fb2711 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -143,7 +143,7 @@ def run_system(self, system): Parameters ---------- - system: :class:`vermouth.System` + system: :class:`vermouth.system.System` """ if not (self.idr_regions or self.auto_bias): return system From 486c13edf798bcc7d35a781995e56f6fdd0adfee Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:20:05 +0100 Subject: [PATCH 73/95] Update martinize2_workflow.rst Update documentation considering restructured Go model --- doc/source/martinize2_workflow.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/martinize2_workflow.rst b/doc/source/martinize2_workflow.rst index 418b7454..aca44068 100644 --- a/doc/source/martinize2_workflow.rst +++ b/doc/source/martinize2_workflow.rst @@ -277,7 +277,7 @@ There can be any number of post processing steps. For example to add an elastic network, or to generate Go virtual sites. We will not describe their function here in detail. Instead, see for example :class:`~vermouth.processors.apply_rubber_band.ApplyRubberBand` and -:class:`~vermouth.processors.go_vs_includes.GoVirtIncludes`. +:class:`~vermouth.processors.rcsu.go_vs_includes.VirtualSiteCreator`. Relevant CLI options: ``-elastic``, ``-ef``, ``-el``, ``-eu``, ``-ermd``, ``-ea``, ``-ep``, ``-em``, ``-eb``, ``-eunit``, ``-govs-include``, From b6ca0a1cb256d64afc7931806df2f122af81acc8 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:23:08 +0100 Subject: [PATCH 74/95] add doi for c-code --- vermouth/rcsu/contact_map.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index ca593f26..a75aec80 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -19,8 +19,9 @@ def read_go_map(file_path): """ Read a RCSU contact map from the c code as published in - doi:zzzz. The format requires all contacts to have 18 - columns and the first column to be a capital R. + doi:10.5281/zenodo.3817447. The format requires all + contacts to have 18 columns and the first column to be + a capital R. Paraemters --------- From 169927687b752ff1aca1d39a36c5009a5e9ab35f Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:29:52 +0100 Subject: [PATCH 75/95] fix docs according to new go --- doc/source/martinize2_workflow.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/martinize2_workflow.rst b/doc/source/martinize2_workflow.rst index aca44068..9e29df80 100644 --- a/doc/source/martinize2_workflow.rst +++ b/doc/source/martinize2_workflow.rst @@ -277,11 +277,11 @@ There can be any number of post processing steps. For example to add an elastic network, or to generate Go virtual sites. We will not describe their function here in detail. Instead, see for example :class:`~vermouth.processors.apply_rubber_band.ApplyRubberBand` and -:class:`~vermouth.processors.rcsu.go_vs_includes.VirtualSiteCreator`. +:class:`~vermouth.rcsu.go_vs_includes.VirtualSiteCreator`. Relevant CLI options: ``-elastic``, ``-ef``, ``-el``, ``-eu``, ``-ermd``, -``-ea``, ``-ep``, ``-em``, ``-eb``, ``-eunit``, ``-govs-include``, -``-govs-moltype`` +``-ea``, ``-ep``, ``-em``, ``-eb``, ``-eunit``, ``-go``, +``-go-eps``, ``-go-moltype``, ``-go-low``, ``-go-up``, ``-go-res-dist`` 6) Write output =============== From dacbdf8de9633ee459af3ffbd5c36c334118f274 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 13:08:12 +0100 Subject: [PATCH 76/95] Create __init__.py --- vermouth/rcsu/__init__.py | 1 + 1 file changed, 1 insertion(+) create mode 100644 vermouth/rcsu/__init__.py diff --git a/vermouth/rcsu/__init__.py b/vermouth/rcsu/__init__.py new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/vermouth/rcsu/__init__.py @@ -0,0 +1 @@ + From 6e8382d851e31aa458f30819373ff8a0e8a34d36 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Tue, 5 Dec 2023 13:11:53 +0100 Subject: [PATCH 77/95] Update contact_map.py --- vermouth/rcsu/contact_map.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index a75aec80..29914f6d 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -23,8 +23,8 @@ def read_go_map(file_path): contacts to have 18 columns and the first column to be a capital R. - Paraemters - --------- + Parameters + ---------- file_path: :cls:pathlib.Path path to the contact map file From 806d1f5cd72d4d9972f0e703a4b6999ea90f697c Mon Sep 17 00:00:00 2001 From: Peter Kroon Date: Tue, 5 Dec 2023 13:19:20 +0100 Subject: [PATCH 78/95] Fix sphinx references --- vermouth/rcsu/__init__.py | 0 vermouth/rcsu/contact_map.py | 8 ++++---- vermouth/rcsu/go_structure_bias.py | 10 +++++----- vermouth/rcsu/go_utils.py | 2 +- vermouth/rcsu/go_vs_includes.py | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-) create mode 100644 vermouth/rcsu/__init__.py diff --git a/vermouth/rcsu/__init__.py b/vermouth/rcsu/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index a75aec80..96ccbb5a 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -23,14 +23,14 @@ def read_go_map(file_path): contacts to have 18 columns and the first column to be a capital R. - Paraemters - --------- - file_path: :cls:pathlib.Path + Parameters + ---------- + file_path: :class:`pathlib.Path` path to the contact map file Returns ------- - list(tuple(4)) + list(tuple) contact as chain id, res id, chain id, res id """ with open(file_path, "r", encoding='UTF-8') as _file: diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 67f786f5..0bbc0d7e 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -75,10 +75,10 @@ def __init__(self, into account disulfide bridges for example moltype: str name of the molecule to treat - res_graph: :class:vermouth.Molecule + res_graph: :class:`vermouth.molecule.Molecule` residue graph of the molecule; if None it - get's generated automatically - system: :class:vermouth.System + gets generated automatically + system: :class:`vermouth.system.System` the system magic_number: float magic number for Go contacts from the old @@ -142,11 +142,11 @@ def contact_selector(self, molecule): Parameters ---------- - molecule: :class:vermouth.Molecule + molecule: :class:`vermouth.molecule.Molecule` Returns ------- - list[(abc.hashable, abc.hashable, float)] + list[(collections.abc.Hashable, collections.abc.Hashable, float)] list of node keys and distance """ # distance_matrix of elegible pairs as tuple(node, node, dist) diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index 7a12095f..772f4139 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -23,7 +23,7 @@ def get_go_type_from_attributes(molecule, prefix, **kwargs): Parameters ---------- - molecule: :class:vermouth.Molecule + molecule: :class:`vermouth.molecule.Molecule` prefix: str the atom-type prefix of the Go virtual side kwargs: diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 2331242e..60fcb76d 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -29,7 +29,7 @@ class VirtualSiteCreator(Processor): Create virtual-sites for the Martini Go model implementation or the specific water biasing options. - See :mod:`vermouth.processors.go_vs_includes` for more details. + See :mod:`vermouth.rcsu` for more details. Every molecule must have a moltype name under the "moltype" key of the molecule meta. From 0f31eedfa6a8f8da44cdd165c22dfb816d038f23 Mon Sep 17 00:00:00 2001 From: Peter C Kroon Date: Wed, 6 Dec 2023 11:16:05 +0100 Subject: [PATCH 79/95] fix CLI typo --- bin/martinize2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/martinize2 b/bin/martinize2 index c60c0b8c..bb811420 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -571,7 +571,7 @@ def entry(): dest="go_res_dist", type=int, default=3, - help=("Minimum graph distance (similar seqeuence distance) below which" + help=("Minimum graph distance (similar sequence distance) below which" "contacts are removed. "), ) From 71f19aa8e132cf86dccb4c824cc872a91c5f2097 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Wed, 6 Dec 2023 12:56:01 +0100 Subject: [PATCH 80/95] Update bin/martinize2 Co-authored-by: Peter C Kroon --- bin/martinize2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/martinize2 b/bin/martinize2 index bb811420..c60747cc 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -590,7 +590,7 @@ def entry(): type=lambda s: s.split(":"), default=[], help=("Define the strength of the water bias by secondary structure type. " - "For example, use H:3.6, C:2.1 to bias helixes and coils. " + "For example, use `H:3.6 C:2.1` to bias helixes and coils. " "Using the idr option (e.g. idr:2.1) intrinsically disordered regions " "are biased seperately."), ) From 317f813eaa8eb3ae2c49cd7616b5c584cec4dd48 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Mon, 11 Dec 2023 09:15:52 +0100 Subject: [PATCH 81/95] Apply suggestions from code review changes not relating to tests Co-authored-by: Peter C Kroon --- vermouth/processors/water_bias.py | 5 +++-- vermouth/rcsu/contact_map.py | 7 ++----- vermouth/rcsu/go_structure_bias.py | 11 ++++++----- vermouth/rcsu/go_utils.py | 6 +++--- vermouth/rcsu/go_vs_includes.py | 4 +--- 5 files changed, 15 insertions(+), 18 deletions(-) diff --git a/vermouth/processors/water_bias.py b/vermouth/processors/water_bias.py index 80fb2711..859a1cb4 100644 --- a/vermouth/processors/water_bias.py +++ b/vermouth/processors/water_bias.py @@ -32,7 +32,8 @@ class ComputeWaterBias(Processor): This Processor updates the system.gmx_topology_params attribute. - ** Subclassing ** + Subclassing + ----------- If the procedure by which to assign the water bias is to be changed this processor is best subclassed and the assign_residue_water_bias method overwritten. @@ -94,7 +95,7 @@ def assign_residue_water_bias(self, molecule, res_graph): else: continue - if eps == 0.0: + if abs(eps) <= 1e-12: continue vs_go_node = next(get_go_type_from_attributes(res_graph.nodes[res_node]['graph'], diff --git a/vermouth/rcsu/contact_map.py b/vermouth/rcsu/contact_map.py index 96ccbb5a..111f0c94 100644 --- a/vermouth/rcsu/contact_map.py +++ b/vermouth/rcsu/contact_map.py @@ -43,11 +43,8 @@ def read_go_map(file_path): if tokens[0] == "R" and len(tokens) == 18: # this is a bad place to filter but follows # the old script - if tokens[11] == "1": - # this is a OV contact we take it - contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) - if tokens[11] == "0" and tokens[14] == "1": - # this is a rCSU contact we take it + if tokens[11] == "1" or (tokens[11] == "0" and tokens[14] == "1"): + # this is a OV or rCSU contact we take it contacts.append((int(tokens[5]), tokens[4], int(tokens[9]), tokens[8])) if len(contacts) == 0: diff --git a/vermouth/rcsu/go_structure_bias.py b/vermouth/rcsu/go_structure_bias.py index 0bbc0d7e..6f754424 100644 --- a/vermouth/rcsu/go_structure_bias.py +++ b/vermouth/rcsu/go_structure_bias.py @@ -35,13 +35,14 @@ class ComputeStructuralGoBias(Processor): be written out using the `vermouth.gmx.write_topology` function. - ** Subclassing ** + Subclassing + ----------- In order to customize the Go-model structural bias it is recommended to subclass this function and - overwrite the .contact_selector method and/or - the .compute_bias method. This subclassed Processor - then has to be added to the into the /bin/martinize2 - pipline in place of the StructuralBiasWriter or as + overwrite the ``contact_selector`` method and/or + the ``compute_bias`` method. This subclassed Processor + then has to be added to the into the martinize2 + pipeline in place of the StructuralBiasWriter or as replacement in the GoPipeline. """ def __init__(self, diff --git a/vermouth/rcsu/go_utils.py b/vermouth/rcsu/go_utils.py index 772f4139..01646617 100644 --- a/vermouth/rcsu/go_utils.py +++ b/vermouth/rcsu/go_utils.py @@ -36,9 +36,9 @@ def get_go_type_from_attributes(molecule, prefix, **kwargs): Raises ------ - IOError + KeyError If no node can be found that matches attributes - and prefix an IOError is raised. + and prefix an KeyError is raised. """ for node in molecule.nodes: attrs = molecule.nodes[node] @@ -57,7 +57,7 @@ def _in_resid_region(resid, regions): ---------- resid: int the resid of a molecule - regions: list[tuple(int)] + regions: list[tuple(int, int)] a list of the intervals Returns diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 60fcb76d..31a6696d 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -54,7 +54,7 @@ def run_molecule(self, molecule): raise ValueError('The molecule does not have a moltype name.') if not self.system: - raise IOError('This processor requires a system.') + raise ValueError('This processor requires a system.') self.add_virtual_sites(molecule, prefix=moltype) @@ -132,7 +132,5 @@ def add_virtual_sites(self, molecule, prefix, backbone='BB', atomname='CA', char molecule.add_nodes_from(virtual_site_nodes) - if 'virtual_sitesn' not in molecule.interactions: - molecule.interactions['virtual_sitesn'] = [] molecule.interactions['virtual_sitesn'] += virtual_sites From 484f9048be58f98c29c649594051efca7c917f26 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Mon, 11 Dec 2023 09:20:04 +0100 Subject: [PATCH 82/95] Apply suggestions from code review Co-authored-by: Peter C Kroon --- vermouth/tests/helper_functions.py | 4 ++-- vermouth/tests/integration_tests/test_integration.py | 2 +- vermouth/tests/rcsu/test_go_structure_bias.py | 2 +- vermouth/tests/test_vs_generation.py | 4 ++-- vermouth/tests/test_water_bias.py | 8 ++++---- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 1cec5933..3982c314 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -93,7 +93,7 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): Parameters ---------- - molecule: :class:vermouth.Molecule + molecule: :class:`vermouth.molecule.Molecule` moltype: str sets meta['moltype'] secstruc: dict[int, str] @@ -107,7 +107,7 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): Returns ------- - :class:vermouth.System + :class:`vermouth.system.System` """ # set mol meta molecule.meta['moltype'] = moltype diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index 74588260..0d7bed13 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -118,7 +118,7 @@ def compare_nbparams(fileref, filecomp): ref = parse_gofiles(fileref) compare = parse_gofiles(filecomp) - assert(set(ref.keys())==set(compare.keys())) ## assert correct nb pairs + assert set(ref.keys()) == set(compare.keys()) # assert correct nb pairs for key in ref.keys(): assert(is_equal(list(ref[key]),list(compare[key]))) ##assert correct sigma and eps diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 973c97c9..84d27c7b 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -21,7 +21,7 @@ def test_compute_go_interaction(test_molecule): system = vermouth.System() - system.molecules.append(test_molecule) + system.add_molecule(test_molecule) go_processor = ComputeStructuralGoBias(contact_map=None, cutoff_short=None, cutoff_long=None, diff --git a/vermouth/tests/test_vs_generation.py b/vermouth/tests/test_vs_generation.py index 793fcc73..bbdaedd3 100644 --- a/vermouth/tests/test_vs_generation.py +++ b/vermouth/tests/test_vs_generation.py @@ -34,7 +34,7 @@ def test_no_moltype_error(test_molecule): def test_no_system_error(test_molecule): """ - Test that various high level IOErrors are + Test that various high level errors are properly raised. """ # set up processor @@ -49,5 +49,5 @@ def test_return_no_nodes(): processor = VirtualSiteCreator() mol.meta['moltype'] = "random" system = vermouth.System() - system.molecules.append(mol) + system.add_molecule(mol) assert processor.run_system(system) is None diff --git a/vermouth/tests/test_water_bias.py b/vermouth/tests/test_water_bias.py index a5b3901f..1064c74a 100644 --- a/vermouth/tests/test_water_bias.py +++ b/vermouth/tests/test_water_bias.py @@ -99,7 +99,7 @@ def test_assign_residue_water_bias(test_molecule, def test_no_moltype_error(test_molecule): """ - Test that various high level IOErrors are + Test that various high level errors are properly raised. """ # set up processor @@ -108,13 +108,13 @@ def test_no_moltype_error(test_molecule): idr_regions=None) # no moltype set system = vermouth.System() - system.molecules.append(test_molecule) + system.add_molecule(test_molecule) with pytest.raises(ValueError): processor.run_system(system) def test_no_system_error(test_molecule): """ - Test that various high level IOErrors are + Test that various high level errors are properly raised. """ # set up processor @@ -133,5 +133,5 @@ def test_clean_return(test_molecule): idr_regions=None) test_molecule.meta['moltype'] = "random" system = vermouth.System() - system.molecules.append(test_molecule) + system.add_molecule(test_molecule) assert processor.run_system(system) == system From 372f2262f2a132070cdf5210b17ea435adaee146 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Mon, 11 Dec 2023 09:21:50 +0100 Subject: [PATCH 83/95] Apply suggestions from code review Co-authored-by: Peter C Kroon --- vermouth/tests/gmx/test_topology.py | 2 -- vermouth/tests/helper_functions.py | 22 +++++++++---------- .../integration_tests/test_integration.py | 9 ++++---- vermouth/tests/rcsu/test_go_structure_bias.py | 6 ++--- vermouth/tests/test_vs_generation.py | 4 ++-- 5 files changed, 19 insertions(+), 24 deletions(-) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index 516bb075..b77c13c7 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -207,6 +207,4 @@ def test_toplevel_topology(tmp_path, dummy_molecule): ref_lines = textwrap.dedent(reference).splitlines() with open(str(outpath)) as infile: for line, ref_line in zip(infile, ref_lines): - print('l', line.strip()) - print('lr', ref_line.strip()) assert line.strip() == ref_line diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 3982c314..56ace336 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -163,17 +163,17 @@ def parse_gofiles(file, atomtypes=False): Parser of go_nbparams.itp & go_atomtypes.itp files into an easy to assert dictionary. ''' with open(file) as my_file: - tt = my_file.readlines() - vals = {} - for line in tt[1:]: - if atomtypes: - ## Key is atomname str, value is atomdef str - vals[line.split()[0]]=' '.join(line.split()[1:]) - else: - ## Key is tuple with nb pair, value is tuple with nb sigma and eps - tup = tuple(sorted((line.split()[0], - line.split()[1]))) - vals[tup]=tuple((float(line.split()[3]), float(line.split()[4]))) + next(my_file) # Skip header + vals = {} + for line in my_file: + line = line.split() + if atomtypes: + # Key is atomname str, value is atomdef str + vals[line[0]] = ' '.join(line[1:]) + else: + # Key is tuple with nb pair, value is tuple with nb sigma and eps + tup = tuple(sorted((line[0], line[1]))) + vals[tup] = tuple((float(line[3]), float(line[4]))) return vals @pytest.fixture diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index 0d7bed13..9c37ee95 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -131,10 +131,10 @@ def compare_goatomtypes(fileref, filecomp): ref = parse_gofiles(fileref, atomtypes=True) compare = parse_gofiles(filecomp, atomtypes=True) - assert(set(ref.keys())==set(compare.keys())) ## assert correct atomtypes + assert set(ref.keys()) == set(compare.keys()) # assert correct atomtypes for key in ref.keys(): - assert(ref[key] == compare[key]) ##assert correct atom definition string + assert ref[key] == compare[key] #assert correct atom definition string GOCOMPARERS = {'go_nbparams.itp': compare_nbparams, 'virtual_sites_nonbond_params.itp': compare_nbparams, @@ -236,9 +236,8 @@ def test_integration_protein(tmp_path, monkeypatch, tier, protein): filename = new_file.name reference_file = data_path/filename assert reference_file.is_file() - if filename in ['go_nbparams.itp','go_atomtypes.itp', - 'virtual_sites_nonbond_params.itp','virtual_sites_atomtypes.itp']: - ## compare the extra go/vs model files + if filename in GOCOMPARERS: + # compare the extra go/vs model files GOCOMPARERS[filename](str(reference_file), str(new_file)) else: ext = new_file.suffix.lower() diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 84d27c7b..1e6ffba4 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -15,9 +15,7 @@ def test_compute_go_interaction(test_molecule): ("atom_a", "atom_c", 4.1), ("atom_q", "atom_p", 0.0)] denom = 2**(1/6.) - expected = {("atom_a", "atom_b"): 2.3/denom, - ("atom_a", "atom_c"): 4.1/denom, - ("atom_q", "atom_p"): 0/denom} + expected = {(k1, k2): v/denom for k1, k2, v in contacts} system = vermouth.System() @@ -33,7 +31,7 @@ def test_compute_go_interaction(test_molecule): go_processor.compute_go_interaction(contacts) for nb_params in system.gmx_topology_params['nonbond_params']: assert nb_params.atoms in expected - assert np.isclose(nb_params.sigma, expected[nb_params.atoms]) + assert pytest.approx(expected[nb_params.atoms]) == nb_params.sigma assert nb_params.epsilon == 2.1 @pytest.mark.parametrize('cmap, cshort, clong, rdist, expected',( diff --git a/vermouth/tests/test_vs_generation.py b/vermouth/tests/test_vs_generation.py index bbdaedd3..e8abcb5d 100644 --- a/vermouth/tests/test_vs_generation.py +++ b/vermouth/tests/test_vs_generation.py @@ -21,14 +21,14 @@ def test_no_moltype_error(test_molecule): """ - Test that various high level IOErrors are + Test that various high level errors are properly raised. """ # set up processor processor = VirtualSiteCreator() # no moltype set system = vermouth.System() - system.molecules.append(test_molecule) + system.add_molecule(test_molecule) with pytest.raises(ValueError): processor.run_system(system) From 01b32b5244495c3d67a93cbbeb8d052de69a015b Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:31:01 +0100 Subject: [PATCH 84/95] Update vermouth/tests/rcsu/test_go_utils.py Co-authored-by: Peter C Kroon --- vermouth/tests/rcsu/test_go_utils.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/vermouth/tests/rcsu/test_go_utils.py b/vermouth/tests/rcsu/test_go_utils.py index 2d08b2c5..3233ed9b 100644 --- a/vermouth/tests/rcsu/test_go_utils.py +++ b/vermouth/tests/rcsu/test_go_utils.py @@ -51,13 +51,8 @@ def test_in_region(regions, resid, result): @hypothesis.given(random_molecule()) def test_get_go_type_from_attributes(mol): vs_node = len(mol.nodes) + with pytest.raises(KeyError): + next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) mol.add_node(vs_node, atype="prefix_0", chain="A", resid=5) found_atype = next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) assert found_atype == "prefix_0" - -@hypothesis.settings(suppress_health_check=[hypothesis.HealthCheck.too_slow]) -@hypothesis.given(random_molecule()) -def test_error_get_go_type_from_attributes(mol): - vs_node = len(mol.nodes) - with pytest.raises(KeyError): - next(get_go_type_from_attributes(mol, prefix="prefix", chain="A", resid=5)) From 023e457475ee79d27b8fdc985d285bc4773a5ae3 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:32:15 +0100 Subject: [PATCH 85/95] Update vermouth/tests/helper_functions.py Co-authored-by: Peter C Kroon --- vermouth/tests/helper_functions.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/vermouth/tests/helper_functions.py b/vermouth/tests/helper_functions.py index 56ace336..3e44c81d 100644 --- a/vermouth/tests/helper_functions.py +++ b/vermouth/tests/helper_functions.py @@ -151,11 +151,6 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs): system.molecules.append(molecule) return system -def is_equal(floats_a, floats_b, precision=1e-3): - ''' - Convenience comparisson of two floats within specified precision. - ''' - return all((abs(a-b) < precision) for a, b in zip(floats_a, floats_b)) def parse_gofiles(file, atomtypes=False): From cf400224befb15b7562ae4f680b1560956a9e126 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:32:38 +0100 Subject: [PATCH 86/95] Update vermouth/tests/rcsu/test_go_structure_bias.py Co-authored-by: Peter C Kroon --- vermouth/tests/rcsu/test_go_structure_bias.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/rcsu/test_go_structure_bias.py b/vermouth/tests/rcsu/test_go_structure_bias.py index 1e6ffba4..75f4bbea 100644 --- a/vermouth/tests/rcsu/test_go_structure_bias.py +++ b/vermouth/tests/rcsu/test_go_structure_bias.py @@ -7,7 +7,7 @@ import vermouth from vermouth.rcsu.go_vs_includes import VirtualSiteCreator from vermouth.tests.test_water_bias import create_sys_all_attrs -from vermouth.tests.test_apply_rubber_band import test_molecule +from vermouth.tests.helper_functions import test_molecule from vermouth.rcsu.go_structure_bias import ComputeStructuralGoBias def test_compute_go_interaction(test_molecule): From aaf8ee2004d85035cc4ca34a382b5b36d2b79653 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:33:18 +0100 Subject: [PATCH 87/95] Update vermouth/tests/integration_tests/test_integration.py Co-authored-by: Peter C Kroon --- vermouth/tests/integration_tests/test_integration.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index 9c37ee95..eaa82cde 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -121,7 +121,7 @@ def compare_nbparams(fileref, filecomp): assert set(ref.keys()) == set(compare.keys()) # assert correct nb pairs for key in ref.keys(): - assert(is_equal(list(ref[key]),list(compare[key]))) ##assert correct sigma and eps + assert compare[key] == pytest.approx(ref[key]) # assert correct sigma and eps def compare_goatomtypes(fileref, filecomp): From 69ae01170d14784f4a3e32a6c40f159d925dbac2 Mon Sep 17 00:00:00 2001 From: "Dr. Fabian Grunewald" <32294573+fgrunewald@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:33:36 +0100 Subject: [PATCH 88/95] Update vermouth/tests/integration_tests/test_integration.py Co-authored-by: Peter C Kroon --- vermouth/tests/integration_tests/test_integration.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index eaa82cde..2d73a0b3 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -28,7 +28,7 @@ from vermouth.forcefield import ForceField from .. import datafiles -from ..helper_functions import find_in_path, is_equal, parse_gofiles +from ..helper_functions import find_in_path, parse_gofiles INTEGRATION_DATA = Path(datafiles.TEST_DATA/'integration_tests') From 393e1bb53fd5da6ddb42300fa11f8e5dd2fb42fa Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 13:43:06 +0100 Subject: [PATCH 89/95] put comment --- vermouth/gmx/topology.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 9d850ecb..6a5c653a 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -46,9 +46,13 @@ def write_atomtypes(system, itp_path, C6C12=False): itp_file.write("[ atomtypes ]\n") grouped_types = _group_by_conditionals(system.gmx_topology_params['atomtypes']) for (conditional, group), interactions_in_group in grouped_types: + # conditionals are things like #ifdef; for more details on how this + # works see the molecule_itp_writer if conditional: conditional_key = conditional_keys[conditional[1]] itp_file.write('{} {}\n'.format(conditional_key, conditional[0])) + # groups are collections of interactions that are written bunched + # together and indicated by a comment line if group: itp_file.write('; {}\n'.format(group)) From 72a38178a12412d783031c11aa2dfa283d9810a8 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 13:45:42 +0100 Subject: [PATCH 90/95] fix docstring go vs includes --- vermouth/rcsu/go_vs_includes.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 31a6696d..3402441f 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -34,11 +34,6 @@ class VirtualSiteCreator(Processor): Every molecule must have a moltype name under the "moltype" key of the molecule meta. - Parameters - ---------- - sections: collections.abc.Iterable[str], optional - The sections to which to add an include statement. - See Also -------- :class:`~vermouth.processors.name_moltype.NameMolType` From e2491d07b99b5d7d6027370eb0e815ead00ac4b7 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 13:48:50 +0100 Subject: [PATCH 91/95] fix spelling --- vermouth/gmx/topology.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 6a5c653a..1245c9c3 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -182,7 +182,7 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), with deferred_open("{}.itp".format(moltype), "w") as outfile: # here we format and merge all citations header[-1] = header[-1] + "\n" - header.append("Pleas cite the following papers:") + header.append("Please cite the following papers:") for citation in molecule.citations: cite_string = citation_formatter( molecule.force_field.citations[citation] From 2a36e6341a905e0e7a69659ab4857b9102f0bbd4 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 14:09:45 +0100 Subject: [PATCH 92/95] make itp_paths dict in write_gmx_topology --- bin/martinize2 | 6 ++++-- vermouth/gmx/topology.py | 17 ++++++++++++----- 2 files changed, 16 insertions(+), 7 deletions(-) diff --git a/bin/martinize2 b/bin/martinize2 index 1ab934d3..f6e4f8d3 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -961,7 +961,8 @@ def entry(): res_dist=args.go_res_dist,) defines = ("GO_VIRT",) - itp_paths = ["go_atomtypes.itp", "go_nbparams.itp"] + itp_paths = {"atomtypes": "go_atomtypes.itp", + "nonbond_params": "go_nbparams.itp"} else: # don't write non-bonded interactions itp_paths = [] @@ -1029,7 +1030,8 @@ def entry(): # sites for the biasing if not args.go: vermouth.rcsu.go_vs_includes.VirtualSiteCreator().run_system(system) - itp_paths = ["virtual_sites_atomtypes.itp", "virtual_sites_nonbond_params.itp"] + itp_paths = {"atomtypes": "virtual_sites_atomtypes.itp", + "nonbond_params": "virtual_sites_nonbond_params.itp"} # now we add a bias by defining specific virtual-site water interactions vermouth.processors.ComputeWaterBias(args.water_bias, { s:float(eps) for s, eps in args.water_bias_eps}, diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index 1245c9c3..cfa52624 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -110,7 +110,13 @@ def write_nonbond_params(system, itp_path, C6C12=False): comments = "" itp_file.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n") -def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), header=()): +def write_gmx_topology(system, + top_path, + itp_paths={"nonbond_params": "extra_nbparams.itp", + "atomtypes": "extra_atomtypes.itp"}, + C6C12=False, + defines=(), + header=()): """ Writes a Gromacs .top file for the specified system. Gromacs topology files are defined by directives for example `[ atomtypes ]`. However, @@ -126,9 +132,10 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), system: vermouth.system.System top_path: pathlib.Path path for topology file - itp_paths: list[pathlib.Path] + itp_paths: dict[str, pathlib.Path] list of paths for writing the topology parameters - like atomtypes. + like atomtypes with the key being the name of the + directive. C6C12: bool write non-bonded interaction parameters using LJ C6C12 form @@ -144,12 +151,12 @@ def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), include_string = "" # First we write the atomtypes directive if "atomtypes" in system.gmx_topology_params: - _path = itp_paths.pop() + _path = itp_paths['atomtypes'] write_atomtypes(system, _path, C6C12) include_string += f'\n #include "{_path}"' # Next we write the nonbond_params directive if "nonbond_params" in system.gmx_topology_params: - _path = itp_paths.pop() + _path = itp_paths['nonbond_params'] write_nonbond_params(system, _path, C6C12) include_string += f'\n #include "{_path}"\n' # Write the ITP files for the molecule types, and prepare writing the From daa792b7bb7c177e461a6a65de2bc686694346ce Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 14:22:18 +0100 Subject: [PATCH 93/95] fix error type in test --- vermouth/tests/test_vs_generation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/test_vs_generation.py b/vermouth/tests/test_vs_generation.py index e8abcb5d..d942d537 100644 --- a/vermouth/tests/test_vs_generation.py +++ b/vermouth/tests/test_vs_generation.py @@ -41,7 +41,7 @@ def test_no_system_error(test_molecule): processor = VirtualSiteCreator() test_molecule.meta['moltype'] = "random" # no system - with pytest.raises(IOError): + with pytest.raises(ValueError): processor.run_molecule(test_molecule) def test_return_no_nodes(): From f5f5dead41a343c8a01d5751a8c56be9374d4bb9 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 14:29:46 +0100 Subject: [PATCH 94/95] fix bug in topology regarding itp_paths --- vermouth/gmx/topology.py | 1 - 1 file changed, 1 deletion(-) diff --git a/vermouth/gmx/topology.py b/vermouth/gmx/topology.py index cfa52624..ccd537c3 100644 --- a/vermouth/gmx/topology.py +++ b/vermouth/gmx/topology.py @@ -147,7 +147,6 @@ def write_gmx_topology(system, if not system.molecules: raise ValueError("No molecule in the system. Nothing to write.") - itp_paths = itp_paths[::-1] include_string = "" # First we write the atomtypes directive if "atomtypes" in system.gmx_topology_params: From 2fb282179167818903905c2695fc2cf786d7f935 Mon Sep 17 00:00:00 2001 From: Fabian Gruenewald Date: Thu, 14 Dec 2023 14:45:47 +0100 Subject: [PATCH 95/95] fix bug in topology regarding itp_paths --- vermouth/tests/gmx/test_topology.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vermouth/tests/gmx/test_topology.py b/vermouth/tests/gmx/test_topology.py index b77c13c7..659612f0 100644 --- a/vermouth/tests/gmx/test_topology.py +++ b/vermouth/tests/gmx/test_topology.py @@ -185,7 +185,7 @@ def test_toplevel_topology(tmp_path, dummy_molecule): outpath, header=['first header comment', 'second header comment'], defines=('random', ), - itp_paths=[atompath, nbpath], + itp_paths={"atomtypes": atompath, "nonbond_params": nbpath}, # at this level C6C12 doesn't matter; it gets # checked in previous texts C6C12=False)