In [16]:
import sys
import modeller
import _modeller
import modeller.automodel
import numpy as np
import warnings
warnings.filterwarnings('ignore') # make the notebook nicer
from __future__ import print_function
import pytraj as pt
import nglview as nv
from IPython.display import display, Image
In [2]:
env = modeller.environ()
env.io.hetatm = True
MODELLER 9.19, 2017/07/19, r11078
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux shadbox 3.2.0-29-generic x86_64
Date and time of compilation : 2017/07/19 14:40:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/12/24 06:02:33
Возьмем лизоцим гориллы (P79179 (LYSC_GORGO)):
In [3]:
%%bash
wget http://www.pdb.org/pdb/files/1lmp.pdb
wget http://www.uniprot.org/uniprot/P79179.fasta
--2017-12-24 06:02:38-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.244.52
Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-12-24 06:02:39-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 132.249.213.110
Connecting to www.rcsb.org (www.rcsb.org)|132.249.213.110|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-12-24 06:02:40-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 132.249.213.140
Connecting to files.rcsb.org (files.rcsb.org)|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb'
0K .......... .......... .......... .......... .......... 108K
50K .......... .......... .......... .......... .......... 108K
100K .......... .......... ........ 122K=1.2s
2017-12-24 06:02:42 (110 KB/s) - `1lmp.pdb' saved [131301]
--2017-12-24 06:02:42-- http://www.uniprot.org/uniprot/P79179.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.211, 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.211|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 228 [text/plain]
Saving to: `P79179.fasta'
0K 100% 40.1M=0s
2017-12-24 06:02:42 (40.1 MB/s) - `P79179.fasta' saved [228/228]
Создадим объект выравнивание и добавим последовательность и структуру:
In [4]:
alignm = modeller.alignment(env)
alignm.append(file = 'P79179.fasta', align_codes = 'all', alignment_format = 'FASTA')
## создадим модель
mdl = modeller.model(env, file = '1lmp.pdb', model_segment = ('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files = '1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'model'
alignm[1].code = 'aligment'
alignm.salign()
alignm.write(file = 'all_in_one.ali', alignment_format = 'PIR')
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
SALIGN_____> adding the next group to the alignment; iteration 1
In [5]:
with open('all_in_one.ali') as f:
print(f.readlines())
['\n', '>P1;model\n', 'sequence:: : : : :::-1.00:-1.00\n', 'MKALIVLGLVLLSVMVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIF\n', 'QINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV--\n', '-*\n', '\n', '>P1;aligment\n', 'structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16\n', '------------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNT-DGSTDYGIF\n', 'QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV..\n', '.*\n']
In [7]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
# print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile = 'all_in_one.ali', knowns = pdb.code, sequence = s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 1 #2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13197 12190
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 1158 1158
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12190 12190
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2361
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 870.5908
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1178 0 0 0.006 0.006 11.963 1.000
2 Bond angle potential : 1592 0 7 2.042 2.042 135.67 1.000
3 Stereochemical cosine torsion poten: 736 0 25 48.046 48.046 266.29 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.312 1.312 18.881 1.000
5 Soft-sphere overlap restraints : 2361 0 0 0.001 0.001 0.56495 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.135 0.135 46.168 1.000
10 Distance restraints 2 (N-O) : 2564 2 10 0.196 0.196 120.58 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 3 4.361 4.361 32.970 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 1 67.969 67.969 24.753 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 63.212 63.212 31.786 1.000
16 Sidechain Chi_3 dihedral restraints: 36 0 0 93.940 93.940 22.159 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 98.390 98.390 13.630 1.000
18 Disulfide distance restraints : 4 0 0 0.011 0.011 0.78846E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.908 1.908 0.64309 1.000
20 Disulfide dihedral angle restraints: 4 0 0 26.451 26.451 2.7758 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.421 0.421 38.614 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 16 16 23.218 59.765 40.285 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 0 0.680 0.680 62.783 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: model.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 14735.9307
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7443 45N 38Y N O 337 294 11.73 9.41 2.31 4.85 9.41 2.31 4.85
2 7472 46W 38Y N O 345 294 11.04 8.62 2.43 5.49 8.62 2.43 5.49
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 1M 2K C N 7 9 -74.63 -70.20 6.44 0.39 -62.90 174.51 23.32
1 2K 2K N CA 9 10 145.08 140.40 -40.80
2 4004 2K 3A C N 16 18 -130.60 -134.00 3.84 0.20 -62.50 -176.58 33.71
2 3A 3A N CA 18 19 148.79 147.00 -40.90
3 4005 3A 4L C N 21 23 -88.83 -108.50 32.88 1.52 -63.50 149.52 19.45
3 4L 4L N CA 23 24 106.15 132.50 -41.20
4 4008 6V 7L C N 44 46 -143.48 -108.50 68.42 3.25 -63.50 150.51 25.80
4 7L 7L N CA 46 47 -168.70 132.50 -41.20
5 4010 8G 9L C N 56 58 -54.95 -70.70 18.11 1.30 -63.50 174.07 24.67
5 9L 9L N CA 58 59 132.66 141.60 -41.20
6 4012 10V 11L C N 71 73 -84.98 -108.50 38.19 1.76 -63.50 145.21 19.04
6 11L 11L N CA 73 74 102.41 132.50 -41.20
7 4013 11L 12L C N 79 81 -112.71 -108.50 4.75 0.21 -63.50 -177.35 23.05
7 12L 12L N CA 81 82 134.70 132.50 -41.20
8 4014 12L 13S C N 87 89 -118.87 -136.60 21.88 0.67 -64.10 -178.18 11.21
8 13S 13S N CA 89 90 138.37 151.20 -35.00
9 4016 14V 15M C N 100 102 -72.28 -73.00 24.51 1.67 -63.40 152.26 23.43
9 15M 15M N CA 102 103 167.50 143.00 -40.50
10 4018 16V 17Q C N 115 117 -137.36 -121.10 29.49 1.06 -63.80 171.93 29.12
10 17Q 17Q N CA 117 118 164.30 139.70 -40.30
11 4019 17Q 18G C N 124 126 -153.76 -167.20 27.96 0.83 82.20 -171.77 14.23
11 18G 18G N CA 126 127 150.09 174.60 8.50
12 4020 18G 19K C N 128 130 -137.04 -118.00 19.23 0.78 -62.90 -167.95 22.16
12 19K 19K N CA 130 131 136.36 139.10 -40.80
13 4039 37G 38Y C N 281 283 -60.66 -63.50 13.00 1.92 -98.40 179.53 18.55
13 38Y 38Y N CA 283 284 -56.08 -43.40 128.40
14 4040 38Y 39R C N 293 295 -121.67 -125.20 86.80 4.12 57.30 179.67 20.18
14 39R 39R N CA 295 296 53.87 140.60 38.00
15 4055 53E 54S C N 416 418 -137.75 -64.10 81.01 8.59 -64.10 81.01 8.59
15 54S 54S N CA 418 419 -1.25 -35.00 -35.00
16 4067 65A 66G C N 509 511 -66.54 -62.40 4.53 0.86 82.20 157.42 11.98
16 66G 66G N CA 511 512 -43.05 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 4 8 37 68 116 107 121 166 177 199
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
model.B99990001.pdb 870.59076
In [8]:
nv.show_structure_file('model.B99990001.pdb')
In [17]:
Image('./1.png')
Out[17]:
In [9]:
# nv.show_structure_file('model.B99990002.pdb')
Добавляем лиганд:
In [10]:
## Получить список остаков
alignm[0].residues[:]
Out[10]:
[Residue MET, Residue LYS, Residue ALA, Residue LEU, Residue ILE, Residue VAL, Residue LEU, Residue GLY, Residue LEU, Residue VAL, Residue LEU, Residue LEU, Residue SER, Residue VAL, Residue MET, Residue VAL, Residue GLN, Residue GLY, Residue LYS, Residue VAL, Residue PHE, Residue GLU, Residue ARG, Residue CYS, Residue GLU, Residue LEU, Residue ALA, Residue ARG, Residue THR, Residue LEU, Residue LYS, Residue ARG, Residue LEU, Residue GLY, Residue MET, Residue ASP, Residue GLY, Residue TYR, Residue ARG, Residue GLY, Residue ILE, Residue SER, Residue LEU, Residue ALA, Residue ASN, Residue TRP, Residue MET, Residue CYS, Residue LEU, Residue ALA, Residue LYS, Residue TRP, Residue GLU, Residue SER, Residue GLY, Residue TYR, Residue ASN, Residue THR, Residue ARG, Residue ALA, Residue THR, Residue ASN, Residue TYR, Residue ASN, Residue ALA, Residue GLY, Residue ASP, Residue ARG, Residue SER, Residue THR, Residue ASP, Residue TYR, Residue GLY, Residue ILE, Residue PHE, Residue GLN, Residue ILE, Residue ASN, Residue SER, Residue ARG, Residue TYR, Residue TRP, Residue CYS, Residue ASN, Residue ASP, Residue GLY, Residue LYS, Residue THR, Residue PRO, Residue GLY, Residue ALA, Residue VAL, Residue ASN, Residue ALA, Residue CYS, Residue HIS, Residue LEU, Residue SER, Residue CYS, Residue SER, Residue ALA, Residue LEU, Residue LEU, Residue GLN, Residue ASP, Residue ASN, Residue ILE, Residue ALA, Residue ASP, Residue ALA, Residue VAL, Residue ALA, Residue CYS, Residue ALA, Residue LYS, Residue ARG, Residue VAL, Residue VAL, Residue ARG, Residue ASP, Residue PRO, Residue GLN, Residue GLY, Residue ILE, Residue ARG, Residue ALA, Residue TRP, Residue VAL, Residue ALA, Residue TRP, Residue ARG, Residue ASN, Residue ARG, Residue CYS, Residue GLN, Residue ASN, Residue ARG, Residue ASP, Residue VAL, Residue ARG, Residue GLN, Residue TYR, Residue VAL, Residue GLN, Residue GLY, Residue CYS, Residue GLY, Residue VAL]
In [11]:
seq = ''
for i in alignm[0].residues:
seq += i.code
seq += '...'
alignm.append_sequence(seq)
seq
Out[11]:
'MKALIVLGLVLLSVMVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV...'
In [12]:
# повторяем
alignm.salign()
alignm.write(file = 'all_in_one_and_ligand.ali', alignment_format = 'PIR')
## Выбираем объект для моделирования
s = alignm[2]
pdb = alignm[1]
# print s.code, pdb.code
## Создаем объект automodel с лигандом
a = modeller.automodel.automodel(env, alnfile = 'all_in_one_and_ligand.ali', knowns = pdb.code, sequence = s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 1 #2
a.make()
SALIGN_____> adding the next group to the alignment; iteration 1
SALIGN_____> adding the next group to the alignment; iteration 2
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 148
atom names : C +N
atom indices : 1156 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 148
atom names : C CA +N O
atom indices : 1156 1152 0 1157
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14598 13591
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 151
Number of all, selected real atoms : 1201 1201
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13591 13591
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2545
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 859.5407
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1178 0 0 0.006 0.006 12.800 1.000
2 Bond angle potential : 1592 0 10 2.163 2.163 151.76 1.000
3 Stereochemical cosine torsion poten: 736 0 22 47.422 47.422 262.08 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.329 1.329 19.397 1.000
5 Soft-sphere overlap restraints : 2545 2 2 0.008 0.008 17.429 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.121 0.121 37.581 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.149 0.149 63.872 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 147 0 3 4.812 4.812 40.145 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 1 68.839 68.839 22.180 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 63.678 63.678 39.337 1.000
16 Sidechain Chi_3 dihedral restraints: 36 0 0 79.723 79.723 24.668 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 98.916 98.916 13.332 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.46799E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.816 2.816 1.4007 1.000
20 Disulfide dihedral angle restraints: 4 0 0 24.692 24.692 2.4001 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1691 0 0 0.432 0.432 45.067 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 146 13 16 19.199 56.846 22.750 1.000
26 Distance restraints 4 (SDCH-SDCH) : 972 0 0 0.696 0.696 69.193 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 14.103 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: .V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 14851.0059
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 1M 2K C N 7 9 -84.44 -70.20 33.37 2.10 -62.90 150.17 20.74
1 2K 2K N CA 9 10 170.58 140.40 -40.80
2 4004 2K 3A C N 16 18 -61.70 -68.20 11.59 1.12 -62.50 164.20 26.87
2 3A 3A N CA 18 19 154.90 145.30 -40.90
3 4005 3A 4L C N 21 23 -61.90 -70.70 9.23 0.74 -63.50 179.98 24.90
3 4L 4L N CA 23 24 138.82 141.60 -41.20
4 4008 6V 7L C N 44 46 -64.39 -70.70 10.70 1.04 -63.50 168.55 23.45
4 7L 7L N CA 46 47 150.25 141.60 -41.20
5 4009 7L 8G C N 52 54 115.88 78.70 37.30 1.81 82.20 -179.29 7.08
5 8G 8G N CA 54 55 -169.04 -166.10 8.50
6 4010 8G 9L C N 56 58 -111.66 -108.50 3.19 0.16 -63.50 179.86 22.70
6 9L 9L N CA 58 59 132.09 132.50 -41.20
7 4012 10V 11L C N 71 73 -123.67 -108.50 15.18 0.73 -63.50 -176.75 22.80
7 11L 11L N CA 73 74 131.89 132.50 -41.20
8 4013 11L 12L C N 79 81 -86.97 -70.70 21.45 1.41 -63.50 164.90 24.31
8 12L 12L N CA 81 82 155.58 141.60 -41.20
9 4014 12L 13S C N 87 89 -58.56 -72.40 46.15 2.28 -64.10 143.49 10.73
9 13S 13S N CA 89 90 108.38 152.40 -35.00
10 4016 14V 15M C N 100 102 -62.94 -73.00 14.48 0.92 -63.40 173.09 25.88
10 15M 15M N CA 102 103 132.59 143.00 -40.50
11 4018 16V 17Q C N 115 117 -120.46 -121.10 3.08 0.16 -63.80 -174.16 30.34
11 17Q 17Q N CA 117 118 142.71 139.70 -40.30
12 4020 18G 19K C N 128 130 -119.43 -118.00 6.38 0.32 -62.90 -177.35 21.34
12 19K 19K N CA 130 131 132.89 139.10 -40.80
13 4067 65A 66G C N 509 511 -73.73 -62.40 11.38 1.99 82.20 163.35 12.34
13 66G 66G N CA 511 512 -40.15 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 10 55 85 132 111 146 167 187 217
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
.B99990001.pdb 859.54071
In [13]:
nv.show_structure_file('.B99990001.pdb')
In [18]:
Image('./2.png')
Out[18]:
In [14]:
# nv.show_structure_file('.B99990002.pdb')