Гомологичное моделирование комплекса белка с лигандом¶
Импортируем все необходимые для работы модули. Установка модуля modeller производилась с помощью следующих команд:
conda config --add channels salilab conda install modellerДалее необходимо было получить ключ доступа для вноса его в конфигурационные файлы modeller.
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
Зададим некторые дополнительные параметры
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.21, 2018/12/06, r11301
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2018 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 alexander-HP-Notebook 4.17.19-041719-generic x86_64
Date and time of compilation : 2018/12/06 09:58:12
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2019/05/30 02:44:54
Далее скачаем белок-заготовку (лизоцим радужной форели(Oncorhynchus mykiss)):
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2019-05-30 02:44:56-- http://www.pdb.org/pdb/files/1lmp.pdb Распознаётся www.pdb.org (www.pdb.org)… 128.6.244.52 Подключение к www.pdb.org (www.pdb.org)|128.6.244.52|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 301 Moved Permanently Адрес: https://www.rcsb.org/pdb/files/1lmp.pdb [переход] --2019-05-30 02:44:56-- https://www.rcsb.org/pdb/files/1lmp.pdb Распознаётся www.rcsb.org (www.rcsb.org)… 132.249.213.190 Подключение к www.rcsb.org (www.rcsb.org)|132.249.213.190|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 301 Moved Permanently Адрес: http://files.rcsb.org/view/1lmp.pdb [переход] --2019-05-30 02:44:57-- http://files.rcsb.org/view/1lmp.pdb Распознаётся files.rcsb.org (files.rcsb.org)… 132.249.213.91 Подключение к files.rcsb.org (files.rcsb.org)|132.249.213.91|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 200 OK Длина: нет данных [text/plain] Сохранение в: «1lmp.pdb» 1lmp.pdb [ <=> ] 127,35K 154KB/s за 0,8s 2019-05-30 02:44:59 (154 KB/s) - «1lmp.pdb» сохранён [130410]
А теперь скачаем последовательность лизоцима из Bombyx mori (LYS_BOMMO):
In [4]:
! wget http://www.uniprot.org/uniprot/P48816.fasta
URL transformed to HTTPS due to an HSTS policy --2019-05-30 02:45:00-- https://www.uniprot.org/uniprot/P48816.fasta Распознаётся www.uniprot.org (www.uniprot.org)… 128.175.245.185, 193.62.193.81 Подключение к www.uniprot.org (www.uniprot.org)|128.175.245.185|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 200 Длина: 203 [text/plain] Сохранение в: «P48816.fasta» P48816.fasta 100%[===================>] 203 --.-KB/s за 0s 2019-05-30 02:45:00 (11,5 MB/s) - «P48816.fasta» сохранён [203/203]
Создадим объект выравнивание:
In [5]:
alignm=modeller.alignment(env)
Теперь последовательность и структуру, а также изменяем идентификаторы:
In [6]:
alignm.append(file='P48816.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 = 'BOMMO'
alignm[1].code = '1lmp'
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.
Далее делаем выравнивание и сохраняем:
In [7]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Проверим содержимое получившегося файла:
In [8]:
! cat all_in_one.ali
>P1;BOMMO sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC-------* >P1;1lmp 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 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
В LYS_BOMMO нет лиганда, добавляем его в файл вручную.
Попробуем построить модель:
In [9]:
## 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 = 2
a.make()
BOMMO 1lmp
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
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
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: 3
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: 13094 12134
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2441
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 : 981.9435
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 : 1119 0 2 0.009 0.009 27.602 1.000
2 Bond angle potential : 1504 1 10 2.195 2.195 147.58 1.000
3 Stereochemical cosine torsion poten: 713 0 28 47.908 47.908 257.01 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.213 1.213 15.141 1.000
5 Soft-sphere overlap restraints : 2441 1 2 0.008 0.008 17.908 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) : 2215 0 4 0.292 0.292 95.691 1.000
10 Distance restraints 2 (N-O) : 2371 0 7 0.323 0.323 127.75 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: 136 0 3 4.692 4.692 35.312 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 77.529 77.529 30.094 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 68.371 68.371 34.429 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 65.387 65.387 20.307 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 99.401 99.401 14.422 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.43978 1.000
19 Disulfide angle restraints : 6 0 0 5.194 5.194 3.5746 1.000
20 Disulfide dihedral angle restraints: 3 0 0 35.678 35.678 2.5594 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) : 1316 0 0 0.368 0.368 29.910 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: 135 16 14 27.779 61.199 68.850 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.580 0.580 27.834 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 25.531 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: BOMMO.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: 15234.8779
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 128.29 107.00 21.29 6.12 107.00 21.29 6.12
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -74.94 -73.00 11.67 0.72 -63.80 167.86 25.27
1 2Q 2Q N CA 9 10 152.21 140.70 -40.30
2 3811 2Q 3K C N 16 18 -70.90 -70.20 1.53 0.13 -62.90 -179.99 22.95
2 3K 3K N CA 18 19 139.03 140.40 -40.80
3 3812 3K 4L C N 25 27 -78.71 -70.70 8.17 0.69 -63.50 176.25 25.37
3 4L 4L N CA 27 28 143.21 141.60 -41.20
4 3815 6I 7F C N 49 51 -76.99 -71.40 28.90 2.46 -63.20 157.25 20.92
4 7F 7F N CA 51 52 112.34 140.70 -44.30
5 3816 7F 8A C N 60 62 -173.52 -134.00 45.15 1.04 -62.50 -173.15 36.46
5 8A 8A N CA 62 63 168.81 147.00 -40.90
6 3817 8A 9L C N 65 67 -70.64 -70.70 3.54 0.27 -63.50 173.81 24.55
6 9L 9L N CA 67 68 145.14 141.60 -41.20
7 3820 11V 12L C N 87 89 -73.20 -70.70 10.64 0.72 -63.50 167.14 23.78
7 12L 12L N CA 89 90 151.94 141.60 -41.20
8 3821 12L 13C C N 95 97 -58.93 -63.00 5.78 0.66 -117.90 -176.56 7.94
8 13C 13C N CA 97 98 -45.20 -41.10 141.10
9 3823 14V 15G C N 108 110 -77.03 -80.20 6.83 0.16 82.20 -134.58 7.04
9 15G 15G N CA 110 111 168.06 174.10 8.50
10 3824 15G 16S C N 112 114 -119.88 -136.60 22.32 0.70 -64.10 -179.73 11.11
10 16S 16S N CA 114 115 136.42 151.20 -35.00
11 3844 35F 36E C N 274 276 60.37 54.60 14.68 0.76 -63.60 141.98 24.42
11 36E 36E N CA 276 277 28.90 42.40 -40.30
12 3859 50E 51S C N 405 407 -139.21 -64.10 84.45 8.70 -64.10 84.45 8.70
12 51S 51S N CA 407 408 3.63 -35.00 -35.00
13 3860 51S 52S C N 411 413 60.11 56.90 5.63 0.26 -64.10 141.02 18.66
13 52S 52S N CA 413 414 31.77 36.40 -35.00
14 3896 87K 88D C N 695 697 -142.90 -63.30 83.98 14.22 -63.30 83.98 14.22
14 88D 88D N CA 697 698 -66.77 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -45.14 -98.40 59.64 3.71 -63.50 146.12 24.13
15 112Y 112Y N CA 874 875 101.56 128.40 -43.40
16 3935 126H 127C C N 1020 1022 -115.45 -63.00 53.45 8.30 -63.00 53.45 8.30
16 127C 127C N CA 1022 1023 -30.79 -41.10 -41.10
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 1 10 10 53 73 100 141 140 157 178 208
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2451
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 : 1179.6171
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 : 1119 0 3 0.010 0.010 31.219 1.000
2 Bond angle potential : 1504 1 11 2.485 2.485 181.93 1.000
3 Stereochemical cosine torsion poten: 713 0 31 48.523 48.523 266.72 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.498 1.498 21.806 1.000
5 Soft-sphere overlap restraints : 2451 1 2 0.008 0.008 18.760 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) : 2215 0 4 0.341 0.341 132.27 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.365 0.365 166.36 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: 136 0 1 4.659 4.659 34.820 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 76.147 76.147 45.144 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 70.553 70.553 37.836 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 87.135 87.135 27.396 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 85.938 85.938 16.355 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.33424 1.000
19 Disulfide angle restraints : 6 0 0 4.132 4.132 2.2624 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.107 22.107 1.4162 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) : 1316 0 0 0.376 0.376 32.619 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: 135 22 19 32.564 69.494 93.012 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.736 0.736 44.076 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.046 0.046 25.273 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: BOMMO.V99990002
# 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: 16943.4551
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2080 88D 88D N CA 697 698 128.22 107.00 21.22 6.10 107.00 21.22 6.10
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -78.52 -73.00 11.74 0.68 -63.80 169.28 25.67
1 2Q 2Q N CA 9 10 151.06 140.70 -40.30
2 3811 2Q 3K C N 16 18 -60.16 -70.20 19.43 1.60 -62.90 162.18 20.91
2 3K 3K N CA 18 19 157.04 140.40 -40.80
3 3812 3K 4L C N 25 27 -63.58 -70.70 8.39 0.59 -63.50 178.35 24.76
3 4L 4L N CA 27 28 137.15 141.60 -41.20
4 3815 6I 7F C N 49 51 -153.80 -124.20 39.76 1.05 -63.20 171.71 29.50
4 7F 7F N CA 51 52 169.84 143.30 -44.30
5 3816 7F 8A C N 60 62 -100.55 -68.20 43.37 4.28 -62.50 161.85 24.95
5 8A 8A N CA 62 63 116.42 145.30 -40.90
6 3817 8A 9L C N 65 67 -112.53 -108.50 39.64 2.18 -63.50 142.94 17.74
6 9L 9L N CA 67 68 93.07 132.50 -41.20
7 3819 10V 11V C N 80 82 -63.46 -62.40 3.86 0.44 -125.40 -171.52 10.54
7 11V 11V N CA 82 83 -38.68 -42.40 143.30
8 3820 11V 12L C N 87 89 85.47 -70.70 156.17 14.22 -63.50 -129.09 29.03
8 12L 12L N CA 89 90 142.38 141.60 -41.20
9 3823 14V 15G C N 108 110 -90.58 -80.20 37.92 1.02 82.20 -125.91 18.08
9 15G 15G N CA 110 111 -149.43 174.10 8.50
10 3824 15G 16S C N 112 114 -72.44 -72.40 26.87 1.58 -64.10 160.75 11.18
10 16S 16S N CA 114 115 125.53 152.40 -35.00
11 3844 35F 36E C N 274 276 52.32 54.60 3.08 0.39 -63.60 141.20 24.28
11 36E 36E N CA 276 277 40.32 42.40 -40.30
12 3859 50E 51S C N 405 407 -138.07 -64.10 84.59 8.53 -64.10 84.59 8.53
12 51S 51S N CA 407 408 6.05 -35.00 -35.00
13 3860 51S 52S C N 411 413 56.20 56.90 2.60 0.11 -64.10 141.18 18.52
13 52S 52S N CA 413 414 38.90 36.40 -35.00
14 3896 87K 88D C N 695 697 -146.12 -63.30 84.58 14.08 -63.30 84.58 14.08
14 88D 88D N CA 697 698 -57.15 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -45.03 -98.40 59.11 3.59 -63.50 147.55 24.36
15 112Y 112Y N CA 874 875 102.99 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -130.81 -63.20 86.69 10.21 -63.20 86.69 10.21
16 126H 126H N CA 1012 1013 11.95 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -134.67 -63.00 77.15 10.98 -63.00 77.15 10.98
17 127C 127C N CA 1022 1023 -12.52 -41.10 -41.10
18 3936 127C 128Q C N 1026 1028 -63.28 -63.80 7.09 1.07 -121.10 -177.66 7.54
18 128Q 128Q N CA 1028 1029 -33.23 -40.30 139.70
19 3937 128Q 129G C N 1035 1037 -61.66 -62.40 11.26 1.72 82.20 148.92 11.13
19 129G 129G N CA 1037 1038 -29.96 -41.20 8.50
20 3938 129G 130S C N 1039 1041 83.30 56.90 32.67 2.38 -72.40 -153.77 10.07
20 130S 130S N CA 1041 1042 17.17 36.40 152.40
21 3939 130S 131L C N 1045 1047 -66.99 -63.50 4.39 0.59 -108.50 175.99 9.02
21 131L 131L N CA 1047 1048 -38.53 -41.20 132.50
22 3940 131L 132P C N 1053 1055 -41.08 -64.50 78.94 4.84 -58.70 103.82 10.03
22 132P 132P N CA 1055 1056 71.81 147.20 -30.50
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 10 12 63 93 120 154 153 155 191 187
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
BOMMO.B99990001.pdb 981.94354
BOMMO.B99990002.pdb 1179.61707
Теперь проверим результат:
In [16]:
from IPython.display import Image
Image(filename='mod_1.jpg') # 1-ая модель
Out[16]:
In [36]:
from IPython.display import Image
Image(filename='foru2.png') # 2-ая модель
Out[36]:
Перемещение лиганда¶
Необходимо переместить лиганд в другое место
In [33]:
! rm BOMMO.rsr
rm: невозможно удалить 'BOMMO.rsr': Нет такого файла или каталога
In [51]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:123','CA:114')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
Замена всех аминокислот на аланин¶
Необходимо было заменить все аминокислоты лизоцима на аланин. Добавляем исходный лизоцим радужной форели, далее создаем alanin с последовательностью только из аланинов. Выравниваем, проверяем содержимое файла, создаем модель.
In [23]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alanin = 'A' * 120 + '...'
alignm.append_sequence(alanin)
alignm[0].code = 'pdb'
alignm[1].code = 'alanin'
In [24]:
alignm.salign()
alignm.write(file='align_alanin.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [25]:
! cat align_alanin.ali
>P1;pdb 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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;alanin sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [26]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_alanin.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
alanin pdb
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
----------------------------------------------
55 1 55 65 A A 16.730
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C +N
atom indices : 599 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C CA +N O
atom indices : 599 597 0 600
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.)
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: 8748 8155
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1138
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 : 1024.6859
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 : 600 0 1 0.008 0.008 11.661 1.000
2 Bond angle potential : 839 0 2 2.043 2.043 72.183 1.000
3 Stereochemical cosine torsion poten: 244 0 34 76.087 76.087 233.14 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.832 0.832 4.6123 1.000
5 Soft-sphere overlap restraints : 1138 1 2 0.011 0.011 15.716 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) : 1968 8 23 0.771 0.771 259.39 1.000
10 Distance restraints 2 (N-O) : 2093 8 28 0.737 0.737 317.46 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: 119 0 2 4.468 4.468 28.016 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 668 0 0 0.337 0.337 7.8380 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: 118 23 15 33.430 71.179 51.767 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.034 1.034 4.2678 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.042 0.042 18.631 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: alanin.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: 11953.0938
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 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3583 56A 63A CA CA 277 312 13.37 7.04 6.33 5.97 7.04 6.33 5.97
2 3584 56A 64A CA CA 277 317 13.91 7.69 6.22 4.84 7.69 6.22 4.84
3 3585 56A 65A CA CA 277 322 11.08 5.45 5.64 6.48 5.45 5.64 6.48
4 3588 56A 68A CA CA 277 337 12.21 7.46 4.75 4.61 7.46 4.75 4.61
5 3589 56A 69A CA CA 277 342 9.94 6.07 3.87 5.44 6.07 3.87 5.44
6 3590 56A 70A CA CA 277 347 9.07 4.69 4.38 6.25 4.69 4.38 6.25
-------------------------------------------------------------------------------------------------
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 4905 38A 55A N O 186 275 8.23 5.51 2.72 4.64 5.51 2.72 4.64
2 5216 56A 63A N O 276 315 14.22 7.89 6.33 5.14 7.89 6.33 5.14
3 5217 56A 64A N O 276 320 13.33 7.21 6.12 4.65 7.21 6.12 4.65
4 5218 56A 65A N O 276 325 13.23 6.37 6.87 6.49 6.37 6.87 6.49
5 5221 56A 68A N O 276 340 12.46 7.02 5.44 5.08 7.02 5.44 5.08
6 5222 56A 69A N O 276 345 8.64 2.70 5.95 11.62 2.70 5.95 11.62
7 5389 71A 56A N O 351 280 5.72 2.97 2.75 5.81 2.97 2.75 5.81
8 5427 73A 70A N O 361 350 5.97 3.17 2.80 4.54 3.17 2.80 4.54
-------------------------------------------------------------------------------------------------
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 1938 15A 16A C N 74 76 78.31 55.40 26.58 1.95 -62.50 155.35 31.56
1 16A 16A N CA 76 77 24.73 38.20 -40.90
2 1941 18A 19A C N 89 91 65.37 55.40 22.28 0.81 -62.50 140.90 28.62
2 19A 19A N CA 91 92 18.28 38.20 -40.90
3 1943 20A 21A C N 99 101 54.25 55.40 4.53 0.37 -62.50 138.61 28.16
3 21A 21A N CA 101 102 33.82 38.20 -40.90
4 1944 21A 22A C N 104 106 62.28 55.40 10.54 0.50 -62.50 143.61 29.21
4 22A 22A N CA 106 107 30.21 38.20 -40.90
5 1959 36A 37A C N 179 181 66.24 55.40 13.97 0.85 -62.50 146.68 29.83
5 37A 37A N CA 181 182 29.39 38.20 -40.90
6 1960 37A 38A C N 184 186 61.13 55.40 8.87 0.41 -62.50 143.23 29.13
6 38A 38A N CA 186 187 31.43 38.20 -40.90
7 1971 48A 49A C N 239 241 158.44 -134.00 71.85 1.67 -62.50 -157.19 40.35
7 49A 49A N CA 241 242 171.47 147.00 -40.90
8 1972 49A 50A C N 244 246 85.11 -134.00 141.22 4.32 -68.20 153.74 13.41
8 50A 50A N CA 246 247 156.72 147.00 145.30
9 1976 53A 54A C N 264 266 59.57 -68.20 143.90 13.94 -62.50 162.73 25.52
9 54A 54A N CA 266 267 -148.51 145.30 -40.90
10 1979 56A 57A C N 279 281 -143.33 -134.00 40.82 2.06 -62.50 155.10 29.72
10 57A 57A N CA 281 282 -173.26 147.00 -40.90
11 1980 57A 58A C N 284 286 -72.09 -68.20 16.37 1.18 -62.50 158.19 26.41
11 58A 58A N CA 286 287 161.21 145.30 -40.90
12 1984 61A 62A C N 304 306 57.29 55.40 2.29 0.16 -62.50 142.84 29.02
12 62A 62A N CA 306 307 36.91 38.20 -40.90
13 1986 63A 64A C N 314 316 -76.70 -68.20 8.50 0.72 -62.50 174.47 29.31
13 64A 64A N CA 316 317 145.22 145.30 -40.90
14 1987 64A 65A C N 319 321 -96.10 -68.20 50.40 4.88 -62.50 148.09 22.87
14 65A 65A N CA 321 322 103.33 145.30 -40.90
15 1988 65A 66A C N 324 326 -67.90 -68.20 12.57 1.02 -62.50 161.32 26.71
15 66A 66A N CA 326 327 157.87 145.30 -40.90
16 1989 66A 67A C N 329 331 51.26 -68.20 133.54 9.21 -62.50 170.13 33.74
16 67A 67A N CA 331 332 85.61 145.30 -40.90
17 1990 67A 68A C N 334 336 -64.08 -68.20 35.07 2.68 -62.50 151.38 24.73
17 68A 68A N CA 336 337 110.47 145.30 -40.90
18 1992 69A 70A C N 344 346 -67.79 -62.50 23.28 4.09 -134.00 163.45 10.09
18 70A 70A N CA 346 347 -63.57 -40.90 147.00
19 1993 70A 71A C N 349 351 -167.50 -62.50 106.05 19.71 -62.50 106.05 19.71
19 71A 71A N CA 351 352 -26.02 -40.90 -40.90
20 2017 94A 95A C N 469 471 80.97 -134.00 159.81 3.63 -62.50 177.78 28.55
20 95A 95A N CA 471 472 -145.89 147.00 -40.90
21 2030 107A 108A C N 534 536 51.50 55.40 7.23 0.28 -62.50 142.31 28.82
21 108A 108A N CA 536 537 44.29 38.20 -40.90
22 2039 116A 117A C N 579 581 68.50 55.40 32.78 1.19 -62.50 139.88 28.31
22 117A 117A N CA 581 582 8.15 38.20 -40.90
23 2041 118A 119A C N 589 591 66.16 55.40 15.18 0.80 -62.50 145.71 29.63
23 119A 119A N CA 591 592 27.50 38.20 -40.90
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 3 8 35 49 63 67 75 89 95 73
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1111
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 : 1030.4675
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 : 600 0 1 0.008 0.008 12.104 1.000
2 Bond angle potential : 839 0 4 2.189 2.189 82.819 1.000
3 Stereochemical cosine torsion poten: 244 0 27 74.761 74.761 225.49 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.809 0.809 4.3248 1.000
5 Soft-sphere overlap restraints : 1111 1 2 0.011 0.011 15.535 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) : 1968 8 31 0.797 0.797 282.22 1.000
10 Distance restraints 2 (N-O) : 2093 7 36 0.759 0.759 340.54 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: 119 0 5 5.086 5.086 36.303 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 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) : 668 0 0 0.258 0.258 4.9947 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: 118 17 10 24.861 63.466 4.9907 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.009 1.009 3.9849 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.040 0.040 17.160 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: alanin.V99990002
# 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: 11050.6143
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 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3583 56A 63A CA CA 277 312 13.04 7.04 6.00 5.66 7.04 6.00 5.66
2 3584 56A 64A CA CA 277 317 13.65 7.69 5.96 4.64 7.69 5.96 4.64
3 3585 56A 65A CA CA 277 322 11.04 5.45 5.59 6.43 5.45 5.59 6.43
4 3588 56A 68A CA CA 277 337 12.26 7.46 4.80 4.66 7.46 4.80 4.66
5 3589 56A 69A CA CA 277 342 10.06 6.07 3.99 5.60 6.07 3.99 5.60
6 3590 56A 70A CA CA 277 347 9.73 4.69 5.04 7.19 4.69 5.04 7.19
-------------------------------------------------------------------------------------------------
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 4905 38A 55A N O 186 275 8.36 5.51 2.85 4.86 5.51 2.85 4.86
2 5216 56A 63A N O 276 315 14.73 7.89 6.84 5.55 7.89 6.84 5.55
3 5217 56A 64A N O 276 320 13.39 7.21 6.17 4.69 7.21 6.17 4.69
4 5218 56A 65A N O 276 325 13.63 6.37 7.27 6.87 6.37 7.27 6.87
5 5221 56A 68A N O 276 340 13.13 7.02 6.10 5.69 7.02 6.10 5.69
6 5222 56A 69A N O 276 345 8.82 2.70 6.13 11.97 2.70 6.13 11.97
7 5389 71A 56A N O 351 280 5.80 2.97 2.83 5.98 2.97 2.83 5.98
-------------------------------------------------------------------------------------------------
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 1938 15A 16A C N 74 76 79.24 55.40 26.92 2.08 -62.50 156.61 31.82
1 16A 16A N CA 76 77 25.70 38.20 -40.90
2 1940 17A 18A C N 84 86 -56.66 -62.50 8.56 1.31 -134.00 -177.01 11.29
2 18A 18A N CA 86 87 -47.15 -40.90 147.00
3 1943 20A 21A C N 99 101 57.33 55.40 11.75 0.56 -62.50 137.53 27.97
3 21A 21A N CA 101 102 26.61 38.20 -40.90
4 1944 21A 22A C N 104 106 63.31 55.40 16.76 0.61 -62.50 141.30 28.73
4 22A 22A N CA 106 107 23.42 38.20 -40.90
5 1959 36A 37A C N 179 181 65.36 55.40 12.65 0.79 -62.50 146.39 29.77
5 37A 37A N CA 181 182 30.40 38.20 -40.90
6 1960 37A 38A C N 184 186 60.51 55.40 6.88 0.39 -62.50 143.81 29.24
6 38A 38A N CA 186 187 33.60 38.20 -40.90
7 1971 48A 49A C N 239 241 85.31 55.40 38.63 2.35 -62.50 157.59 31.89
7 49A 49A N CA 241 242 13.75 38.20 -40.90
8 1976 53A 54A C N 264 266 57.58 -68.20 142.76 13.86 -62.50 160.35 25.13
8 54A 54A N CA 266 267 -147.17 145.30 -40.90
9 1979 56A 57A C N 279 281 -145.57 -134.00 14.24 0.78 -62.50 -162.12 29.70
9 57A 57A N CA 281 282 138.70 147.00 -40.90
10 1984 61A 62A C N 304 306 59.05 55.40 4.04 0.48 -62.50 145.97 29.64
10 62A 62A N CA 306 307 39.92 38.20 -40.90
11 1986 63A 64A C N 314 316 -111.75 -134.00 22.36 0.66 -62.50 -178.79 32.31
11 64A 64A N CA 316 317 144.71 147.00 -40.90
12 1987 64A 65A C N 319 321 -79.87 -68.20 36.04 3.29 -62.50 153.09 24.29
12 65A 65A N CA 321 322 111.21 145.30 -40.90
13 1990 67A 68A C N 334 336 63.97 55.40 12.13 0.64 -62.50 144.79 29.45
13 68A 68A N CA 336 337 29.61 38.20 -40.90
14 2017 94A 95A C N 469 471 79.64 -134.00 160.97 3.66 -62.50 176.78 28.35
14 95A 95A N CA 471 472 -146.00 147.00 -40.90
15 2030 107A 108A C N 534 536 50.48 55.40 9.90 0.37 -62.50 143.02 28.93
15 108A 108A N CA 536 537 46.79 38.20 -40.90
16 2039 116A 117A C N 579 581 66.33 55.40 29.45 1.08 -62.50 138.83 28.14
16 117A 117A N CA 581 582 10.85 38.20 -40.90
17 2041 118A 119A C N 589 591 64.80 55.40 12.29 0.73 -62.50 145.85 29.66
17 119A 119A N CA 591 592 30.28 38.20 -40.90
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 3 3 34 51 71 63 76 102 83 75
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
alanin.B99990001.pdb 1024.68591
alanin.B99990002.pdb 1030.46753
Визуализируем полученый результат:
In [40]:
from IPython.display import Image
Image(filename='ala_1.jpg') # 1-ая модель
Out[40]:
In [42]:
from IPython.display import Image
Image(filename='ala2.png') # 2-ая модель
Out[42]:
