In [47]:
Image('superimposition.png')
Out[47]:
import sys
import modeller
import _modeller
import modeller.automodel
Согласно данной нам теоретической информации, программе MODELLER для моделирования структуры белков, в качестве входных данных нужны:
- управляющий скрипт,
- файл pdb со структурой-образцом,
- файл выравнивания с дополнительной информацией
env=modeller.Environ()
env.io.hetatm=True
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 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 ripper 5.8.0-43-generic x86_64
Date and time of compilation : 2021/03/12 00:18:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/05/25 15:54:26
import os
os.chdir('/home/domain/julybel/rem/')
%%bash
wget http://www.pdb.org/pdb/files/1lmp.pdb
wget http://www.uniprot.org/uniprot/LYS_BPAPS.fasta # LYS_BPAPS
--2021-05-25 15:20:38-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.159.96
Connecting to www.pdb.org (www.pdb.org)|128.6.159.96|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2021-05-25 15:20:38-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 128.6.159.248
Connecting to www.rcsb.org (www.rcsb.org)|128.6.159.248|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://files.rcsb.org/download/1lmp.pdb [following]
--2021-05-25 15:20:39-- https://files.rcsb.org/download/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 128.6.158.49
Connecting to files.rcsb.org (files.rcsb.org)|128.6.158.49|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/octet-stream]
Saving to: ‘1lmp.pdb.4’
0K .......... .......... .......... .......... .......... 206K
50K .......... .......... .......... .......... .......... 408K
100K .......... .......... ..... 74.3M=0.4s
2021-05-25 15:20:40 (345 KB/s) - ‘1lmp.pdb.4’ saved [128871]
URL transformed to HTTPS due to an HSTS policy
--2021-05-25 15:20:40-- https://www.uniprot.org/uniprot/LYS_BPAPS.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.206, 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.206|:443... connected.
HTTP request sent, awaiting response... 302
Location: /uniprot/Q9T1T5.fasta [following]
URL transformed to HTTPS due to an HSTS policy
--2021-05-25 15:20:40-- https://www.uniprot.org/uniprot/Q9T1T5.fasta
Reusing existing connection to www.uniprot.org:443.
HTTP request sent, awaiting response... 200
Length: 261 [text/plain]
Saving to: ‘LYS_BPAPS.fasta.2’
0K 100% 52.5M=0s
2021-05-25 15:20:40 (52.5 MB/s) - ‘LYS_BPAPS.fasta.2’ saved [261/261]
Создадим объект выравнивание:
alignm=modeller.Alignment(env)
Добавим последовательность и структуру:
alignm.append(file='LYS_BPAPS.fasta', align_codes='all',alignment_format='FASTA')
# Создадим модель
mdl = modeller.Model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
# Добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
read_pd_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.
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.
# Присвоим нужные идентификаторы
alignm[0].code = 'sequence'
alignm[1].code = 'model'
Делаем выравнивание, сохраняем:
alignm.salign()
alignm.write(file='./all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Посмотрим, что получилось с выравниванием:
! cat all_in_one.ali
>P1;sequence sequence::: :: :::-1.00:-1.00 MHISEKGLVLIKRYEGLRLKAYQCRAGRWTLGYGHTHNLNIGDVITQEQAEAFLREDIAQVTALLNTQIKVPLTQ NQYDAICSLVFNIGMTAFTTSTLLKKLNVGDYSGASAEFMKWSKAKVNGKRTPLPGLIKRRQAEKALF-ESA* >P1;model structureX:1lmp.pdb:1:A:+132:B: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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQIN--SRYWCDDGRTPGAK NVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDL------------RSYVAGCGV/...*
Выглядит вполне неплохо (кроме отсутствия лиганда) в sequence.
Построим модель:
# Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
sequence model
# 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
# Проводим моделирование
a.make()
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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.)
transfe_404W> At least one template is aligned with model residue 144:A
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 145:A
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 146:A
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
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: 11428 10412
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 146
Number of all, selected real atoms : 1149 1149
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10412 10412
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2897
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 : 1422.6954
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 : 1168 0 0 0.006 0.006 13.717 1.000
2 Bond angle potential : 1574 2 10 2.443 2.443 185.41 1.000
3 Stereochemical cosine torsion poten: 705 0 44 50.799 50.799 283.81 1.000
4 Stereochemical improper torsion pot: 477 0 1 1.598 1.598 23.475 1.000
5 Soft-sphere overlap restraints : 2897 0 0 0.005 0.005 8.3511 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) : 2406 0 14 0.744 0.744 195.39 1.000
10 Distance restraints 2 (N-O) : 2566 0 29 0.858 0.858 312.61 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: 145 0 4 5.213 5.213 46.462 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 79.127 79.127 54.360 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 4 91.080 91.080 61.528 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 81.987 81.987 35.434 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 82.399 82.399 17.384 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) : 838 0 0 0.534 0.534 18.992 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: 144 41 27 40.761 88.299 148.85 1.000
26 Distance restraints 4 (SDCH-SDCH) : 112 0 1 1.184 1.184 16.920 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: sequence.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: 21579.0234
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 1843 61V 62T C N 492 494 140.99 120.00 20.99 4.77 120.00 20.99 4.77
-------------------------------------------------------------------------------------------------
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 3942 18R 19L C N 148 150 66.43 60.20 16.17 0.56 -63.50 141.44 26.03
1 19L 19L N CA 150 151 14.68 29.60 -41.20
2 3944 20K 21A C N 165 167 56.72 55.40 6.93 0.32 -62.50 139.43 28.35
2 21A 21A N CA 167 168 31.40 38.20 -40.90
3 3945 21A 22Y C N 170 172 63.13 55.90 9.20 0.63 -63.50 148.32 28.03
3 22Y 22Y N CA 172 173 33.81 39.50 -43.40
4 3959 35H 36T C N 287 289 -136.18 -63.20 91.69 10.62 -63.20 91.69 10.62
4 36T 36T N CA 289 290 13.41 -42.10 -42.10
5 3960 36T 37H C N 294 296 59.20 56.30 9.33 0.67 -63.20 143.15 24.58
5 37H 37H N CA 296 297 31.93 40.80 -42.30
6 3964 40N 41I C N 328 330 -100.81 -120.60 69.05 3.22 -63.40 114.06 17.61
6 41I 41I N CA 330 331 64.15 130.30 -43.60
7 3972 48E 49Q C N 388 390 80.56 55.10 34.11 2.29 -121.10 -160.05 9.97
7 49Q 49Q N CA 390 391 17.60 40.30 139.70
8 3977 53F 54L C N 427 429 84.08 60.20 153.30 11.20 -108.50 174.31 7.83
8 54L 54L N CA 429 430 -178.97 29.60 132.50
9 3981 57D 58I C N 463 465 -60.87 -63.40 23.26 3.73 -120.60 173.57 12.13
9 58I 58I N CA 465 466 -66.73 -43.60 130.30
10 3982 58I 59A C N 471 473 62.71 -62.50 153.87 24.80 -68.20 155.74 15.26
10 59A 59A N CA 473 474 -130.33 -40.90 145.30
11 3983 59A 60Q C N 476 478 120.71 -121.10 153.31 4.83 -63.80 -166.15 34.99
11 60Q 60Q N CA 478 479 -122.65 139.70 -40.30
12 3984 60Q 61V C N 485 487 -61.74 -62.40 18.99 2.37 -125.40 167.86 9.49
12 61V 61V N CA 487 488 -61.37 -42.40 143.30
13 3985 61V 62T C N 492 494 176.44 -63.20 128.19 17.23 -63.20 128.19 17.23
13 62T 62T N CA 494 495 2.00 -42.10 -42.10
14 3991 67T 68Q C N 535 537 -111.22 -121.10 12.20 0.60 -63.80 179.23 28.89
14 68Q 68Q N CA 537 538 146.86 139.70 -40.30
15 3995 71V 72P C N 568 570 -51.96 -58.70 38.52 2.67 -64.50 144.92 11.49
15 72P 72P N CA 570 571 -68.43 -30.50 147.20
16 3996 72P 73L C N 575 577 -107.62 -108.50 38.17 2.05 -63.50 142.55 17.81
16 73L 73L N CA 577 578 94.35 132.50 -41.20
17 3998 74T 75Q C N 590 592 -124.59 -121.10 33.35 1.64 -63.80 158.92 20.77
17 75Q 75Q N CA 592 593 106.53 139.70 -40.30
18 3999 75Q 76N C N 599 601 -53.02 -63.20 10.92 1.44 55.90 137.88 16.75
18 76N 76N N CA 601 602 -45.05 -41.10 39.50
19 4000 76N 77Q C N 607 609 70.92 -63.80 142.86 21.32 -63.80 142.86 21.32
19 77Q 77Q N CA 609 610 -87.83 -40.30 -40.30
20 4027 103N 104V C N 815 817 -68.24 -125.40 57.65 2.02 -62.40 178.23 22.22
20 104V 104V N CA 817 818 135.73 143.30 -42.40
21 4028 104V 105G C N 822 824 116.98 82.20 52.34 1.54 -62.40 179.69 32.51
21 105G 105G N CA 824 825 -30.62 8.50 -41.20
22 4029 105G 106D C N 826 828 51.36 -63.30 144.40 17.28 -63.30 144.40 17.28
22 106D 106D N CA 828 829 -127.78 -40.00 -40.00
23 4045 121K 122V C N 952 954 -79.95 -125.40 72.29 2.18 -62.40 130.67 15.59
23 122V 122V N CA 954 955 87.09 143.30 -42.40
24 4046 122V 123N C N 959 961 -131.18 -119.90 35.68 1.34 -63.20 162.91 24.21
24 123N 123N N CA 961 962 170.85 137.00 -41.10
25 4047 123N 124G C N 967 969 -123.31 -80.20 43.23 2.78 82.20 -131.17 17.39
25 124G 124G N CA 969 970 177.31 174.10 8.50
26 4048 124G 125K C N 971 973 -87.65 -70.20 34.32 2.11 -62.90 151.29 21.08
26 125K 125K N CA 973 974 169.95 140.40 -40.80
27 4049 125K 126R C N 980 982 -61.13 -72.10 20.09 1.33 -63.00 166.17 22.57
27 126R 126R N CA 982 983 125.07 141.90 -41.10
28 4050 126R 127T C N 991 993 -99.41 -124.80 42.23 1.31 -63.20 156.12 17.86
28 127T 127T N CA 993 994 109.76 143.50 -42.10
29 4051 127T 128P C N 998 1000 -55.07 -58.70 6.46 0.39 -64.50 177.20 13.73
29 128P 128P N CA 1000 1001 -35.85 -30.50 147.20
30 4052 128P 129L C N 1005 1007 -70.06 -70.70 11.61 0.90 -63.50 165.73 23.39
30 129L 129L N CA 1007 1008 153.20 141.60 -41.20
31 4054 130P 131G C N 1020 1022 -70.13 -80.20 57.22 1.77 82.20 -172.53 7.14
31 131G 131G N CA 1022 1023 117.77 174.10 8.50
32 4055 131G 132L C N 1024 1026 -123.15 -108.50 78.83 4.09 -63.50 124.11 20.91
32 132L 132L N CA 1026 1027 -150.04 132.50 -41.20
33 4057 133I 134K C N 1040 1042 129.80 -118.00 118.18 3.98 -62.90 -139.92 37.89
33 134K 134K N CA 1042 1043 176.21 139.10 -40.80
34 4058 134K 135R C N 1049 1051 -116.84 -125.20 15.18 0.84 -63.00 174.17 27.25
34 135R 135R N CA 1051 1052 153.26 140.60 -41.10
35 4059 135R 136R C N 1060 1062 -137.18 -125.20 80.72 3.62 -63.00 123.29 21.49
35 136R 136R N CA 1062 1063 -139.57 140.60 -41.10
36 4060 136R 137Q C N 1071 1073 -54.60 -121.10 73.96 3.46 -63.80 147.93 21.28
36 137Q 137Q N CA 1073 1074 172.05 139.70 -40.30
37 4063 139E 140K C N 1094 1096 58.57 56.60 10.44 0.61 -62.90 139.77 24.41
37 140K 140K N CA 1096 1097 28.34 38.60 -40.80
38 4064 140K 141A C N 1103 1105 -134.20 -134.00 26.65 1.52 -62.50 176.47 26.52
38 141A 141A N CA 1105 1106 120.35 147.00 -40.90
39 4065 141A 142L C N 1108 1110 -71.25 -70.70 41.61 3.17 -63.50 141.41 19.20
39 142L 142L N CA 1110 1111 100.00 141.60 -41.20
40 4066 142L 143F C N 1116 1118 -65.12 -63.20 5.27 0.62 -124.20 -173.12 9.97
40 143F 143F N CA 1118 1119 -39.40 -44.30 143.30
41 4067 143F 144E C N 1127 1129 -97.08 -117.80 41.26 1.57 -63.60 145.33 17.75
41 144E 144E N CA 1129 1130 101.12 136.80 -40.30
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 12 21 102 99 175 161 178 178 202 201
<< 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 : 146
Number of all, selected real atoms : 1149 1149
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10412 10412
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2999
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 : 1250.7488
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 : 1168 0 0 0.006 0.006 12.006 1.000
2 Bond angle potential : 1574 0 8 2.257 2.257 157.28 1.000
3 Stereochemical cosine torsion poten: 705 0 42 50.708 50.708 287.86 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.429 1.429 19.423 1.000
5 Soft-sphere overlap restraints : 2999 0 0 0.005 0.005 9.5766 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) : 2406 2 12 0.695 0.695 168.58 1.000
10 Distance restraints 2 (N-O) : 2566 0 19 0.777 0.777 235.40 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: 145 0 4 5.378 5.378 49.460 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 79.319 79.319 42.613 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 82.435 82.435 37.059 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 2 86.693 86.693 32.597 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 103.923 103.923 13.606 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) : 838 0 0 0.415 0.415 12.687 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: 144 35 23 43.055 87.126 161.69 1.000
26 Distance restraints 4 (SDCH-SDCH) : 112 0 0 0.950 0.950 10.914 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: sequence.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: 19692.2656
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 3942 18R 19L C N 148 150 74.57 60.20 27.99 1.03 -63.50 145.78 26.68
1 19L 19L N CA 150 151 5.58 29.60 -41.20
2 3944 20K 21A C N 165 167 62.87 -68.20 151.14 14.73 -62.50 159.46 25.37
2 21A 21A N CA 167 168 -139.44 145.30 -40.90
3 3945 21A 22Y C N 170 172 -116.53 -98.40 59.44 5.98 -63.50 126.81 17.85
3 22Y 22Y N CA 172 173 71.79 128.40 -43.40
4 3959 35H 36T C N 287 289 -134.39 -63.20 89.00 10.34 -63.20 89.00 10.34
4 36T 36T N CA 289 290 11.30 -42.10 -42.10
5 3960 36T 37H C N 294 296 60.68 56.30 10.04 0.73 -63.20 144.33 24.79
5 37H 37H N CA 296 297 31.77 40.80 -42.30
6 3972 48E 49Q C N 388 390 79.19 55.10 35.29 2.12 -121.10 -157.07 10.14
6 49Q 49Q N CA 390 391 14.51 40.30 139.70
7 3977 53F 54L C N 427 429 60.47 -70.70 146.27 14.68 -108.50 -175.60 9.73
7 54L 54L N CA 429 430 -153.66 141.60 132.50
8 3982 58I 59A C N 471 473 179.36 -62.50 127.12 25.76 -68.20 169.54 10.66
8 59A 59A N CA 473 474 -87.81 -40.90 145.30
9 3983 59A 60Q C N 476 478 66.67 -63.80 150.83 21.10 -63.80 150.83 21.10
9 60Q 60Q N CA 478 479 -115.97 -40.30 -40.30
10 3984 60Q 61V C N 485 487 -64.89 -62.40 24.18 3.21 -125.40 161.97 9.14
10 61V 61V N CA 487 488 -66.45 -42.40 143.30
11 3985 61V 62T C N 492 494 144.78 -63.20 155.02 22.41 -63.20 155.02 22.41
11 62T 62T N CA 494 495 -11.77 -42.10 -42.10
12 3991 67T 68Q C N 535 537 -106.53 -121.10 34.09 1.78 -63.80 155.18 25.10
12 68Q 68Q N CA 537 538 170.51 139.70 -40.30
13 3993 69I 70K C N 552 554 -137.04 -118.00 48.09 2.49 -62.90 154.67 17.77
13 70K 70K N CA 554 555 94.94 139.10 -40.80
14 3995 71V 72P C N 568 570 -52.52 -58.70 35.71 2.48 -64.50 147.62 11.66
14 72P 72P N CA 570 571 -65.67 -30.50 147.20
15 3996 72P 73L C N 575 577 -111.28 -108.50 34.66 1.90 -63.50 147.13 18.32
15 73L 73L N CA 577 578 97.95 132.50 -41.20
16 4027 103N 104V C N 815 817 -63.05 -125.40 62.68 2.25 -62.40 179.26 22.65
16 104V 104V N CA 817 818 136.86 143.30 -42.40
17 4028 104V 105G C N 822 824 113.35 82.20 45.97 1.38 -62.40 176.46 32.12
17 105G 105G N CA 824 825 -25.32 8.50 -41.20
18 4029 105G 106D C N 826 828 43.74 -70.90 138.45 11.57 -63.30 141.19 16.46
18 106D 106D N CA 828 829 -132.07 150.30 -40.00
19 4045 121K 122V C N 952 954 -162.94 -125.40 41.06 1.15 -62.40 -173.00 29.74
19 122V 122V N CA 954 955 159.93 143.30 -42.40
20 4046 122V 123N C N 959 961 -126.43 -119.90 43.11 1.80 -63.20 152.97 22.70
20 123N 123N N CA 961 962 179.61 137.00 -41.10
21 4047 123N 124G C N 967 969 -86.38 -80.20 10.11 0.27 82.20 -118.01 7.45
21 124G 124G N CA 969 970 -177.89 174.10 8.50
22 4048 124G 125K C N 971 973 -164.54 -118.00 51.67 1.71 -62.90 -172.43 30.39
22 125K 125K N CA 973 974 161.56 139.10 -40.80
23 4049 125K 126R C N 980 982 -173.82 -125.20 49.00 1.81 -63.00 -155.24 35.03
23 126R 126R N CA 982 983 146.72 140.60 -41.10
24 4050 126R 127T C N 991 993 -147.34 -124.80 27.14 0.99 -63.20 -179.86 28.54
24 127T 127T N CA 993 994 158.62 143.50 -42.10
25 4051 127T 128P C N 998 1000 -68.83 -58.70 13.05 1.02 -64.50 169.52 12.88
25 128P 128P N CA 1000 1001 -22.27 -30.50 147.20
26 4052 128P 129L C N 1005 1007 -77.92 -70.70 11.12 1.09 -63.50 174.94 23.50
26 129L 129L N CA 1007 1008 133.14 141.60 -41.20
27 4054 130P 131G C N 1020 1022 -152.50 -167.20 28.00 0.80 82.20 -170.42 14.35
27 131G 131G N CA 1022 1023 150.77 174.60 8.50
28 4057 133I 134K C N 1040 1042 176.42 -118.00 65.98 2.62 -62.90 -149.41 24.46
28 134K 134K N CA 1042 1043 131.78 139.10 -40.80
29 4058 134K 135R C N 1049 1051 -146.42 -125.20 33.55 1.86 -63.00 176.65 20.03
29 135R 135R N CA 1051 1052 114.61 140.60 -41.10
30 4059 135R 136R C N 1060 1062 -139.46 -125.20 55.88 2.96 -63.00 148.81 16.84
30 136R 136R N CA 1062 1063 86.57 140.60 -41.10
31 4060 136R 137Q C N 1071 1073 64.60 -121.10 177.08 6.05 -63.80 -163.49 25.36
31 137Q 137Q N CA 1073 1074 170.93 139.70 -40.30
32 4063 139E 140K C N 1094 1096 111.19 56.60 155.18 7.95 -62.90 -173.87 26.92
32 140K 140K N CA 1096 1097 -106.66 38.60 -40.80
33 4064 140K 141A C N 1103 1105 -59.05 -68.20 21.05 1.39 -62.50 167.28 27.58
33 141A 141A N CA 1105 1106 126.35 145.30 -40.90
34 4065 141A 142L C N 1108 1110 -121.94 -108.50 18.92 1.06 -63.50 170.71 21.18
34 142L 142L N CA 1110 1111 119.19 132.50 -41.20
35 4067 143F 144E C N 1127 1129 -105.66 -117.80 12.31 0.41 -63.60 -179.91 21.97
35 144E 144E N CA 1129 1130 134.80 136.80 -40.30
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 17 21 110 113 167 163 175 204 215 229
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sequence.B99990001.pdb 1422.69543
sequence.B99990002.pdb 1250.74878
Посмотрим на результат:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('sequence.B99990001.pdb')
w1
w2 = nglview.show_structure_file('sequence.B99990002.pdb')
w2
Посмотрим на исходную модель лизоцима:
pre = nglview.show_structure_file('1lmp.pdb')
pre
В смоделированных структурах лиганда мы действительно не видим.
Чтобы добавить его в модель, нужно добавить его в изначальную последовательность - LYS_BPAPS.fasta.
['/',alignm[1].residues[-3],alignm[1].residues[-2],alignm[1].residues[-1]]
['/', Residue 1:B (type NDG), Residue 2:B (type NAG), Residue 3:B (type NAG)]
new_seq = ''.join([i.code for i in alignm[0].residues])
new_seq += '/' + ''.join([i.code for i in [alignm[1].residues[-3],alignm[1].residues[-2],alignm[1].residues[-1]]])
alignm.append_sequence(new_seq)
del alignm[0]
alignm[1].code = 'newseq'
alignm.salign()
alignm.write(file='all_in_one_new.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat all_in_one_new.ali
>P1;model structureX:1lmp.pdb:1:A:+132:B: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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQIN--SRYWCDDGRTPGAK NVCGIRCSQLLT---DDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGC------------GV/...* >P1;newseq sequence::1:A:+149:B:undefined:undefined:-1.00:-1.00 MHISEKGLVLIKRYEGLRLKAYQCRAGRWTLGYGHTHNLNIGDVITQEQAEAFLREDIAQVTALLNTQIKVPLTQ NQYDAICSLVFNIGMTAFTTSTLLKKLNVGDYSGASAEFMKWSKAKVNGKRTPLPGLIKRRQAEKALFESA/...*
Теперь лиганд есть в обоих последовательностях.
Повторяем наши предыдущие действия:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one_new.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
newseq model
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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
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: 12858 11842
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 : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11842 11842
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2935
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 : 1016.7914
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 : 1168 0 0 0.005 0.005 8.4647 1.000
2 Bond angle potential : 1574 1 5 2.116 2.116 136.41 1.000
3 Stereochemical cosine torsion poten: 705 0 40 51.842 51.842 289.86 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.234 1.234 14.903 1.000
5 Soft-sphere overlap restraints : 2935 1 2 0.008 0.008 22.885 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) : 2407 0 0 0.281 0.281 45.600 1.000
10 Distance restraints 2 (N-O) : 2568 0 3 0.481 0.481 126.19 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: 145 1 5 5.309 5.309 48.204 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 83.793 83.793 40.574 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 86.812 86.812 43.505 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 91.428 91.428 32.599 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 81.279 81.279 12.339 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) : 857 0 0 0.403 0.403 14.994 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: 144 33 26 42.346 78.551 152.02 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 0 1.079 1.079 15.102 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.031 0.031 13.134 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: newseq.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: 19094.1016
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 3942 18R 19L C N 148 150 65.08 60.20 9.75 0.35 -63.50 142.90 26.34
1 19L 19L N CA 150 151 21.15 29.60 -41.20
2 3944 20K 21A C N 165 167 56.35 55.40 4.83 0.22 -62.50 140.19 28.49
2 21A 21A N CA 167 168 33.47 38.20 -40.90
3 3945 21A 22Y C N 170 172 65.83 55.90 13.31 0.85 -63.50 149.02 28.12
3 22Y 22Y N CA 172 173 30.63 39.50 -43.40
4 3959 35H 36T C N 287 289 -138.96 -63.20 93.55 10.95 -63.20 93.55 10.95
4 36T 36T N CA 289 290 12.79 -42.10 -42.10
5 3960 36T 37H C N 294 296 57.21 56.30 2.94 0.21 -63.20 144.74 24.81
5 37H 37H N CA 296 297 38.01 40.80 -42.30
6 3964 40N 41I C N 328 330 -101.57 -120.60 71.04 3.35 -63.40 112.16 17.29
6 41I 41I N CA 330 331 61.86 130.30 -43.60
7 3972 48E 49Q C N 388 390 148.53 55.10 107.74 9.15 -121.10 177.74 9.29
7 49Q 49Q N CA 390 391 -13.35 40.30 139.70
8 3977 53F 54L C N 427 429 88.33 60.20 146.56 11.16 -108.50 168.22 7.60
8 54L 54L N CA 429 430 173.43 29.60 132.50
9 3983 59A 60Q C N 476 478 -134.98 -63.80 81.37 11.46 -63.80 81.37 11.46
9 60Q 60Q N CA 478 479 -0.88 -40.30 -40.30
10 3984 60Q 61V C N 485 487 -73.33 -62.40 11.56 1.62 -125.40 -174.49 10.26
10 61V 61V N CA 487 488 -38.64 -42.40 143.30
11 3985 61V 62T C N 492 494 91.43 -124.80 148.42 8.59 -63.20 -145.45 36.51
11 62T 62T N CA 494 495 106.63 143.50 -42.10
12 3992 68Q 69I C N 544 546 46.60 -97.30 148.03 7.37 -63.40 175.00 32.49
12 69I 69I N CA 546 547 92.50 127.20 -43.60
13 3993 69I 70K C N 552 554 179.41 -62.90 117.90 19.00 -62.90 117.90 19.00
13 70K 70K N CA 554 555 -33.78 -40.80 -40.80
14 3995 71V 72P C N 568 570 -67.34 -58.70 9.80 1.38 -64.50 177.71 13.11
14 72P 72P N CA 570 571 -35.11 -30.50 147.20
15 3998 74T 75Q C N 590 592 -146.39 -121.10 82.99 4.27 -63.80 130.43 16.78
15 75Q 75Q N CA 592 593 60.65 139.70 -40.30
16 3999 75Q 76N C N 599 601 -41.93 -71.20 62.38 3.35 55.90 109.06 9.12
16 76N 76N N CA 601 602 87.71 142.80 39.50
17 4009 85V 86F C N 676 678 -105.57 -124.20 59.16 2.27 -63.20 138.11 16.61
17 86F 86F N CA 678 679 87.15 143.30 -44.30
18 4013 89G 90M C N 707 709 -159.49 -125.60 37.55 1.14 -63.40 -170.94 35.65
18 90M 90M N CA 709 710 156.68 140.50 -40.50
19 4014 90M 91T C N 715 717 -92.15 -124.80 72.03 2.29 -63.20 124.79 14.28
19 91T 91T N CA 717 718 79.29 143.50 -42.10
20 4044 120A 121K C N 943 945 20.70 -70.20 118.64 9.91 -118.00 158.90 7.44
20 121K 121K N CA 945 946 -143.35 140.40 139.10
21 4048 124G 125K C N 971 973 -104.35 -62.90 86.93 9.99 -62.90 86.93 9.99
21 125K 125K N CA 973 974 35.62 -40.80 -40.80
22 4056 132L 133I C N 1032 1034 76.06 -120.60 163.48 11.57 -120.60 163.48 11.57
22 133I 133I N CA 1034 1035 123.40 130.30 130.30
23 4057 133I 134K C N 1040 1042 -148.10 -118.00 36.51 1.76 -62.90 -179.40 20.75
23 134K 134K N CA 1042 1043 118.44 139.10 -40.80
24 4058 134K 135R C N 1049 1051 -140.34 -125.20 15.15 0.60 -63.00 -166.06 31.50
24 135R 135R N CA 1051 1052 141.05 140.60 -41.10
25 4060 136R 137Q C N 1071 1073 -124.43 -121.10 8.06 0.42 -63.80 -177.01 24.20
25 137Q 137Q N CA 1073 1074 132.36 139.70 -40.30
26 4061 137Q 138A C N 1080 1082 -69.13 -68.20 5.93 0.45 -62.50 168.08 27.87
26 138A 138A N CA 1082 1083 151.16 145.30 -40.90
27 4062 138A 139E C N 1085 1087 -126.68 -117.80 13.00 0.43 -63.60 -175.49 28.16
27 139E 139E N CA 1087 1088 146.30 136.80 -40.30
28 4063 139E 140K C N 1094 1096 58.36 -70.20 133.12 10.47 -62.90 -171.55 22.32
28 140K 140K N CA 1096 1097 174.95 140.40 -40.80
29 4064 140K 141A C N 1103 1105 -72.12 -68.20 18.46 1.62 -62.50 168.44 27.15
29 141A 141A N CA 1105 1106 127.26 145.30 -40.90
30 4065 141A 142L C N 1108 1110 -158.02 -108.50 77.46 3.55 -63.50 158.10 27.67
30 142L 142L N CA 1110 1111 -167.94 132.50 -41.20
31 4066 142L 143F C N 1116 1118 -137.71 -124.20 68.57 2.87 -63.20 128.89 22.45
31 143F 143F N CA 1118 1119 -149.47 143.30 -44.30
32 4067 143F 144E C N 1127 1129 -51.67 -69.30 17.63 1.34 -63.60 177.39 23.02
32 144E 144E N CA 1129 1130 142.71 142.50 -40.30
33 4068 144E 145S C N 1136 1138 -131.50 -136.60 10.97 0.62 -64.10 177.38 17.63
33 145S 145S N CA 1138 1139 160.92 151.20 -35.00
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 21 22 108 116 170 153 162 219 195 201
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11842 11842
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2877
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 : 1086.2111
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 : 1168 0 0 0.007 0.007 14.916 1.000
2 Bond angle potential : 1574 2 14 2.415 2.415 175.32 1.000
3 Stereochemical cosine torsion poten: 705 0 42 52.065 52.065 285.43 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.401 1.401 18.737 1.000
5 Soft-sphere overlap restraints : 2877 2 5 0.010 0.010 37.305 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) : 2407 0 0 0.276 0.276 50.019 1.000
10 Distance restraints 2 (N-O) : 2568 0 10 0.478 0.478 161.05 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: 145 1 5 4.760 4.760 38.741 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 81.686 81.686 40.655 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 87.738 87.738 37.735 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 78.835 78.835 30.283 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 92.752 92.752 11.272 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) : 857 0 2 0.468 0.468 27.011 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: 144 31 23 34.057 78.432 111.34 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 0 1.041 1.041 13.151 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.054 0.054 33.251 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: newseq.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: 18996.2910
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 1833 60Q 61V C N 485 487 140.70 120.00 20.70 4.70 120.00 20.70 4.70
2 1843 61V 62T C N 492 494 149.21 120.00 29.21 6.64 120.00 29.21 6.64
-------------------------------------------------------------------------------------------------
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 3942 18R 19L C N 148 150 64.41 60.20 7.33 0.30 -63.50 143.38 26.44
1 19L 19L N CA 150 151 23.59 29.60 -41.20
2 3944 20K 21A C N 165 167 57.51 55.40 7.40 0.30 -62.50 139.96 28.46
2 21A 21A N CA 167 168 31.11 38.20 -40.90
3 3945 21A 22Y C N 170 172 65.34 55.90 15.15 0.81 -63.50 147.14 27.74
3 22Y 22Y N CA 172 173 27.65 39.50 -43.40
4 3959 35H 36T C N 287 289 -133.69 -63.20 86.63 10.18 -63.20 86.63 10.18
4 36T 36T N CA 289 290 8.26 -42.10 -42.10
5 3960 36T 37H C N 294 296 59.15 56.30 7.79 0.56 -63.20 143.95 24.71
5 37H 37H N CA 296 297 33.54 40.80 -42.30
6 3964 40N 41I C N 328 330 -104.25 -120.60 70.72 3.43 -63.40 112.76 17.34
6 41I 41I N CA 330 331 61.50 130.30 -43.60
7 3972 48E 49Q C N 388 390 80.10 55.10 35.84 2.21 -121.10 -157.85 10.11
7 49Q 49Q N CA 390 391 14.62 40.30 139.70
8 3977 53F 54L C N 427 429 67.21 -70.70 150.29 15.02 -108.50 -171.29 9.87
8 54L 54L N CA 429 430 -158.67 141.60 132.50
9 3985 61V 62T C N 492 494 -72.59 -63.20 77.28 9.32 -63.20 77.28 9.32
9 62T 62T N CA 494 495 34.61 -42.10 -42.10
10 3991 67T 68Q C N 535 537 -107.56 -121.10 23.05 1.20 -63.80 167.18 26.92
10 68Q 68Q N CA 537 538 158.35 139.70 -40.30
11 3992 68Q 69I C N 544 546 -102.54 -97.30 57.38 5.93 -63.40 120.22 18.57
11 69I 69I N CA 546 547 70.06 127.20 -43.60
12 3993 69I 70K C N 552 554 -159.94 -62.90 103.89 15.00 -62.90 103.89 15.00
12 70K 70K N CA 554 555 -3.72 -40.80 -40.80
13 3996 72P 73L C N 575 577 49.67 60.20 35.60 1.34 -63.50 154.24 27.95
13 73L 73L N CA 577 578 63.60 29.60 -41.20
14 4012 88I 89G C N 703 705 69.61 78.70 45.17 0.92 82.20 130.96 6.99
14 89G 89G N CA 705 706 -121.85 -166.10 8.50
15 4013 89G 90M C N 707 709 -63.17 -73.00 16.18 1.01 -63.40 170.65 25.50
15 90M 90M N CA 709 710 130.15 143.00 -40.50
16 4014 90M 91T C N 715 717 -99.04 -124.80 53.43 1.68 -63.20 143.35 16.27
16 91T 91T N CA 717 718 96.69 143.50 -42.10
17 4027 103N 104V C N 815 817 -69.48 -125.40 57.06 2.58 -62.40 163.12 21.06
17 104V 104V N CA 817 818 154.64 143.30 -42.40
18 4028 104V 105G C N 822 824 108.18 82.20 43.76 1.21 -62.40 171.19 31.13
18 105G 105G N CA 824 825 -26.71 8.50 -41.20
19 4047 123N 124G C N 967 969 -64.40 -62.40 2.46 0.46 -167.20 175.93 6.96
19 124G 124G N CA 969 970 -42.64 -41.20 174.60
20 4048 124G 125K C N 971 973 42.86 -62.90 126.69 22.07 -62.90 126.69 22.07
20 125K 125K N CA 973 974 28.94 -40.80 -40.80
21 4057 133I 134K C N 1040 1042 -70.31 -70.20 13.74 0.99 -62.90 165.23 21.87
21 134K 134K N CA 1042 1043 154.14 140.40 -40.80
22 4058 134K 135R C N 1049 1051 -63.97 -72.10 8.31 0.60 -63.00 178.71 24.21
22 135R 135R N CA 1051 1052 140.19 141.90 -41.10
23 4059 135R 136R C N 1060 1062 -134.98 -125.20 27.55 1.09 -63.00 168.67 27.70
23 136R 136R N CA 1062 1063 166.36 140.60 -41.10
24 4060 136R 137Q C N 1071 1073 -68.79 -73.00 4.80 0.37 -63.80 176.77 26.25
24 137Q 137Q N CA 1073 1074 143.00 140.70 -40.30
25 4061 137Q 138A C N 1080 1082 -62.25 -68.20 10.49 0.67 -62.50 177.55 29.11
25 138A 138A N CA 1082 1083 136.65 145.30 -40.90
26 4062 138A 139E C N 1085 1087 -172.92 -117.80 98.13 3.56 -63.60 149.31 25.41
26 139E 139E N CA 1087 1088 -142.01 136.80 -40.30
27 4063 139E 140K C N 1094 1096 -59.01 -70.20 13.00 1.07 -62.90 172.23 22.16
27 140K 140K N CA 1096 1097 147.01 140.40 -40.80
28 4065 141A 142L C N 1108 1110 57.79 -70.70 134.27 13.20 -63.50 -176.11 23.23
28 142L 142L N CA 1110 1111 -179.42 141.60 -41.20
29 4066 142L 143F C N 1116 1118 -79.93 -71.40 31.41 2.72 -63.20 155.68 20.51
29 143F 143F N CA 1118 1119 110.48 140.70 -44.30
30 4067 143F 144E C N 1127 1129 -130.73 -117.80 63.95 3.40 -63.60 132.70 15.33
30 144E 144E N CA 1129 1130 74.17 136.80 -40.30
31 4068 144E 145S C N 1136 1138 179.17 -136.60 53.99 1.65 -64.10 -175.52 21.78
31 145S 145S N CA 1138 1139 -177.85 151.20 -35.00
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 22 20 96 112 183 167 165 199 197 192
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
newseq.B99990001.pdb 1016.79138
newseq.B99990002.pdb 1086.21106
Посмотрим на модель гомолога с лигандом:
w1 = nglview.show_structure_file('newseq.B99990001.pdb')
w1
w2 = nglview.show_structure_file('newseq.B99990002.pdb')
w2
Теперь лиганд есть везде.
pre = nglview.show_structure_file('1lmp.pdb')
pre
Лиганд у исходного белка и его гомолога располагается примерно в одной и той же области, чего и следовало ожидать.
# Делаем некоторого рода 'backup'
! mv newseq.B99990001.pdb newseq.B99990001.pre.pdb
! mv newseq.B99990002.pdb newseq.B99990002.pre.pdb
# Удалим файл с рестрейнтами, который генерируется автоматически
! rm newseq.rsr
Поместим лиганд в другое место, переназначив объект automodel:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:14:A','O6:2:B')]:
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_new.ali', knowns=pdb.code, sequence=s.code)
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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()
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 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
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
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12859 11843
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11843 11843
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2868
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 : 1418.6398
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 : 1168 1 1 0.009 0.009 25.024 1.000
2 Bond angle potential : 1574 0 13 2.283 2.283 158.94 1.000
3 Stereochemical cosine torsion poten: 705 0 40 52.423 52.423 294.95 1.000
4 Stereochemical improper torsion pot: 477 0 1 1.610 1.610 23.535 1.000
5 Soft-sphere overlap restraints : 2868 2 2 0.008 0.008 23.687 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) : 2407 2 14 0.553 0.553 205.67 1.000
10 Distance restraints 2 (N-O) : 2568 0 15 0.608 0.608 247.38 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: 145 1 3 5.213 5.213 46.468 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 83.567 83.567 38.156 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 95.314 95.314 49.039 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 87.168 87.168 28.825 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 90.154 90.154 11.556 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) : 857 0 0 0.461 0.461 14.838 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: 144 37 23 37.253 85.877 157.33 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 1 1.091 1.091 12.306 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.056 0.056 80.926 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: newseq.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: 21237.5547
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 1 : Bond length 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 1025 129L 129L CB CA 1009 1008 1.72 1.54 0.18 4.96 1.54 0.18 4.96
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4129 61V 61V CA C 488 492 -152.11 -180.00 27.89 5.58 -180.00 27.89 5.58
-------------------------------------------------------------------------------------------------
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 3942 18R 19L C N 148 150 65.63 60.20 12.27 0.42 -63.50 142.30 26.22
1 19L 19L N CA 150 151 18.59 29.60 -41.20
2 3944 20K 21A C N 165 167 56.16 55.40 6.11 0.31 -62.50 139.33 28.32
2 21A 21A N CA 167 168 32.14 38.20 -40.90
3 3945 21A 22Y C N 170 172 61.37 55.90 6.09 0.51 -63.50 148.41 28.08
3 22Y 22Y N CA 172 173 36.81 39.50 -43.40
4 3956 32G 33Y C N 261 263 -68.30 -98.40 39.23 2.79 -63.50 163.11 26.13
4 33Y 33Y N CA 263 264 153.56 128.40 -43.40
5 3957 33Y 34G C N 273 275 95.54 82.20 74.39 2.94 -62.40 159.68 27.47
5 34G 34G N CA 275 276 -64.68 8.50 -41.20
6 3959 35H 36T C N 287 289 -136.88 -63.20 87.69 10.54 -63.20 87.69 10.54
6 36T 36T N CA 289 290 5.44 -42.10 -42.10
7 3960 36T 37H C N 294 296 57.87 56.30 3.81 0.28 -63.20 144.90 24.85
7 37H 37H N CA 296 297 37.33 40.80 -42.30
8 3964 40N 41I C N 328 330 -102.53 -120.60 73.53 3.53 -63.40 109.84 16.90
8 41I 41I N CA 330 331 59.03 130.30 -43.60
9 3972 48E 49Q C N 388 390 74.59 55.10 25.76 1.76 -121.10 -158.73 9.93
9 49Q 49Q N CA 390 391 23.46 40.30 139.70
10 3977 53F 54L C N 427 429 96.72 60.20 150.06 12.09 -108.50 160.55 7.23
10 54L 54L N CA 429 430 175.15 29.60 132.50
11 3982 58I 59A C N 471 473 -176.02 -134.00 99.81 4.34 -68.20 141.88 9.04
11 59A 59A N CA 473 474 -122.47 147.00 145.30
12 3983 59A 60Q C N 476 478 108.64 -63.80 172.67 29.19 -63.80 172.67 29.19
12 60Q 60Q N CA 478 479 -31.33 -40.30 -40.30
13 3984 60Q 61V C N 485 487 -166.78 -62.40 107.14 15.71 -125.40 166.76 9.14
13 61V 61V N CA 487 488 -18.24 -42.40 143.30
14 3985 61V 62T C N 492 494 90.71 -63.20 164.44 27.98 -63.20 164.44 27.98
14 62T 62T N CA 494 495 15.81 -42.10 -42.10
15 3991 67T 68Q C N 535 537 -105.84 -121.10 36.00 1.88 -63.80 153.27 24.78
15 68Q 68Q N CA 537 538 172.30 139.70 -40.30
16 3992 68Q 69I C N 544 546 -105.67 -97.30 61.67 6.33 -63.40 117.57 18.08
16 69I 69I N CA 546 547 66.10 127.20 -43.60
17 3993 69I 70K C N 552 554 -179.18 -118.00 114.76 5.93 -62.90 142.75 18.50
17 70K 70K N CA 554 555 42.01 139.10 -40.80
18 3995 71V 72P C N 568 570 -41.33 -58.70 57.97 3.61 -64.50 129.09 10.89
18 72P 72P N CA 570 571 -85.81 -30.50 147.20
19 3996 72P 73L C N 575 577 -113.44 -108.50 39.37 2.17 -63.50 143.60 17.80
19 73L 73L N CA 577 578 93.44 132.50 -41.20
20 3998 74T 75Q C N 590 592 -129.13 -121.10 53.65 2.67 -63.80 142.77 18.43
20 75Q 75Q N CA 592 593 86.65 139.70 -40.30
21 3999 75Q 76N C N 599 601 -61.83 -71.20 34.47 1.97 55.90 137.03 10.64
21 76N 76N N CA 601 602 109.63 142.80 39.50
22 4012 88I 89G C N 703 705 79.80 78.70 6.48 0.14 82.20 179.02 8.57
22 89G 89G N CA 705 706 -172.49 -166.10 8.50
23 4013 89G 90M C N 707 709 -89.45 -73.00 37.61 2.84 -63.40 151.93 20.79
23 90M 90M N CA 709 710 109.18 143.00 -40.50
24 4014 90M 91T C N 715 717 -133.19 -124.80 48.12 1.82 -63.20 145.03 23.11
24 91T 91T N CA 717 718 -169.12 143.50 -42.10
25 4045 121K 122V C N 952 954 54.72 55.90 5.00 0.44 -125.40 -149.85 11.23
25 122V 122V N CA 954 955 34.64 39.50 143.30
26 4046 122V 123N C N 959 961 -77.67 -63.20 14.68 2.10 -119.90 -179.36 7.17
26 123N 123N N CA 961 962 -38.64 -41.10 137.00
27 4048 124G 125K C N 971 973 -96.65 -118.00 71.14 3.10 -62.90 117.02 13.74
27 125K 125K N CA 973 974 71.24 139.10 -40.80
28 4057 133I 134K C N 1040 1042 -52.38 -70.20 18.15 1.24 -62.90 178.06 23.71
28 134K 134K N CA 1042 1043 136.94 140.40 -40.80
29 4058 134K 135R C N 1049 1051 -68.74 -72.10 4.80 0.31 -63.00 179.66 23.89
29 135R 135R N CA 1051 1052 138.47 141.90 -41.10
30 4059 135R 136R C N 1060 1062 -85.54 -72.10 16.12 1.06 -63.00 169.61 24.46
30 136R 136R N CA 1062 1063 150.80 141.90 -41.10
31 4060 136R 137Q C N 1071 1073 -83.16 -73.00 21.24 1.59 -63.80 163.50 23.06
31 137Q 137Q N CA 1073 1074 122.05 140.70 -40.30
32 4061 137Q 138A C N 1080 1082 -127.35 -134.00 20.76 1.27 -62.50 165.66 30.62
32 138A 138A N CA 1082 1083 166.66 147.00 -40.90
33 4063 139E 140K C N 1094 1096 -72.79 -70.20 7.67 0.61 -62.90 174.26 22.11
33 140K 140K N CA 1096 1097 133.18 140.40 -40.80
34 4065 141A 142L C N 1108 1110 -76.47 -70.70 13.00 1.20 -63.50 171.65 23.12
34 142L 142L N CA 1110 1111 129.96 141.60 -41.20
35 4066 142L 143F C N 1116 1118 -137.55 -124.20 20.98 1.16 -63.20 -173.15 21.74
35 143F 143F N CA 1118 1119 127.12 143.30 -44.30
36 4067 143F 144E C N 1127 1129 -133.64 -117.80 21.04 0.65 -63.60 -177.02 28.34
36 144E 144E N CA 1129 1130 150.65 136.80 -40.30
37 4068 144E 145S C N 1136 1138 -133.37 -136.60 12.06 0.54 -64.10 -172.18 11.62
37 145S 145S N CA 1138 1139 139.58 151.20 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11843 14Y 129L N CB 106 1009 4.44 3.00 1.44 14.36 3.00 1.44 14.36
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 18 14 106 102 156 169 168 195 201 186
<< 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 : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11843 11843
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2905
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 : 1604.6903
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 : 1168 1 1 0.009 0.009 23.858 1.000
2 Bond angle potential : 1574 1 14 2.358 2.358 171.18 1.000
3 Stereochemical cosine torsion poten: 705 0 42 52.855 52.855 299.07 1.000
4 Stereochemical improper torsion pot: 477 0 1 1.516 1.516 21.769 1.000
5 Soft-sphere overlap restraints : 2905 2 2 0.008 0.008 23.618 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) : 2407 2 16 0.598 0.598 231.31 1.000
10 Distance restraints 2 (N-O) : 2568 0 31 0.662 0.662 324.37 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: 145 0 5 5.406 5.406 49.983 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 89.598 89.598 48.383 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 87.465 87.465 46.582 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 89.160 89.160 30.521 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 83.335 83.335 10.437 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) : 857 0 0 0.377 0.377 13.717 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: 144 45 32 42.154 89.567 217.96 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 0 0.979 0.979 10.411 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.058 0.058 81.514 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: newseq.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: 22750.0293
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 1 : Bond length 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 1025 129L 129L CB CA 1009 1008 1.72 1.54 0.18 4.98 1.54 0.18 4.98
-------------------------------------------------------------------------------------------------
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 3938 14Y 15E C N 116 118 -70.14 -63.60 53.65 7.52 -63.60 53.65 7.52
1 15E 15E N CA 118 119 -93.55 -40.30 -40.30
2 3939 15E 16G C N 125 127 -98.31 -62.40 36.46 6.23 82.20 -175.34 10.55
2 16G 16G N CA 127 128 -34.92 -41.20 8.50
3 3942 18R 19L C N 148 150 67.70 60.20 14.85 0.54 -63.50 143.44 26.41
3 19L 19L N CA 150 151 16.78 29.60 -41.20
4 3944 20K 21A C N 165 167 57.20 55.40 11.22 0.54 -62.50 137.67 28.00
4 21A 21A N CA 167 168 27.12 38.20 -40.90
5 3945 21A 22Y C N 170 172 66.10 55.90 14.68 0.86 -63.50 148.43 27.99
5 22Y 22Y N CA 172 173 28.95 39.50 -43.40
6 3956 32G 33Y C N 261 263 -69.62 -98.40 37.65 2.69 -63.50 164.04 26.34
6 33Y 33Y N CA 263 264 152.67 128.40 -43.40
7 3957 33Y 34G C N 273 275 95.15 82.20 73.81 2.93 -62.40 159.22 27.42
7 34G 34G N CA 275 276 -64.17 8.50 -41.20
8 3959 35H 36T C N 287 289 -135.22 -63.20 85.27 10.29 -63.20 85.27 10.29
8 36T 36T N CA 289 290 3.54 -42.10 -42.10
9 3960 36T 37H C N 294 296 58.56 56.30 5.88 0.42 -63.20 144.43 24.78
9 37H 37H N CA 296 297 35.38 40.80 -42.30
10 3964 40N 41I C N 328 330 -103.16 -120.60 85.44 4.22 -63.40 98.64 15.10
10 41I 41I N CA 330 331 46.66 130.30 -43.60
11 3972 48E 49Q C N 388 390 80.28 55.10 33.66 2.27 -121.10 -160.05 9.97
11 49Q 49Q N CA 390 391 17.96 40.30 139.70
12 3977 53F 54L C N 427 429 86.08 60.20 148.57 11.09 -108.50 171.01 7.71
12 54L 54L N CA 429 430 175.90 29.60 132.50
13 3982 58I 59A C N 471 473 -173.40 -134.00 93.74 4.08 -68.20 136.36 8.72
13 59A 59A N CA 473 474 -127.94 147.00 145.30
14 3983 59A 60Q C N 476 478 103.72 -121.10 165.24 5.12 -63.80 -172.17 26.78
14 60Q 60Q N CA 478 479 -125.26 139.70 -40.30
15 3984 60Q 61V C N 485 487 -72.60 -62.40 26.96 2.98 -125.40 169.20 6.90
15 61V 61V N CA 487 488 -17.45 -42.40 143.30
16 3985 61V 62T C N 492 494 106.75 -124.80 177.00 10.65 -63.20 -178.47 30.88
16 62T 62T N CA 494 495 21.72 143.50 -42.10
17 3991 67T 68Q C N 535 537 -135.94 -121.10 72.82 3.67 -63.80 130.47 16.72
17 68Q 68Q N CA 537 538 68.41 139.70 -40.30
18 3992 68Q 69I C N 544 546 -14.39 -97.30 84.72 4.09 -63.40 161.03 28.20
18 69I 69I N CA 546 547 109.79 127.20 -43.60
19 3993 69I 70K C N 552 554 161.44 -62.90 137.96 21.37 -62.90 137.96 21.37
19 70K 70K N CA 554 555 -15.71 -40.80 -40.80
20 3995 71V 72P C N 568 570 -46.63 -58.70 42.90 2.71 -64.50 142.26 11.58
20 72P 72P N CA 570 571 -71.67 -30.50 147.20
21 3996 72P 73L C N 575 577 -107.93 -108.50 33.98 1.83 -63.50 146.62 18.35
21 73L 73L N CA 577 578 98.52 132.50 -41.20
22 3998 74T 75Q C N 590 592 -135.86 -121.10 78.35 3.94 -63.80 125.76 16.12
22 75Q 75Q N CA 592 593 62.76 139.70 -40.30
23 3999 75Q 76N C N 599 601 -41.83 -71.20 59.37 3.17 55.90 110.56 9.01
23 76N 76N N CA 601 602 91.20 142.80 39.50
24 4001 77Q 78Y C N 616 618 -101.49 -63.50 79.26 11.04 -63.50 79.26 11.04
24 78Y 78Y N CA 618 619 26.15 -43.40 -43.40
25 4004 80A 81I C N 641 643 -68.00 -63.40 11.81 1.81 -120.60 171.30 7.88
25 81I 81I N CA 643 644 -32.73 -43.60 130.30
26 4005 81I 82C C N 649 651 87.98 -63.00 151.00 25.31 -63.00 151.00 25.31
26 82C 82C N CA 651 652 -38.35 -41.10 -41.10
27 4009 85V 86F C N 676 678 -82.51 -63.20 81.00 10.03 -63.20 81.00 10.03
27 86F 86F N CA 678 679 34.36 -44.30 -44.30
28 4012 88I 89G C N 703 705 -61.85 -62.40 4.20 0.65 82.20 151.08 11.42
28 89G 89G N CA 705 706 -37.04 -41.20 8.50
29 4014 90M 91T C N 715 717 -85.90 -124.80 48.37 2.93 -63.20 147.41 20.42
29 91T 91T N CA 717 718 172.24 143.50 -42.10
30 4027 103N 104V C N 815 817 -68.08 -125.40 59.48 2.80 -62.40 158.47 20.39
30 104V 104V N CA 817 818 159.23 143.30 -42.40
31 4028 104V 105G C N 822 824 105.22 82.20 43.18 1.19 -62.40 168.14 30.54
31 105G 105G N CA 824 825 -28.03 8.50 -41.20
32 4048 124G 125K C N 971 973 -119.29 -118.00 82.63 4.03 -62.90 112.44 12.93
32 125K 125K N CA 973 974 56.48 139.10 -40.80
33 4053 129L 130P C N 1013 1015 -65.78 -58.70 7.32 0.82 -64.50 175.85 13.19
33 130P 130P N CA 1015 1016 -28.65 -30.50 147.20
34 4054 130P 131G C N 1020 1022 -61.85 -62.40 16.57 2.50 82.20 147.81 10.93
34 131G 131G N CA 1022 1023 -24.64 -41.20 8.50
35 4057 133I 134K C N 1040 1042 -137.59 -118.00 37.77 1.48 -62.90 165.60 25.97
35 134K 134K N CA 1042 1043 171.40 139.10 -40.80
36 4058 134K 135R C N 1049 1051 -113.64 -125.20 34.61 1.87 -63.00 154.23 24.33
36 135R 135R N CA 1051 1052 173.22 140.60 -41.10
37 4059 135R 136R C N 1060 1062 73.26 57.30 33.48 1.66 -63.00 145.03 26.14
37 136R 136R N CA 1062 1063 8.57 38.00 -41.10
38 4061 137Q 138A C N 1080 1082 -133.24 -134.00 1.65 0.07 -62.50 -172.56 34.51
38 138A 138A N CA 1082 1083 145.53 147.00 -40.90
39 4062 138A 139E C N 1085 1087 -84.60 -69.30 18.12 1.05 -63.60 168.80 23.68
39 139E 139E N CA 1087 1088 152.21 142.50 -40.30
40 4063 139E 140K C N 1094 1096 54.79 56.60 2.33 0.17 -62.90 142.78 24.84
40 140K 140K N CA 1096 1097 40.05 38.60 -40.80
41 4064 140K 141A C N 1103 1105 -154.40 -134.00 21.80 0.50 -62.50 -171.62 35.78
41 141A 141A N CA 1105 1106 154.66 147.00 -40.90
42 4065 141A 142L C N 1108 1110 -127.46 -108.50 21.20 1.13 -63.50 176.22 21.79
42 142L 142L N CA 1110 1111 123.00 132.50 -41.20
43 4066 142L 143F C N 1116 1118 -112.90 -124.20 11.57 0.52 -63.20 177.04 27.90
43 143F 143F N CA 1118 1119 145.78 143.30 -44.30
44 4067 143F 144E C N 1127 1129 -107.95 -117.80 15.46 0.84 -63.60 176.65 26.06
44 144E 144E N CA 1129 1130 148.71 136.80 -40.30
45 4068 144E 145S C N 1136 1138 -134.28 -136.60 16.50 0.88 -64.10 172.39 17.49
45 145S 145S N CA 1138 1139 167.53 151.20 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11843 14Y 129L N CB 106 1009 4.40 3.00 1.40 14.05 3.00 1.40 14.05
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 18 22 123 131 167 147 158 188 196 224
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
newseq.B99990001.pdb 1418.63977
newseq.B99990002.pdb 1604.69031
Сопоставим в PyMol структуру модели гомолога, построенной с дополнительными ограничениями с той, что была построена без них:
from IPython.display import Image
Image('superimposition.png')
Мы видим, что структура, полученная при использовании рестрейнтов на расстояния между остатками белка и лиганда (deepteal) имеет несколько иную геометрию, что выражается в небольшом сдвиге петлевых участков белка в области лиганд-связывающего кармана. Примечательно, что наблюдается достаточно значительное отклонение С-концевого участка (слева)
Теперь нам нужно построить структуру лизоцима с лигандом, где все аминокислоты - аланин, после чего нужно сравнить скор-функцию с "нативной" последовательностью
! cat all_in_one_new.ali
>P1;model structureX:1lmp.pdb:1:A:+132:B: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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQIN--SRYWCDDGRTPGAK NVCGIRCSQLLT---DDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGC------------GV/...* >P1;newseq sequence::1:A:+149:B:undefined:undefined:-1.00:-1.00 MHISEKGLVLIKRYEGLRLKAYQCRAGRWTLGYGHTHNLNIGDVITQEQAEAFLREDIAQVTALLNTQIKVPLTQ NQYDAICSLVFNIGMTAFTTSTLLKKLNVGDYSGASAEFMKWSKAKVNGKRTPLPGLIKRRQAEKALFESA/...*
poly_a = 'A'*146 + '...' ; del alignm[1]
alignm.append_sequence(poly_a)
alignm[1].code = 'poly_a'
alignm.salign()
alignm.write(file='poly_a.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat poly_a.ali
>P1;model structureX:1lmp.pdb:1:A:+132:B: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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------------- ----WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...* >P1;poly_a sequence::1:A:+149:A:undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-...*
Получили полиаланиновую последовательность. Посмотрим, что за модель у нас получится.
Повторяем уже знакомые нам действия:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='poly_a.ali',
knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
poly_a model
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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: 1 146
atom names : C +N
atom indices : 729 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 146
atom names : C CA +N O
atom indices : 729 727 0 730
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: 10506 9783
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1412
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 : 911.6770
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 : 730 0 0 0.007 0.007 11.915 1.000
2 Bond angle potential : 1021 1 6 2.439 2.439 123.12 1.000
3 Stereochemical cosine torsion poten: 296 0 43 78.657 78.657 297.48 1.000
4 Stereochemical improper torsion pot: 292 0 0 1.258 1.258 11.803 1.000
5 Soft-sphere overlap restraints : 1412 2 2 0.012 0.012 24.984 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 1 0.286 0.286 75.576 1.000
10 Distance restraints 2 (N-O) : 2564 0 8 0.421 0.421 172.71 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: 145 2 6 6.444 6.444 71.010 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) : 722 0 0 0.267 0.267 6.1931 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: 144 37 22 33.879 86.620 92.370 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.489 0.489 1.3317 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.044 0.044 23.182 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: poly_a.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: 16113.7402
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 2354 15A 16A C N 74 76 78.72 55.40 26.71 2.01 -62.50 155.91 31.68
1 16A 16A N CA 76 77 25.17 38.20 -40.90
2 2356 17A 18A C N 84 86 -52.82 -62.50 9.71 1.90 -134.00 -168.98 11.79
2 18A 18A N CA 86 87 -40.08 -40.90 147.00
3 2357 18A 19A C N 89 91 -126.86 -134.00 55.85 2.99 -62.50 147.30 22.09
3 19A 19A N CA 91 92 91.60 147.00 -40.90
4 2360 21A 22A C N 104 106 -176.96 -134.00 106.92 6.60 -62.50 145.61 23.17
4 22A 22A N CA 106 107 49.09 147.00 -40.90
5 2375 36A 37A C N 179 181 65.75 55.40 11.75 0.90 -62.50 147.84 30.07
5 37A 37A N CA 181 182 32.64 38.20 -40.90
6 2376 37A 38A C N 184 186 63.33 55.40 11.85 0.58 -62.50 144.13 29.31
6 38A 38A N CA 186 187 29.39 38.20 -40.90
7 2387 48A 49A C N 239 241 86.93 55.40 45.33 2.33 -62.50 156.51 31.54
7 49A 49A N CA 241 242 5.64 38.20 -40.90
8 2392 53A 54A C N 264 266 91.57 -134.00 140.61 3.38 -62.50 -157.84 31.85
8 54A 54A N CA 266 267 -171.78 147.00 -40.90
9 2395 56A 57A C N 279 281 61.11 55.40 10.44 1.07 -62.50 151.63 30.75
9 57A 57A N CA 281 282 46.94 38.20 -40.90
10 2401 62A 63A C N 309 311 -66.05 -68.20 59.29 4.71 -62.50 127.00 20.64
10 63A 63A N CA 311 312 86.05 145.30 -40.90
11 2402 63A 64A C N 314 316 -168.07 -134.00 34.39 1.32 -62.50 -154.09 39.37
11 64A 64A N CA 316 317 142.31 147.00 -40.90
12 2403 64A 65A C N 319 321 -42.77 -68.20 30.09 2.00 -62.50 171.25 29.07
12 65A 65A N CA 321 322 129.21 145.30 -40.90
13 2404 65A 66A C N 324 326 -161.57 -134.00 40.86 1.30 -62.50 173.10 33.60
13 66A 66A N CA 326 327 177.16 147.00 -40.90
14 2405 66A 67A C N 329 331 -114.37 -134.00 27.34 0.81 -62.50 176.66 26.93
14 67A 67A N CA 331 332 127.97 147.00 -40.90
15 2406 67A 68A C N 334 336 178.54 -134.00 47.61 1.44 -62.50 -153.81 40.07
15 68A 68A N CA 336 337 150.69 147.00 -40.90
16 2407 68A 69A C N 339 341 -158.13 -134.00 25.59 1.18 -62.50 -156.70 30.46
16 69A 69A N CA 341 342 138.50 147.00 -40.90
17 2408 69A 70A C N 344 346 -137.12 -134.00 6.96 0.43 -62.50 -166.70 35.68
17 70A 70A N CA 346 347 140.78 147.00 -40.90
18 2409 70A 71A C N 349 351 65.11 -68.20 134.14 11.85 -62.50 -156.21 30.91
18 71A 71A N CA 351 352 160.20 145.30 -40.90
19 2410 71A 72A C N 354 356 -103.65 -134.00 36.22 0.88 -62.50 173.08 26.66
19 72A 72A N CA 356 357 127.21 147.00 -40.90
20 2411 72A 73A C N 359 361 173.85 -134.00 59.36 1.37 -62.50 -170.38 37.48
20 73A 73A N CA 361 362 175.34 147.00 -40.90
21 2412 73A 74A C N 364 366 -105.90 -134.00 32.36 0.75 -62.50 177.24 27.26
21 74A 74A N CA 366 367 130.95 147.00 -40.90
22 2413 74A 75A C N 369 371 -158.62 -134.00 30.09 0.75 -62.50 -177.77 34.98
22 75A 75A N CA 371 372 164.29 147.00 -40.90
23 2414 75A 76A C N 374 376 -149.56 -134.00 15.67 0.59 -62.50 -165.52 36.53
23 76A 76A N CA 376 377 145.20 147.00 -40.90
24 2415 76A 77A C N 379 381 -160.04 -134.00 28.12 0.64 -62.50 -171.35 36.11
24 77A 77A N CA 381 382 157.62 147.00 -40.90
25 2416 77A 78A C N 384 386 -115.35 -134.00 71.29 3.53 -62.50 130.29 19.58
25 78A 78A N CA 386 387 78.19 147.00 -40.90
26 2417 78A 79A C N 389 391 -146.44 -134.00 18.32 1.08 -62.50 -166.40 29.04
26 79A 79A N CA 391 392 133.55 147.00 -40.90
27 2422 83A 84A C N 414 416 77.31 55.40 53.42 1.93 -62.50 143.07 28.55
27 84A 84A N CA 416 417 -10.52 38.20 -40.90
28 2426 87A 88A C N 434 436 48.97 55.40 28.35 1.23 -62.50 154.32 30.91
28 88A 88A N CA 436 437 65.82 38.20 -40.90
29 2429 90A 91A C N 449 451 62.26 55.40 11.04 1.19 -62.50 152.52 30.94
29 91A 91A N CA 451 452 46.85 38.20 -40.90
30 2432 93A 94A C N 464 466 64.75 55.40 10.05 1.19 -62.50 151.81 30.84
30 94A 94A N CA 466 467 41.89 38.20 -40.90
31 2459 120A 121A C N 599 601 80.54 -134.00 158.16 3.60 -62.50 -179.55 28.79
31 121A 121A N CA 601 602 -150.91 147.00 -40.90
32 2471 132A 133A C N 659 661 -54.07 -62.50 16.94 2.54 -68.20 159.74 13.38
32 133A 133A N CA 661 662 -55.59 -40.90 145.30
33 2472 133A 134A C N 664 666 -119.74 -134.00 48.75 2.36 -62.50 152.44 22.97
33 134A 134A N CA 666 667 100.38 147.00 -40.90
34 2473 134A 135A C N 669 671 -161.52 -134.00 34.63 0.90 -68.20 96.05 7.33
34 135A 135A N CA 671 672 168.01 147.00 145.30
35 2480 141A 142A C N 704 706 58.27 -68.20 133.39 12.55 -68.20 133.39 12.55
35 142A 142A N CA 706 707 -172.30 145.30 145.30
36 2481 142A 143A C N 709 711 -81.35 -68.20 72.55 6.30 -62.50 116.39 18.24
36 143A 143A N CA 711 712 73.96 145.30 -40.90
37 2483 144A 145A C N 719 721 69.12 55.40 21.61 0.98 -62.50 145.66 29.60
37 145A 145A N CA 721 722 21.50 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 1 7 13 41 52 83 70 95 109 96 109
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1584
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 : 953.2247
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 : 730 0 0 0.007 0.007 10.952 1.000
2 Bond angle potential : 1021 1 11 2.597 2.597 137.42 1.000
3 Stereochemical cosine torsion poten: 296 0 43 78.894 78.894 296.79 1.000
4 Stereochemical improper torsion pot: 292 0 1 1.359 1.359 13.584 1.000
5 Soft-sphere overlap restraints : 1584 2 5 0.014 0.014 37.274 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 5 0.384 0.384 128.56 1.000
10 Distance restraints 2 (N-O) : 2564 1 7 0.453 0.453 177.10 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: 145 1 4 5.228 5.228 46.729 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) : 722 0 0 0.265 0.265 5.3354 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: 144 37 20 31.684 83.061 66.052 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 1 0.932 0.932 4.7253 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.049 0.049 28.700 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: poly_a.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: 16240.6475
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 1299 82A 82A N CA 406 407 125.16 107.00 18.16 5.22 107.00 18.16 5.22
-------------------------------------------------------------------------------------------------
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 6593 91A 81A N O 451 405 8.31 4.64 3.67 5.47 4.64 3.67 5.47
-------------------------------------------------------------------------------------------------
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 2354 15A 16A C N 74 76 78.23 55.40 26.25 1.96 -62.50 155.50 31.60
1 16A 16A N CA 76 77 25.25 38.20 -40.90
2 2357 18A 19A C N 89 91 65.17 55.40 22.48 0.81 -62.50 140.58 28.56
2 19A 19A N CA 91 92 17.95 38.20 -40.90
3 2359 20A 21A C N 99 101 53.86 55.40 4.63 0.40 -62.50 138.29 28.10
3 21A 21A N CA 101 102 33.83 38.20 -40.90
4 2360 21A 22A C N 104 106 62.79 55.40 9.53 0.58 -62.50 145.05 29.50
4 22A 22A N CA 106 107 32.19 38.20 -40.90
5 2375 36A 37A C N 179 181 65.85 55.40 13.35 0.83 -62.50 146.57 29.81
5 37A 37A N CA 181 182 29.89 38.20 -40.90
6 2376 37A 38A C N 184 186 61.85 55.40 10.35 0.46 -62.50 143.20 29.12
6 38A 38A N CA 186 187 30.11 38.20 -40.90
7 2387 48A 49A C N 239 241 84.44 55.40 39.69 2.20 -62.50 155.88 31.51
7 49A 49A N CA 241 242 11.14 38.20 -40.90
8 2392 53A 54A C N 264 266 89.46 -134.00 141.81 3.47 -62.50 -157.52 31.76
8 54A 54A N CA 266 267 -174.71 147.00 -40.90
9 2395 56A 57A C N 279 281 59.39 55.40 14.84 1.22 -62.50 153.55 31.07
9 57A 57A N CA 281 282 52.49 38.20 -40.90
10 2401 62A 63A C N 309 311 6.60 -62.50 112.73 22.09 -62.50 112.73 22.09
10 63A 63A N CA 311 312 48.17 -40.90 -40.90
11 2402 63A 64A C N 314 316 -72.11 -68.20 74.71 6.16 -62.50 112.01 17.91
11 64A 64A N CA 316 317 70.69 145.30 -40.90
12 2403 64A 65A C N 319 321 -132.61 -134.00 1.40 0.04 -62.50 -173.99 34.24
12 65A 65A N CA 321 322 146.82 147.00 -40.90
13 2404 65A 66A C N 324 326 -97.45 -68.20 41.80 2.63 -62.50 148.11 26.12
13 66A 66A N CA 326 327 175.17 145.30 -40.90
14 2405 66A 67A C N 329 331 -59.41 -68.20 12.54 0.79 -62.50 177.29 29.21
14 67A 67A N CA 331 332 136.36 145.30 -40.90
15 2406 67A 68A C N 334 336 -148.59 -134.00 20.03 0.58 -62.50 -179.74 34.14
15 68A 68A N CA 336 337 160.73 147.00 -40.90
16 2407 68A 69A C N 339 341 -71.67 -68.20 8.28 0.55 -62.50 166.53 27.75
16 69A 69A N CA 341 342 152.82 145.30 -40.90
17 2408 69A 70A C N 344 346 -142.28 -134.00 17.41 0.72 -62.50 175.92 33.10
17 70A 70A N CA 346 347 162.31 147.00 -40.90
18 2409 70A 71A C N 349 351 -68.90 -68.20 15.71 1.24 -62.50 158.23 26.25
18 71A 71A N CA 351 352 161.00 145.30 -40.90
19 2410 71A 72A C N 354 356 -57.53 -68.20 24.38 1.61 -62.50 164.35 27.18
19 72A 72A N CA 356 357 123.38 145.30 -40.90
20 2411 72A 73A C N 359 361 158.90 -134.00 84.45 2.19 -62.50 -176.12 37.01
20 73A 73A N CA 361 362 -161.73 147.00 -40.90
21 2412 73A 74A C N 364 366 -63.28 -68.20 7.24 0.71 -62.50 168.49 27.65
21 74A 74A N CA 366 367 150.61 145.30 -40.90
22 2413 74A 75A C N 369 371 -108.19 -134.00 32.03 0.81 -62.50 175.00 26.83
22 75A 75A N CA 371 372 128.03 147.00 -40.90
23 2414 75A 76A C N 374 376 175.74 -134.00 53.36 1.24 -62.50 -163.54 38.56
23 76A 76A N CA 376 377 164.92 147.00 -40.90
24 2415 76A 77A C N 379 381 -139.05 -134.00 9.72 0.60 -62.50 -164.78 29.37
24 77A 77A N CA 381 382 138.69 147.00 -40.90
25 2416 77A 78A C N 384 386 -170.48 -134.00 46.04 2.56 -62.50 -167.12 28.99
25 78A 78A N CA 386 387 118.92 147.00 -40.90
26 2417 78A 79A C N 389 391 172.87 -134.00 57.37 1.31 -62.50 -164.61 38.50
26 79A 79A N CA 391 392 168.62 147.00 -40.90
27 2422 83A 84A C N 414 416 75.46 55.40 33.29 1.43 -62.50 147.62 29.89
27 84A 84A N CA 416 417 11.63 38.20 -40.90
28 2426 87A 88A C N 434 436 55.29 55.40 20.56 1.23 -62.50 154.29 31.10
28 88A 88A N CA 436 437 58.76 38.20 -40.90
29 2429 90A 91A C N 449 451 76.62 55.40 30.18 1.58 -62.50 150.59 30.54
29 91A 91A N CA 451 452 16.74 38.20 -40.90
30 2432 93A 94A C N 464 466 63.49 55.40 11.13 1.26 -62.50 152.96 31.04
30 94A 94A N CA 466 467 45.84 38.20 -40.90
31 2459 120A 121A C N 599 601 80.73 -134.00 159.51 3.62 -62.50 178.32 28.59
31 121A 121A N CA 601 602 -147.12 147.00 -40.90
32 2471 132A 133A C N 659 661 -55.45 -62.50 14.55 2.18 -68.20 161.58 13.48
32 133A 133A N CA 661 662 -53.62 -40.90 145.30
33 2472 133A 134A C N 664 666 -116.19 -134.00 54.06 2.55 -62.50 147.00 22.18
33 134A 134A N CA 666 667 95.95 147.00 -40.90
34 2473 134A 135A C N 669 671 -165.26 -134.00 36.88 0.88 -68.20 99.37 7.67
34 135A 135A N CA 671 672 166.56 147.00 145.30
35 2480 141A 142A C N 704 706 57.22 -68.20 132.61 12.49 -68.20 132.61 12.49
35 142A 142A N CA 706 707 -171.64 145.30 145.30
36 2481 142A 143A C N 709 711 -80.68 -68.20 69.99 6.08 -62.50 118.73 18.65
36 143A 143A N CA 711 712 76.43 145.30 -40.90
37 2483 144A 145A C N 719 721 71.92 55.40 24.39 1.21 -62.50 147.68 29.99
37 145A 145A N CA 721 722 20.27 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 3 5 12 50 75 77 77 89 129 133 107
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
poly_a.B99990001.pdb 911.67700
poly_a.B99990002.pdb 953.22473
poly_a = nglview.show_structure_file('poly_a.B99990001.pdb')
poly_a
Белковая цепочка, представляющая собой полиаланиновую последовательность, сформировала достаточно хорошую структуру, причем лиганд располагается в "нативной" области. Тут можно вспомнить забавную мысль о том, что последовательности с низким уровнем гомологии могут иметь достаточно близкие с геометрической точки зрения структуры.
Теперь посмотрим на значения скор-функции:
import pandas as pd
ligand = [0, 0, 1, 1, 1, 1]
score = [1422.69543, 1250.74878, 1016.79138, 1086.21106, 911.67700, 953.22473]
struc = ['native', 'native', 'native', 'native', 'polyala', 'polyala']
model = ['model1', 'model2', 'model1', 'model2', 'model1', 'model2']
pd.DataFrame({'is_ligand_bound' : ligand, 'molpdf' : score, 'structure' : struc, 'model' : model})
| is_ligand_bound | molpdf | structure | model | |
|---|---|---|---|---|
| 0 | 0 | 1422.69543 | native | model1 |
| 1 | 0 | 1250.74878 | native | model2 |
| 2 | 1 | 1016.79138 | native | model1 |
| 3 | 1 | 1086.21106 | native | model2 |
| 4 | 1 | 911.67700 | polyala | model1 |
| 5 | 1 | 953.22473 | polyala | model2 |
Неожиданно, что структуры, не связанные с лигандом, имеют больший скор. Структуры, построенные из полиаланиновой последовательности, имеют меньший скор, чем те, для которых использовалась "нативная" последовательность.