Гомологичное моделирование комплекса белка с лигандом¶
In [2]:
import sys
import modeller
import _modeller
import modeller.automodel
from IPython.display import display, Image
# установили, прописали лицензионный ключ
In [3]:
env = modeller.environ()
env.io.hetatm = True
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 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 le-comte 4.4.0-177-generic x86_64
Date and time of compilation : 2020/04/06 19:06:24
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2020/04/20 00:40:10
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
# скачиваем белок-заготовку (лизоцим радужной форели(Oncorhynchus mykiss))
--2020-04-20 00:40:14-- http://www.pdb.org/pdb/files/1lmp.pdb Распознаётся www.pdb.org (www.pdb.org)... 128.6.244.52 Подключение к www.pdb.org (www.pdb.org)|128.6.244.52|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа... 301 Moved Permanently Адрес: https://www.rcsb.org/pdb/files/1lmp.pdb [переход] --2020-04-20 00:40:15-- https://www.rcsb.org/pdb/files/1lmp.pdb Распознаётся www.rcsb.org (www.rcsb.org)... 128.6.244.65 Подключение к www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа... 301 Moved Permanently Адрес: http://files.rcsb.org/view/1lmp.pdb [переход] --2020-04-20 00:40:17-- http://files.rcsb.org/view/1lmp.pdb Распознаётся files.rcsb.org (files.rcsb.org)... 128.6.244.12 Подключение к files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа... 200 OK Длина: нет данных [text/plain] Сохранение в каталог: ««1lmp.pdb.5»». 1lmp.pdb.5 [ <=> ] 127,35K 211KB/s in 0,6s 2020-04-20 00:40:18 (211 KB/s) - «1lmp.pdb.5» сохранён [130410]
Для моделирования выбрал наугад лизоцим из Crassostrea gigas (Pacific oyster) (Crassostrea angulata) ID - LYS_CRAGI
In [5]:
! wget http://www.uniprot.org/uniprot/Q6L6Q6.fasta
# скачиваем его последовательность.
URL transformed to HTTPS due to an HSTS policy --2020-04-20 00:40:18-- https://www.uniprot.org/uniprot/Q6L6Q6.fasta Распознаётся www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81 Подключение к www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа... 200 Длина: 219 [text/plain] Сохранение в каталог: ««Q6L6Q6.fasta.4»». Q6L6Q6.fasta.4 100%[===================>] 219 --.-KB/s in 0s 2020-04-20 00:40:19 (43,6 MB/s) - «Q6L6Q6.fasta.4» сохранён [219/219]
In [6]:
alignm=modeller.alignment(env)
In [7]:
alignm.append(file='Q6L6Q6.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [8]:
# выравниваем и сохраняем в формате PIR
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [9]:
! cat all_in_one.ali
# отлично. Получили выравнивание.
>P1;seq sequence:: : : : :::-1.00:-1.00 MQRLLGSIVILATVFTFCEATISSACLRCICNVESGCRPIGCHYDVYSYSCGYFQIKENYWEDCGKPGTSFKACA NDYTCASNCVRAYMKRYIGSSGCPANCESYARIHNGGPRGCRHPSTLRYWEKVHQQGCNVNS* >P1;pdb structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTP----G AKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCG-V...*
In [10]:
# выбираем объект для моделирования.
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq pdb
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 2
transfe_404W> At least one template is aligned with model residue 135:
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 136:
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: 11160 10215
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 : 137
Number of all, selected real atoms : 1062 1062
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10215 10215
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2501
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 : 1296.6768
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 : 1088 0 0 0.007 0.007 15.418 1.000
2 Bond angle potential : 1471 0 3 2.288 2.288 146.78 1.000
3 Stereochemical cosine torsion poten: 723 0 37 49.029 49.029 261.67 1.000
4 Stereochemical improper torsion pot: 472 0 1 1.335 1.335 17.019 1.000
5 Soft-sphere overlap restraints : 2501 0 0 0.004 0.004 5.8392 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 5 11 0.550 0.550 216.04 1.000
10 Distance restraints 2 (N-O) : 2593 8 30 0.709 0.709 364.34 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 1 5.125 5.125 42.118 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 2 85.008 85.008 40.671 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 0 79.868 79.868 31.694 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 78.314 78.314 24.373 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 99.077 99.077 8.0845 1.000
18 Disulfide distance restraints : 2 0 0 0.003 0.003 0.25012E-02 1.000
19 Disulfide angle restraints : 4 0 0 3.173 3.173 0.88939 1.000
20 Disulfide dihedral angle restraints: 2 0 0 9.640 9.640 0.22323 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) : 825 0 0 0.460 0.460 12.255 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 38 27 35.696 92.704 102.10 1.000
26 Distance restraints 4 (SDCH-SDCH) : 122 0 0 0.821 0.821 7.1560 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: seq.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: 19320.2637
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7633 45D 137S N O 329 1061 13.79 8.62 5.17 5.62 8.62 5.17 5.62
2 7647 46V 137S N O 337 1061 13.88 8.17 5.71 7.27 8.17 5.71 7.27
3 7655 47Y 137S N O 344 1061 15.16 9.76 5.39 4.56 9.76 5.39 4.56
4 7693 50S 137S N O 374 1061 14.88 9.99 4.89 5.78 9.99 4.89 5.78
5 7717 51C 137S N O 380 1061 12.63 8.19 4.44 5.98 8.19 4.44 5.98
6 7743 52G 137S N O 386 1061 10.00 6.08 3.91 6.62 6.08 3.91 6.62
-------------------------------------------------------------------------------------------------
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 3776 14V 15F C N 103 105 -95.47 -71.40 53.32 4.73 -63.20 141.17 17.56
1 15F 15F N CA 105 106 93.13 140.70 -44.30
2 3777 15F 16T C N 114 116 -33.90 -78.10 85.32 2.80 -63.20 122.47 17.66
2 16T 16T N CA 116 117 76.82 149.80 -42.10
3 3780 18C 19E C N 138 140 68.09 54.60 27.10 1.38 -63.60 144.38 24.74
3 19E 19E N CA 140 141 18.90 42.40 -40.30
4 3782 20A 21T C N 152 154 51.24 55.90 4.70 0.50 -63.20 140.91 24.26
4 21T 21T N CA 154 155 40.12 39.50 -42.10
5 3783 21T 22I C N 159 161 36.75 -97.30 139.54 7.28 -63.40 165.72 30.67
5 22I 22I N CA 161 162 88.44 127.20 -43.60
6 3785 23S 24S C N 173 175 -67.42 -72.40 8.28 0.64 -64.10 166.02 12.23
6 24S 24S N CA 175 176 159.01 152.40 -35.00
7 3792 30I 31C C N 223 225 -59.96 -63.00 3.23 0.57 -117.90 -171.97 8.11
7 31C 31C N CA 225 226 -40.02 -41.10 141.10
8 3796 34E 35S C N 253 255 -110.66 -136.60 66.28 2.72 -64.10 133.58 8.24
8 35S 35S N CA 255 256 90.20 151.20 -35.00
9 3797 35S 36G C N 259 261 129.08 82.20 61.97 2.11 -62.40 168.77 29.76
9 36G 36G N CA 261 262 -32.03 8.50 -41.20
10 3798 36G 37C C N 263 265 63.19 57.40 14.09 0.45 -117.90 -145.71 9.16
10 37C 37C N CA 265 266 23.15 36.00 141.10
11 3806 44Y 45D C N 327 329 -88.41 -70.90 17.97 1.21 -63.30 167.56 22.27
11 45D 45D N CA 329 330 154.33 150.30 -40.00
12 3810 48S 49Y C N 360 362 75.86 55.90 29.42 1.68 -63.50 152.25 28.48
12 49Y 49Y N CA 362 363 17.89 39.50 -43.40
13 3824 62E 63D C N 489 491 -133.24 -63.30 84.59 10.40 -63.30 84.59 10.40
13 63D 63D N CA 491 492 7.59 -40.00 -40.00
14 3826 64C 65G C N 503 505 -129.51 -167.20 73.12 2.10 82.20 -179.20 14.12
14 65G 65G N CA 505 506 111.94 174.60 8.50
15 3827 65G 66K C N 507 509 -126.49 -118.00 11.59 0.40 -62.90 -176.43 27.64
15 66K 66K N CA 509 510 147.00 139.10 -40.80
16 3829 67P 68G C N 523 525 121.09 82.20 50.86 1.76 -62.40 177.32 30.94
16 68G 68G N CA 525 526 -24.27 8.50 -41.20
17 3832 70S 71F C N 540 542 -156.08 -124.20 49.97 1.42 -63.20 162.97 28.32
17 71F 71F N CA 542 543 -178.22 143.30 -44.30
18 3834 72K 73A C N 560 562 -82.69 -68.20 30.75 2.92 -62.50 160.36 25.36
18 73A 73A N CA 562 563 118.18 145.30 -40.90
19 3836 74C 75A C N 571 573 -114.07 -134.00 42.48 1.76 -62.50 158.98 24.11
19 75A 75A N CA 573 574 109.49 147.00 -40.90
20 3838 76N 77D C N 584 586 -138.08 -96.50 47.05 1.95 -63.30 -168.58 20.44
20 77D 77D N CA 586 587 136.21 114.20 -40.00
21 3839 77D 78Y C N 592 594 -97.81 -98.40 42.23 4.49 -63.50 134.04 19.63
21 78Y 78Y N CA 594 595 86.17 128.40 -43.40
22 3841 79T 80C C N 611 613 -89.48 -117.90 35.83 0.97 -63.00 162.56 18.19
22 80C 80C N CA 613 614 119.29 141.10 -41.10
23 3850 88Y 89M C N 677 679 -64.51 -73.00 20.42 1.53 -63.40 157.93 23.67
23 89M 89M N CA 679 680 161.57 143.00 -40.50
24 3852 90K 91R C N 694 696 -58.74 -63.00 7.08 0.81 -72.10 171.87 13.51
24 91R 91R N CA 696 697 -46.75 -41.10 141.90
25 3853 91R 92Y C N 705 707 76.77 55.90 49.80 2.39 -63.50 145.25 26.59
25 92Y 92Y N CA 707 708 -5.72 39.50 -43.40
26 3859 97G 98C C N 745 747 -66.02 -63.00 9.06 1.33 -117.90 177.03 7.61
26 98C 98C N CA 747 748 -49.64 -41.10 141.10
27 3868 106A 107R C N 809 811 -92.77 -72.10 57.01 4.78 -63.00 133.23 16.20
27 107R 107R N CA 811 812 88.77 141.90 -41.10
28 3869 107R 108I C N 820 822 -62.41 -63.40 22.56 3.66 -120.60 173.60 12.08
28 108I 108I N CA 822 823 -66.14 -43.60 130.30
29 3872 110N 111G C N 846 848 -57.40 -62.40 7.53 1.38 82.20 146.40 11.07
29 111G 111G N CA 848 849 -35.57 -41.20 8.50
30 3877 115G 116C C N 876 878 -64.34 -63.00 1.37 0.21 -117.90 -174.01 7.99
30 116C 116C N CA 878 879 -40.78 -41.10 141.10
31 3879 117R 118H C N 893 895 -121.41 -63.20 58.28 9.11 -63.20 58.28 9.11
31 118H 118H N CA 895 896 -39.65 -42.30 -42.30
32 3884 122L 123R C N 931 933 -69.96 -63.00 10.29 1.20 -125.20 -177.34 7.46
32 123R 123R N CA 933 934 -33.51 -41.10 140.60
33 3885 123R 124Y C N 942 944 35.26 -98.40 141.45 7.55 -63.50 159.71 29.80
33 124Y 124Y N CA 944 945 82.10 128.40 -43.40
34 3891 129H 130Q C N 1003 1005 63.31 55.10 22.20 1.06 -121.10 -147.31 10.45
34 130Q 130Q N CA 1005 1006 19.67 40.30 139.70
35 3892 130Q 131Q C N 1012 1014 -141.48 -121.10 20.90 0.70 -63.80 -168.17 32.28
35 131Q 131Q N CA 1014 1015 144.31 139.70 -40.30
36 3893 131Q 132G C N 1021 1023 -62.78 -62.40 3.34 0.52 82.20 154.37 11.79
36 132G 132G N CA 1023 1024 -44.52 -41.20 8.50
37 3895 133C 134N C N 1031 1033 -157.09 -119.90 80.28 2.71 -63.20 145.20 23.15
37 134N 134N N CA 1033 1034 -151.86 137.00 -41.10
38 3897 135V 136N C N 1046 1048 -141.16 -119.90 21.70 0.79 -63.20 -166.08 28.66
38 136N 136N N CA 1048 1049 141.34 137.00 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 15 14 94 101 145 115 172 139 182 186
<< 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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1062 1062
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10215 10215
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2396
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 : 1382.1478
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 : 1088 0 6 0.010 0.010 31.340 1.000
2 Bond angle potential : 1471 1 9 2.460 2.460 168.34 1.000
3 Stereochemical cosine torsion poten: 723 0 42 50.244 50.244 269.84 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.392 1.392 18.579 1.000
5 Soft-sphere overlap restraints : 2396 0 1 0.006 0.006 11.021 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 3 13 0.540 0.540 204.74 1.000
10 Distance restraints 2 (N-O) : 2593 13 25 0.697 0.697 406.13 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.949 4.949 39.283 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 2 88.408 88.408 49.524 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 0 76.996 76.996 27.313 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 64.243 64.243 18.676 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 95.763 95.763 11.867 1.000
18 Disulfide distance restraints : 2 0 0 0.011 0.011 0.41436E-01 1.000
19 Disulfide angle restraints : 4 0 0 2.990 2.990 0.78973 1.000
20 Disulfide dihedral angle restraints: 2 0 0 14.545 14.545 0.49674 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) : 825 0 0 0.524 0.524 11.742 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 34 25 35.863 91.285 101.90 1.000
26 Distance restraints 4 (SDCH-SDCH) : 122 0 0 0.992 0.992 10.520 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: seq.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: 19398.7070
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 2539 135V 135V N CA 1041 1042 122.93 107.00 15.93 4.58 107.00 15.93 4.58
-------------------------------------------------------------------------------------------------
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 7617 44Y 137S N O 317 1061 14.33 8.18 6.15 6.69 8.18 6.15 6.69
2 7633 45D 137S N O 329 1061 16.07 8.62 7.45 8.10 8.62 7.45 8.10
3 7647 46V 137S N O 337 1061 16.09 8.17 7.92 10.08 8.17 7.92 10.08
4 7655 47Y 137S N O 344 1061 17.25 9.76 7.49 6.33 9.76 7.49 6.33
5 7664 48S 137S N O 356 1061 17.73 10.84 6.89 6.25 10.84 6.89 6.25
6 7693 50S 137S N O 374 1061 17.01 9.99 7.03 8.30 9.99 7.03 8.30
7 7717 51C 137S N O 380 1061 14.97 8.19 6.79 9.14 8.19 6.79 9.14
8 7743 52G 137S N O 386 1061 12.52 6.08 6.43 10.88 6.08 6.43 10.88
9 7772 53Y 137S N O 390 1061 10.77 7.17 3.59 4.95 7.17 3.59 4.95
10 7968 59N 137S N O 448 1061 9.15 5.93 3.23 4.53 5.93 3.23 4.53
11 7999 60Y 137S N O 456 1061 12.67 8.00 4.67 5.16 8.00 4.67 5.16
-------------------------------------------------------------------------------------------------
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 3775 13T 14V C N 96 98 -65.65 -73.50 16.10 1.42 -62.40 164.37 20.99
1 14V 14V N CA 98 99 153.26 139.20 -42.40
2 3776 14V 15F C N 103 105 69.69 58.10 19.41 1.09 -63.20 146.48 26.18
2 15F 15F N CA 105 106 17.33 32.90 -44.30
3 3777 15F 16T C N 114 116 51.31 55.90 6.26 0.39 -63.20 143.12 24.62
3 16T 16T N CA 116 117 43.76 39.50 -42.10
4 3780 18C 19E C N 138 140 62.06 54.60 14.64 0.75 -63.60 143.89 24.75
4 19E 19E N CA 140 141 29.80 42.40 -40.30
5 3782 20A 21T C N 152 154 46.64 55.90 9.75 0.91 -63.20 138.69 23.84
5 21T 21T N CA 154 155 42.58 39.50 -42.10
6 3783 21T 22I C N 159 161 37.38 -97.30 139.80 7.22 -63.40 167.13 30.92
6 22I 22I N CA 161 162 89.72 127.20 -43.60
7 3785 23S 24S C N 173 175 -77.43 -72.40 12.47 0.59 -64.10 161.74 12.56
7 24S 24S N CA 175 176 163.80 152.40 -35.00
8 3798 36G 37C C N 263 265 66.79 57.40 16.00 0.68 -117.90 -148.65 9.05
8 37C 37C N CA 265 266 23.05 36.00 141.10
9 3806 44Y 45D C N 327 329 -107.94 -96.50 21.55 0.91 -63.30 178.14 19.71
9 45D 45D N CA 329 330 132.46 114.20 -40.00
10 3810 48S 49Y C N 360 362 80.32 55.90 40.14 2.10 -63.50 152.61 28.29
10 49Y 49Y N CA 362 363 7.64 39.50 -43.40
11 3826 64C 65G C N 503 505 -108.61 -80.20 56.49 3.58 82.20 -154.43 16.06
11 65G 65G N CA 505 506 125.26 174.10 8.50
12 3827 65G 66K C N 507 509 -130.23 -118.00 44.37 1.96 -62.90 153.05 23.90
12 66K 66K N CA 509 510 -178.25 139.10 -40.80
13 3828 66K 67P C N 516 518 -62.03 -58.70 17.44 1.19 -64.50 160.60 11.85
13 67P 67P N CA 518 519 -13.38 -30.50 147.20
14 3829 67P 68G C N 523 525 135.05 78.70 83.43 1.74 -62.40 -122.19 33.28
14 68G 68G N CA 525 526 132.38 -166.10 -41.20
15 3832 70S 71F C N 540 542 -112.49 -124.20 14.91 0.80 -63.20 170.44 26.95
15 71F 71F N CA 542 543 152.54 143.30 -44.30
16 3833 71F 72K C N 551 553 -172.02 -118.00 69.07 2.35 -62.90 175.20 29.13
16 72K 72K N CA 553 554 -177.87 139.10 -40.80
17 3836 74C 75A C N 571 573 -160.02 -134.00 26.47 0.71 -62.50 -166.38 36.93
17 75A 75A N CA 573 574 151.83 147.00 -40.90
18 3838 76N 77D C N 584 586 -104.83 -96.50 38.41 1.62 -63.30 173.36 24.06
18 77D 77D N CA 586 587 151.69 114.20 -40.00
19 3839 77D 78Y C N 592 594 -121.38 -98.40 54.81 5.26 -63.50 135.07 18.97
19 78Y 78Y N CA 594 595 78.64 128.40 -43.40
20 3842 80C 81A C N 617 619 58.31 55.40 12.34 0.98 -62.50 151.30 30.63
20 81A 81A N CA 619 620 50.19 38.20 -40.90
21 3850 88Y 89M C N 677 679 -60.69 -73.00 16.52 1.32 -63.40 165.51 24.50
21 89M 89M N CA 679 680 154.01 143.00 -40.50
22 3859 97G 98C C N 745 747 -65.65 -63.00 10.20 1.44 -117.90 175.88 7.57
22 98C 98C N CA 747 748 -50.95 -41.10 141.10
23 3863 101N 102C C N 771 773 -62.62 -63.00 1.76 0.24 -117.90 -172.16 8.08
23 102C 102C N CA 773 774 -39.38 -41.10 141.10
24 3869 107R 108I C N 820 822 54.15 -97.30 166.67 9.00 -120.60 -173.03 14.61
24 108I 108I N CA 822 823 -163.23 127.20 130.30
25 3872 110N 111G C N 846 848 -57.32 -62.40 8.14 1.48 82.20 146.10 11.03
25 111G 111G N CA 848 849 -34.84 -41.20 8.50
26 3877 115G 116C C N 876 878 -63.87 -63.00 2.21 0.33 -117.90 -176.12 7.91
26 116C 116C N CA 878 879 -43.13 -41.10 141.10
27 3879 117R 118H C N 893 895 -120.36 -63.20 57.65 8.75 -63.20 57.65 8.75
27 118H 118H N CA 895 896 -34.87 -42.30 -42.30
28 3881 119P 120S C N 910 912 -65.91 -72.40 14.21 0.66 -64.10 174.77 12.56
28 120S 120S N CA 912 913 139.76 152.40 -35.00
29 3882 120S 121T C N 916 918 57.70 55.90 11.21 0.66 -63.20 139.97 24.12
29 121T 121T N CA 918 919 28.44 39.50 -42.10
30 3885 123R 124Y C N 942 944 -114.41 -98.40 66.56 6.82 -63.50 118.67 16.67
30 124Y 124Y N CA 944 945 63.79 128.40 -43.40
31 3892 130Q 131Q C N 1012 1014 -83.80 -121.10 38.21 1.28 -63.80 172.90 24.41
31 131Q 131Q N CA 1014 1015 131.43 139.70 -40.30
32 3893 131Q 132G C N 1021 1023 62.24 78.70 16.47 0.85 82.20 176.40 9.56
32 132G 132G N CA 1023 1024 -166.77 -166.10 8.50
33 3895 133C 134N C N 1031 1033 -163.16 -119.90 68.26 2.06 -63.20 163.28 25.81
33 134N 134N N CA 1033 1034 -170.20 137.00 -41.10
34 3897 135V 136N C N 1046 1048 -130.36 -119.90 65.63 2.73 -63.20 135.00 20.62
34 136N 136N N CA 1048 1049 -158.21 137.00 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 14 14 76 117 127 119 149 163 165 175
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 1296.67676
seq.B99990002.pdb 1382.14783
Получили две модели на выходе. Попробуем посмотреть, что получилось.
In [11]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('seq.B99990001.pdb')
w1
Почему-то ничего не произошло(
In [13]:
command = f"load seq.B99990001.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; "\
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
In [14]:
command = f"load seq.B99990002.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
Скоры большие
seq.B99990001.pdb 1296.67676
seq.B99990002.pdb 1382.14783
Что-то плохо выровнялось.
А ГДЕ ЛИГАНД??
In [15]:
seq_liganded = ''
for res in alignm[0].residues:
seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'plus_ligand'
del alignm[0]
In [16]:
# Делаем выравнивание.
alignm.salign()
# Сохраняем в файл.
alignm.write(file='all_in_one_w_l.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [18]:
! cat all_in_one_w_l.ali
# отлично. Получили выравнивание.
>P1;pdb structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCS--------QLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;plus_ligand sequence::1 : :+140 : :undefined:undefined:-1.00:-1.00 MQRLLGSIVILATVFTFCEATISSACLRCICNVESGCRPIGCHYDVYSYSCGYFQIKENYWEDCGKPGTSFKACA NDYTCASNCVRAYMKRYIGSSGCPANCESYARIHNGGPRGCRHPSTLRYWEKVHQQGCNVNS...*
In [19]:
# Выбираем объект для моделирования.
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one_w_l.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
plus_ligand pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 137
atom names : C +N
atom indices : 1060 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 137
atom names : C CA +N O
atom indices : 1060 1057 0 1061
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 1
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: 12522 11579
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 : 140
Number of all, selected real atoms : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11579 11579
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2638
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 : 1004.2239
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 : 1088 0 0 0.005 0.005 9.2679 1.000
2 Bond angle potential : 1471 0 6 2.171 2.171 133.72 1.000
3 Stereochemical cosine torsion poten: 721 0 33 48.886 48.886 256.69 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.190 1.190 14.523 1.000
5 Soft-sphere overlap restraints : 2638 2 2 0.008 0.008 20.404 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.251 0.251 56.639 1.000
10 Distance restraints 2 (N-O) : 2564 2 12 0.455 0.455 194.52 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 2 4.692 4.692 35.315 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 3 89.010 89.010 47.299 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 0 82.158 82.158 34.412 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 68.240 68.240 20.097 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 90.765 90.765 9.8133 1.000
18 Disulfide distance restraints : 1 0 0 0.022 0.022 0.86201E-01 1.000
19 Disulfide angle restraints : 2 0 0 0.888 0.888 0.34858E-01 1.000
20 Disulfide dihedral angle restraints: 1 0 0 28.750 28.750 0.84114 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) : 828 0 0 0.400 0.400 17.537 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 33 22 35.483 84.021 132.21 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.724 0.724 6.7967 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.032 0.032 14.011 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: plus_ligand.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: 18221.4023
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7345 34E 30I N O 246 224 5.57 3.16 2.42 4.97 3.16 2.42 4.97
-------------------------------------------------------------------------------------------------
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 3761 5L 6G C N 43 45 -65.28 -62.40 3.83 0.55 82.20 154.85 11.72
1 6G 6G N CA 45 46 -38.68 -41.20 8.50
2 3770 14V 15F C N 103 105 -96.17 -71.40 95.96 8.29 -63.20 98.00 11.65
2 15F 15F N CA 105 106 47.99 140.70 -44.30
3 3771 15F 16T C N 114 116 50.00 55.90 10.83 1.18 -63.20 134.44 23.17
3 16T 16T N CA 116 117 30.42 39.50 -42.10
4 3774 18C 19E C N 138 140 58.94 54.60 18.64 1.11 -63.60 138.51 23.81
4 19E 19E N CA 140 141 24.27 42.40 -40.30
5 3776 20A 21T C N 152 154 49.80 -78.10 143.05 9.52 -63.20 153.60 17.11
5 21T 21T N CA 154 155 -146.14 149.80 -42.10
6 3779 23S 24S C N 173 175 -84.44 -72.40 21.12 0.96 -64.10 156.57 12.67
6 24S 24S N CA 175 176 169.75 152.40 -35.00
7 3784 28R 29C C N 209 211 -63.04 -63.00 4.12 0.50 -117.90 -177.86 7.85
7 29C 29C N CA 211 212 -45.21 -41.10 141.10
8 3785 29C 30I C N 215 217 -79.12 -120.60 56.19 4.47 -63.40 149.02 24.99
8 30I 30I N CA 217 218 168.21 130.30 -43.60
9 3786 30I 31C C N 223 225 76.78 57.40 74.30 2.67 -117.90 -117.92 10.72
9 31C 31C N CA 225 226 -35.73 36.00 141.10
10 3791 35S 36G C N 259 261 -170.85 82.20 107.66 6.74 -62.40 114.71 18.65
10 36G 36G N CA 261 262 -3.83 8.50 -41.20
11 3792 36G 37C C N 263 265 62.65 57.40 7.77 0.41 -117.90 -149.08 8.95
11 37C 37C N CA 265 266 30.27 36.00 141.10
12 3800 44Y 45D C N 327 329 -83.14 -70.90 13.99 0.75 -63.30 164.13 21.51
12 45D 45D N CA 329 330 157.08 150.30 -40.00
13 3804 48S 49Y C N 360 362 81.72 55.90 40.30 2.19 -63.50 154.23 28.60
13 49Y 49Y N CA 362 363 8.56 39.50 -43.40
14 3821 65G 66K C N 507 509 -115.08 -118.00 18.67 0.94 -62.90 169.87 25.17
14 66K 66K N CA 509 510 157.54 139.10 -40.80
15 3823 67P 68G C N 523 525 123.13 82.20 53.47 1.85 -62.40 175.13 30.63
15 68G 68G N CA 525 526 -25.91 8.50 -41.20
16 3826 70S 71F C N 540 542 59.14 58.10 1.17 0.18 -63.20 144.94 26.14
16 71F 71F N CA 542 543 33.43 32.90 -44.30
17 3828 72K 73A C N 560 562 -131.18 -134.00 59.92 3.34 -62.50 145.30 21.77
17 73A 73A N CA 562 563 87.14 147.00 -40.90
18 3837 81A 82S C N 622 624 -161.90 -136.60 32.78 1.02 -64.10 -178.45 20.21
18 82S 82S N CA 624 625 172.04 151.20 -35.00
19 3838 82S 83N C N 628 630 -67.39 -71.20 8.97 0.68 -63.20 168.04 21.24
19 83N 83N N CA 630 631 150.92 142.80 -41.10
20 3841 85V 86R C N 649 651 78.97 57.30 117.79 9.38 -63.00 -142.23 25.18
20 86R 86R N CA 651 652 153.77 38.00 -41.10
21 3842 86R 87A C N 660 662 -74.79 -68.20 16.62 1.55 -62.50 171.38 27.51
21 87A 87A N CA 662 663 130.04 145.30 -40.90
22 3843 87A 88Y C N 665 667 -151.53 -124.30 40.87 1.74 -63.50 174.55 31.91
22 88Y 88Y N CA 667 668 165.88 135.40 -43.40
23 3844 88Y 89M C N 677 679 -118.46 -125.60 11.69 0.64 -63.40 178.45 31.03
23 89M 89M N CA 679 680 149.76 140.50 -40.50
24 3845 89M 90K C N 685 687 -125.91 -118.00 33.21 1.49 -62.90 160.71 24.64
24 90K 90K N CA 687 688 171.36 139.10 -40.80
25 3847 91R 92Y C N 705 707 -101.73 -98.40 81.59 8.66 -63.50 98.04 13.88
25 92Y 92Y N CA 707 708 46.88 128.40 -43.40
26 3849 93I 94G C N 725 727 -58.33 -62.40 4.29 0.81 82.20 148.62 11.30
26 94G 94G N CA 727 728 -39.86 -41.20 8.50
27 3852 96S 97G C N 741 743 23.11 78.70 77.87 1.78 -62.40 110.74 16.03
27 97G 97G N CA 743 744 -111.57 -166.10 -41.20
28 3883 127K 128V C N 986 988 -111.57 -125.40 96.91 4.45 -62.40 102.36 11.20
28 128V 128V N CA 988 989 47.38 143.30 -42.40
29 3886 130Q 131Q C N 1012 1014 -77.83 -73.00 48.62 3.28 -63.80 133.36 18.90
29 131Q 131Q N CA 1014 1015 92.32 140.70 -40.30
30 3888 132G 133C C N 1025 1027 -61.23 -63.00 2.65 0.29 -117.90 -175.27 7.97
30 133C 133C N CA 1027 1028 -43.07 -41.10 141.10
31 3889 133C 134N C N 1031 1033 -61.64 -63.20 4.88 0.54 55.90 145.18 17.72
31 134N 134N N CA 1033 1034 -45.72 -41.10 39.50
32 3890 134N 135V C N 1039 1041 -90.23 -73.50 21.20 1.77 -62.40 170.87 20.15
32 135V 135V N CA 1041 1042 126.19 139.20 -42.40
33 3891 135V 136N C N 1046 1048 -85.53 -71.20 42.84 3.14 55.90 154.79 13.40
33 136N 136N N CA 1048 1049 102.43 142.80 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 12 18 88 107 125 140 146 201 203 179
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11579 11579
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2509
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 : 918.7274
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 : 1088 0 0 0.005 0.005 9.1089 1.000
2 Bond angle potential : 1471 0 3 2.108 2.108 125.82 1.000
3 Stereochemical cosine torsion poten: 721 0 38 49.414 49.414 261.84 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.123 1.123 12.446 1.000
5 Soft-sphere overlap restraints : 2509 1 2 0.008 0.008 21.135 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.282 0.282 64.446 1.000
10 Distance restraints 2 (N-O) : 2564 2 9 0.428 0.428 159.64 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 2 4.752 4.752 36.223 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 1 87.162 87.162 39.440 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 1 76.793 76.793 37.936 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 59.433 59.433 19.657 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 91.938 91.938 9.2055 1.000
18 Disulfide distance restraints : 1 0 0 0.000 0.000 0.29565E-04 1.000
19 Disulfide angle restraints : 2 0 0 0.692 0.692 0.21132E-01 1.000
20 Disulfide dihedral angle restraints: 1 0 0 33.818 33.818 1.0787 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) : 828 0 0 0.360 0.360 11.755 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 34 18 34.200 86.669 88.281 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.642 0.642 5.8805 1.000
27 Distance restraints 5 (X-Y) : 1401 0 1 0.034 0.034 14.808 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: plus_ligand.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: 17662.1621
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9036 123R 119P N O 933 911 4.92 2.94 1.98 4.58 2.94 1.98 4.58
2 9054 124Y 119P N O 944 911 5.39 2.79 2.61 5.14 2.79 2.61 5.14
-------------------------------------------------------------------------------------------------
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 3761 5L 6G C N 43 45 -66.47 -62.40 4.92 0.73 82.20 155.90 11.79
1 6G 6G N CA 45 46 -38.44 -41.20 8.50
2 3770 14V 15F C N 103 105 -92.80 -63.20 92.73 11.10 -63.20 92.73 11.10
2 15F 15F N CA 105 106 43.58 -44.30 -44.30
3 3771 15F 16T C N 114 116 54.33 55.90 6.60 0.58 -63.20 139.52 24.05
3 16T 16T N CA 116 117 33.09 39.50 -42.10
4 3774 18C 19E C N 138 140 63.55 54.60 17.43 0.89 -63.60 144.07 24.77
4 19E 19E N CA 140 141 27.44 42.40 -40.30
5 3776 20A 21T C N 152 154 49.47 55.90 6.99 0.61 -63.20 140.75 24.21
5 21T 21T N CA 154 155 42.25 39.50 -42.10
6 3777 21T 22I C N 159 161 43.29 -97.30 144.73 7.23 -63.40 173.18 32.10
6 22I 22I N CA 161 162 92.81 127.20 -43.60
7 3779 23S 24S C N 173 175 -70.42 -72.40 10.24 0.67 -64.10 162.67 12.17
7 24S 24S N CA 175 176 162.45 152.40 -35.00
8 3784 28R 29C C N 209 211 -65.94 -63.00 3.34 0.60 -117.90 -176.29 7.88
8 29C 29C N CA 211 212 -42.69 -41.10 141.10
9 3786 30I 31C C N 223 225 -63.72 -63.00 1.71 0.26 -117.90 -175.61 7.93
9 31C 31C N CA 225 226 -42.64 -41.10 141.10
10 3792 36G 37C C N 263 265 67.57 57.40 16.11 0.76 -117.90 -149.55 9.01
10 37C 37C N CA 265 266 23.51 36.00 141.10
11 3800 44Y 45D C N 327 329 -83.26 -70.90 13.03 0.82 -63.30 166.81 21.84
11 45D 45D N CA 329 330 154.39 150.30 -40.00
12 3804 48S 49Y C N 360 362 78.58 55.90 34.45 1.92 -63.50 153.07 28.52
12 49Y 49Y N CA 362 363 13.56 39.50 -43.40
13 3821 65G 66K C N 507 509 -121.39 -118.00 39.12 1.85 -62.90 152.76 23.34
13 66K 66K N CA 509 510 178.08 139.10 -40.80
14 3822 66K 67P C N 516 518 -65.57 -58.70 22.66 1.41 -64.50 156.11 11.71
14 67P 67P N CA 518 519 -8.91 -30.50 147.20
15 3823 67P 68G C N 523 525 154.27 78.70 115.04 2.30 -62.40 -153.71 28.97
15 68G 68G N CA 525 526 107.16 -166.10 -41.20
16 3826 70S 71F C N 540 542 53.42 58.10 16.35 0.94 -63.20 149.08 26.87
16 71F 71F N CA 542 543 48.57 32.90 -44.30
17 3837 81A 82S C N 622 624 166.96 -136.60 66.59 2.03 -64.10 -170.80 22.96
17 82S 82S N CA 624 625 -173.46 151.20 -35.00
18 3838 82S 83N C N 628 630 -87.32 -71.20 37.71 2.04 -63.20 144.04 19.37
18 83N 83N N CA 630 631 176.89 142.80 -41.10
19 3839 83N 84C C N 636 638 -59.51 -63.00 9.20 0.96 -117.90 179.08 7.75
19 84C 84C N CA 638 639 -49.60 -41.10 141.10
20 3841 85V 86R C N 649 651 -157.09 -125.20 31.95 1.23 -63.00 -160.08 33.37
20 86R 86R N CA 651 652 142.51 140.60 -41.10
21 3843 87A 88Y C N 665 667 -112.86 -124.30 11.80 0.78 -63.50 -177.31 26.65
21 88Y 88Y N CA 667 668 132.50 135.40 -43.40
22 3844 88Y 89M C N 677 679 -77.03 -73.00 22.58 1.46 -63.40 154.88 24.20
22 89M 89M N CA 679 680 165.21 143.00 -40.50
23 3845 89M 90K C N 685 687 -90.75 -62.90 72.41 11.07 -62.90 72.41 11.07
23 90K 90K N CA 687 688 -107.64 -40.80 -40.80
24 3848 92Y 93I C N 717 719 -56.47 -63.40 10.28 1.57 -120.60 -170.33 13.22
24 93I 93I N CA 719 720 -51.19 -43.60 130.30
25 3865 109H 110N C N 838 840 -65.45 -119.90 54.46 2.28 -63.20 179.00 22.26
25 110N 110N N CA 840 841 137.89 137.00 -41.10
26 3866 110N 111G C N 846 848 122.17 82.20 58.21 1.77 -62.40 175.59 31.06
26 111G 111G N CA 848 849 -33.82 8.50 -41.20
27 3874 118H 119P C N 903 905 -75.82 -64.50 33.00 1.98 -58.70 152.27 13.99
27 119P 119P N CA 905 906 178.20 147.20 -30.50
28 3875 119P 120S C N 910 912 63.50 56.90 37.07 1.85 -64.10 132.29 17.67
28 120S 120S N CA 912 913 -0.08 36.40 -35.00
29 3876 120S 121T C N 916 918 -137.91 -63.20 83.25 14.30 -63.20 83.25 14.30
29 121T 121T N CA 918 919 -78.83 -42.10 -42.10
30 3887 131Q 132G C N 1021 1023 -65.84 -62.40 3.72 0.59 82.20 155.71 11.80
30 132G 132G N CA 1023 1024 -39.76 -41.20 8.50
31 3888 132G 133C C N 1025 1027 47.76 -69.10 137.04 12.71 -117.90 -179.26 7.37
31 133C 133C N CA 1027 1028 -146.62 141.80 141.10
32 3889 133C 134N C N 1031 1033 -62.14 -63.20 3.60 0.51 55.90 141.02 17.31
32 134N 134N N CA 1033 1034 -37.66 -41.10 39.50
33 3890 134N 135V C N 1039 1041 -61.57 -73.50 30.32 2.38 -62.40 153.73 19.50
33 135V 135V N CA 1041 1042 111.33 139.20 -42.40
34 3891 135V 136N C N 1046 1048 -84.12 -71.20 34.41 2.55 55.90 157.17 12.99
34 136N 136N N CA 1048 1049 110.90 142.80 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 14 12 82 96 120 129 143 168 200 199
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
plus_ligand.B99990001.pdb 1004.22394
plus_ligand.B99990002.pdb 918.72736
Получили
plus_ligand.B99990001.pdb 699.94702
plus_ligand.B99990002.pdb 731.96399
Отично!
In [20]:
command = f"load plus_ligand.B99990001.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
In [21]:
command = f"load plus_ligand.B99990002.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
Попробуем поместить лиганд в другое место
In [34]:
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd,stored
from IPython.display import Image
import time
In [36]:
cmd.reinitialize()
cmd.do('''
reini
fetch 1lmp, async=0
color palegreen
bg_color white
select s1, resn nag+ndg
util.cbaw s1
set ray_trace_mode, 3
set ray_opaque_background, 0
ray 600,700
remove solvent
extract ligand, het
as cartoon, 1lmp
set cartoon_transparency, 0.5
as sticks, ligand
center ligand
origin ligand
''')
cmd.do('png pr8.png')
In [19]:
Image(filename='pr8.png')
Out[19]:
Выбрал другой карман
In [20]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:123','CA:114')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one_w_l.ali', knowns=pdb.code, sequence=s.code)
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()
In [21]:
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
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 137
atom names : C +N
atom indices : 1060 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 137
atom names : C CA +N O
atom indices : 1060 1057 0 1061
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 1
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: 12523 11580
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 : 140
Number of all, selected real atoms : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11580 11580
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2564
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 : 1226.4092
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 : 1088 0 0 0.007 0.007 13.779 1.000
2 Bond angle potential : 1471 0 3 2.186 2.186 137.78 1.000
3 Stereochemical cosine torsion poten: 721 0 39 49.434 49.434 262.11 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.073 1.073 11.549 1.000
5 Soft-sphere overlap restraints : 2564 2 2 0.009 0.009 22.106 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 1 7 0.395 0.395 135.37 1.000
10 Distance restraints 2 (N-O) : 2564 3 19 0.543 0.543 264.78 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 5.030 5.030 40.585 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 3 88.921 88.921 46.757 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 2 88.898 88.898 44.845 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 74.453 74.453 21.259 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 120.045 120.045 8.2541 1.000
18 Disulfide distance restraints : 1 0 0 0.011 0.011 0.19250E-01 1.000
19 Disulfide angle restraints : 2 0 0 1.199 1.199 0.63495E-01 1.000
20 Disulfide dihedral angle restraints: 1 0 0 26.214 26.214 0.72276 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) : 828 0 0 0.392 0.392 13.160 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 33 23 34.275 88.289 108.74 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.716 0.716 6.8999 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.061 0.061 87.642 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: plus_ligand.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: 19731.6797
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9081 126E 123R N O 970 943 6.13 3.18 2.94 5.34 3.18 2.94 5.34
2 9103 128V 123R N O 988 943 9.36 6.04 3.32 5.34 6.04 3.32 5.34
-------------------------------------------------------------------------------------------------
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 3761 5L 6G C N 43 45 -64.14 -62.40 2.17 0.32 82.20 154.15 11.69
1 6G 6G N CA 45 46 -39.91 -41.20 8.50
2 3769 13T 14V C N 96 98 -71.40 -73.50 25.62 2.21 -62.40 153.13 19.91
2 14V 14V N CA 98 99 164.73 139.20 -42.40
3 3770 14V 15F C N 103 105 73.65 58.10 28.01 1.50 -63.20 147.08 26.09
3 15F 15F N CA 105 106 9.60 32.90 -44.30
4 3771 15F 16T C N 114 116 54.20 55.90 1.71 0.18 -63.20 143.08 24.65
4 16T 16T N CA 116 117 39.70 39.50 -42.10
5 3774 18C 19E C N 138 140 59.28 54.60 15.24 0.85 -63.60 140.54 24.17
5 19E 19E N CA 140 141 27.89 42.40 -40.30
6 3776 20A 21T C N 152 154 48.15 55.90 8.43 0.74 -63.20 140.03 24.08
6 21T 21T N CA 154 155 42.81 39.50 -42.10
7 3777 21T 22I C N 159 161 34.99 -97.30 136.85 6.97 -63.40 167.68 30.95
7 22I 22I N CA 161 162 92.18 127.20 -43.60
8 3779 23S 24S C N 173 175 -69.36 -72.40 8.70 0.61 -64.10 164.53 12.24
8 24S 24S N CA 175 176 160.55 152.40 -35.00
9 3791 35S 36G C N 259 261 -173.81 82.20 104.88 6.49 -62.40 117.09 19.16
9 36G 36G N CA 261 262 -5.19 8.50 -41.20
10 3792 36G 37C C N 263 265 67.52 57.40 18.35 0.72 -117.90 -147.92 9.10
10 37C 37C N CA 265 266 20.69 36.00 141.10
11 3800 44Y 45D C N 327 329 -84.40 -70.90 15.67 0.82 -63.30 163.12 21.46
11 45D 45D N CA 329 330 158.25 150.30 -40.00
12 3804 48S 49Y C N 360 362 78.05 55.90 32.50 1.87 -63.50 153.41 28.63
12 49Y 49Y N CA 362 363 15.72 39.50 -43.40
13 3821 65G 66K C N 507 509 -130.01 -118.00 51.74 2.32 -62.90 146.10 22.99
13 66K 66K N CA 509 510 -170.57 139.10 -40.80
14 3822 66K 67P C N 516 518 -68.55 -58.70 24.84 1.46 -64.50 154.94 11.78
14 67P 67P N CA 518 519 -7.69 -30.50 147.20
15 3823 67P 68G C N 523 525 147.89 78.70 111.90 2.05 -62.40 -150.08 29.66
15 68G 68G N CA 525 526 105.95 -166.10 -41.20
16 3825 69T 70S C N 534 536 -49.65 -64.10 54.99 3.41 -72.40 121.69 7.95
16 70S 70S N CA 536 537 -88.06 -35.00 152.40
17 3826 70S 71F C N 540 542 -102.45 -124.20 48.92 1.67 -63.20 149.05 18.26
17 71F 71F N CA 542 543 99.49 143.30 -44.30
18 3837 81A 82S C N 622 624 168.64 -136.60 55.08 2.03 -64.10 -149.37 24.44
18 82S 82S N CA 624 625 157.15 151.20 -35.00
19 3838 82S 83N C N 628 630 -161.92 -119.90 51.79 1.51 -63.20 -179.07 28.06
19 83N 83N N CA 630 631 167.28 137.00 -41.10
20 3841 85V 86R C N 649 651 -59.67 -72.10 18.15 1.58 -63.00 163.82 21.91
20 86R 86R N CA 651 652 155.12 141.90 -41.10
21 3844 88Y 89M C N 677 679 156.19 -125.60 83.42 2.65 -63.40 -154.53 40.83
21 89M 89M N CA 679 680 169.49 140.50 -40.50
22 3845 89M 90K C N 685 687 -118.41 -118.00 43.22 2.09 -62.90 147.71 22.50
22 90K 90K N CA 687 688 -177.68 139.10 -40.80
23 3848 92Y 93I C N 717 719 -58.52 -63.40 10.12 1.54 -120.60 -172.21 13.04
23 93I 93I N CA 719 720 -52.46 -43.60 130.30
24 3852 96S 97G C N 741 743 23.96 78.70 82.86 1.67 -62.40 106.72 15.73
24 97G 97G N CA 743 744 -103.90 -166.10 -41.20
25 3865 109H 110N C N 838 840 -64.09 -119.90 55.81 2.33 -63.20 178.53 22.27
25 110N 110N N CA 840 841 137.43 137.00 -41.10
26 3866 110N 111G C N 846 848 121.55 82.20 57.76 1.74 -62.40 176.21 31.17
26 111G 111G N CA 848 849 -33.79 8.50 -41.20
27 3878 122L 123R C N 931 933 -113.73 -125.20 60.75 2.66 -63.00 132.17 15.21
27 123R 123R N CA 933 934 80.95 140.60 -41.10
28 3883 127K 128V C N 986 988 -104.32 -73.50 77.83 6.86 -62.40 117.84 13.08
28 128V 128V N CA 988 989 67.73 139.20 -42.40
29 3886 130Q 131Q C N 1012 1014 -76.50 -73.00 20.32 1.40 -63.80 161.48 23.09
29 131Q 131Q N CA 1014 1015 120.68 140.70 -40.30
30 3888 132G 133C C N 1025 1027 -61.07 -63.00 3.31 0.35 -117.90 -175.90 7.94
30 133C 133C N CA 1027 1028 -43.79 -41.10 141.10
31 3889 133C 134N C N 1031 1033 -63.30 -63.20 2.02 0.26 55.90 145.03 17.75
31 134N 134N N CA 1033 1034 -43.12 -41.10 39.50
32 3890 134N 135V C N 1039 1041 -97.12 -73.50 31.31 2.64 -62.40 164.74 19.08
32 135V 135V N CA 1041 1042 118.64 139.20 -42.40
33 3891 135V 136N C N 1046 1048 -79.09 -71.20 32.68 2.31 55.90 152.80 12.44
33 136N 136N N CA 1048 1049 111.09 142.80 39.50
-------------------------------------------------------------------------------------------------
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 11580 123R 114R O CA 943 864 4.44 3.00 1.44 14.38 3.00 1.44 14.38
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 13 10 92 99 142 144 147 180 181 203
<< 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 : 140
Number of all, selected real atoms : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11580 11580
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2447
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 : 1176.4268
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 : 1088 0 0 0.006 0.006 13.109 1.000
2 Bond angle potential : 1471 0 4 2.110 2.110 127.33 1.000
3 Stereochemical cosine torsion poten: 721 0 33 48.958 48.958 252.53 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.083 1.083 12.394 1.000
5 Soft-sphere overlap restraints : 2447 2 2 0.009 0.009 22.189 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 7 0.350 0.350 111.00 1.000
10 Distance restraints 2 (N-O) : 2564 3 27 0.552 0.552 282.56 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.661 4.661 34.836 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 2 80.507 80.507 43.413 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 2 81.699 81.699 38.381 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 61.579 61.579 18.194 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 112.412 112.412 8.7625 1.000
18 Disulfide distance restraints : 1 0 0 0.002 0.002 0.67054E-03 1.000
19 Disulfide angle restraints : 2 0 0 0.918 0.918 0.37252E-01 1.000
20 Disulfide dihedral angle restraints: 1 0 0 42.847 42.847 1.4608 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) : 828 0 0 0.456 0.456 12.024 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 37 30 32.512 84.610 103.97 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.634 0.634 4.4727 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.060 0.060 89.757 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: plus_ligand.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: 18356.3516
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9081 126E 123R N O 970 943 6.16 3.18 2.98 5.40 3.18 2.98 5.40
2 9103 128V 123R N O 988 943 9.50 6.04 3.47 5.57 6.04 3.47 5.57
-------------------------------------------------------------------------------------------------
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 3761 5L 6G C N 43 45 -65.98 -62.40 4.51 0.66 82.20 155.45 11.76
1 6G 6G N CA 45 46 -38.47 -41.20 8.50
2 3771 15F 16T C N 114 116 77.78 55.90 22.46 2.24 -63.20 160.41 27.61
2 16T 16T N CA 116 117 34.44 39.50 -42.10
3 3774 18C 19E C N 138 140 55.55 54.60 2.30 0.12 -63.60 143.86 24.74
3 19E 19E N CA 140 141 40.30 42.40 -40.30
4 3775 19E 20A C N 147 149 -59.79 -62.50 19.70 3.11 -68.20 154.51 12.76
4 20A 20A N CA 149 150 -60.41 -40.90 145.30
5 3776 20A 21T C N 152 154 -89.48 -63.20 69.95 10.70 -63.20 69.95 10.70
5 21T 21T N CA 154 155 -106.92 -42.10 -42.10
6 3777 21T 22I C N 159 161 -109.92 -97.30 72.15 7.35 -63.40 110.08 16.82
6 22I 22I N CA 161 162 56.16 127.20 -43.60
7 3779 23S 24S C N 173 175 -69.76 -72.40 13.64 0.89 -64.10 159.31 11.89
7 24S 24S N CA 175 176 165.78 152.40 -35.00
8 3784 28R 29C C N 209 211 -65.29 -63.00 3.83 0.63 -117.90 -177.52 7.84
8 29C 29C N CA 211 212 -44.16 -41.10 141.10
9 3786 30I 31C C N 223 225 -61.31 -63.00 4.24 0.44 -117.90 -177.12 7.89
9 31C 31C N CA 225 226 -44.99 -41.10 141.10
10 3790 34E 35S C N 253 255 -103.45 -136.60 79.04 3.18 -64.10 121.02 7.45
10 35S 35S N CA 255 256 79.45 151.20 -35.00
11 3791 35S 36G C N 259 261 128.24 82.20 58.59 2.11 -62.40 169.90 29.77
11 36G 36G N CA 261 262 -27.74 8.50 -41.20
12 3792 36G 37C C N 263 265 63.59 57.40 13.23 0.44 -117.90 -146.67 9.11
12 37C 37C N CA 265 266 24.30 36.00 141.10
13 3800 44Y 45D C N 327 329 -86.31 -70.90 16.94 0.98 -63.30 164.30 21.73
13 45D 45D N CA 329 330 157.32 150.30 -40.00
14 3804 48S 49Y C N 360 362 80.06 55.90 40.58 2.09 -63.50 152.11 28.18
14 49Y 49Y N CA 362 363 6.89 39.50 -43.40
15 3821 65G 66K C N 507 509 -136.85 -118.00 57.51 2.96 -62.90 145.72 16.77
15 66K 66K N CA 509 510 84.77 139.10 -40.80
16 3823 67P 68G C N 523 525 136.98 82.20 60.74 2.84 -62.40 162.32 27.95
16 68G 68G N CA 525 526 -17.76 8.50 -41.20
17 3826 70S 71F C N 540 542 53.08 58.10 12.53 0.65 -63.20 146.24 26.38
17 71F 71F N CA 542 543 44.39 32.90 -44.30
18 3828 72K 73A C N 560 562 -125.32 -134.00 64.73 3.46 -62.50 138.78 20.80
18 73A 73A N CA 562 563 82.85 147.00 -40.90
19 3831 75A 76N C N 576 578 -95.39 -119.90 56.22 1.93 -63.20 131.50 14.90
19 76N 76N N CA 578 579 86.40 137.00 -41.10
20 3832 76N 77D C N 584 586 -53.24 -96.50 46.81 1.93 54.50 121.15 10.34
20 77D 77D N CA 586 587 96.30 114.20 40.90
21 3835 79T 80C C N 611 613 -88.44 -63.00 54.24 8.52 -63.00 54.24 8.52
21 80C 80C N CA 613 614 -89.00 -41.10 -41.10
22 3837 81A 82S C N 622 624 -56.63 -72.40 26.27 1.20 -64.10 166.55 12.53
22 82S 82S N CA 624 625 131.38 152.40 -35.00
23 3838 82S 83N C N 628 630 -132.94 -119.90 33.06 1.17 -63.20 166.80 24.79
23 83N 83N N CA 630 631 167.38 137.00 -41.10
24 3840 84C 85V C N 642 644 -63.39 -62.40 7.66 1.03 -125.40 177.86 9.99
24 85V 85V N CA 644 645 -50.00 -42.40 143.30
25 3842 86R 87A C N 660 662 160.86 -134.00 65.24 2.30 -62.50 -137.42 43.63
25 87A 87A N CA 662 663 143.40 147.00 -40.90
26 3843 87A 88Y C N 665 667 -154.88 -124.30 50.30 2.05 -63.50 168.24 30.99
26 88Y 88Y N CA 667 668 175.33 135.40 -43.40
27 3844 88Y 89M C N 677 679 -103.22 -125.60 42.22 1.46 -63.40 150.56 19.76
27 89M 89M N CA 679 680 104.70 140.50 -40.50
28 3845 89M 90K C N 685 687 -129.79 -118.00 28.21 1.16 -62.90 168.33 25.86
28 90K 90K N CA 687 688 164.73 139.10 -40.80
29 3849 93I 94G C N 725 727 -61.85 -62.40 2.09 0.34 82.20 151.74 11.51
29 94G 94G N CA 727 728 -39.19 -41.20 8.50
30 3852 96S 97G C N 741 743 27.69 78.70 76.97 1.56 -62.40 112.43 16.50
30 97G 97G N CA 743 744 -108.46 -166.10 -41.20
31 3878 122L 123R C N 931 933 -112.27 -125.20 59.01 2.54 -63.00 133.54 15.43
31 123R 123R N CA 933 934 83.02 140.60 -41.10
32 3883 127K 128V C N 986 988 -108.64 -125.40 76.96 3.37 -62.40 119.87 13.23
32 128V 128V N CA 988 989 68.19 143.30 -42.40
33 3887 131Q 132G C N 1021 1023 -127.27 -62.40 100.62 13.93 82.20 152.96 11.13
33 132G 132G N CA 1023 1024 35.71 -41.20 8.50
34 3888 132G 133C C N 1025 1027 -62.79 -63.00 7.42 0.89 -117.90 179.07 7.72
34 133C 133C N CA 1027 1028 -48.52 -41.10 141.10
35 3889 133C 134N C N 1031 1033 -62.48 -63.20 2.63 0.30 55.90 144.65 17.69
35 134N 134N N CA 1033 1034 -43.63 -41.10 39.50
36 3890 134N 135V C N 1039 1041 -78.37 -73.50 14.25 1.26 -62.40 168.97 20.50
36 135V 135V N CA 1041 1042 125.81 139.20 -42.40
37 3891 135V 136N C N 1046 1048 -61.80 -63.20 2.71 0.42 55.90 141.35 17.34
37 136N 136N N CA 1048 1049 -38.77 -41.10 39.50
-------------------------------------------------------------------------------------------------
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 11580 123R 114R O CA 943 864 4.50 3.00 1.50 15.04 3.00 1.50 15.04
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 10 12 93 97 109 117 147 181 175 182
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
plus_ligand.B99990001.pdb 1226.40918
plus_ligand.B99990002.pdb 1176.42676
Получили
plus_ligand.B99990001.pdb 1226.40918
plus_ligand.B99990002.pdb 1176.42676
In [22]:
command = f"load plus_ligand.B99990001.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
In [23]:
command = f"load plus_ligand.B99990002.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
Все сломалось
Попробуем заменить аминокислоты на аланин
In [15]:
with open("Q6L6Q6.fasta", 'r') as filik:
lines = filik.read().split("1\n") ##lines[0] is the string with identificator
prot = lines[1].replace("\n", "") ##join the lines of protein sequence into one
Ala = 'A'*len(prot)
with open("polyala.fasta", 'w') as polyala: ##make a new file with old identificator and polyalanine peptide
polyala.write(lines[0] + "1\n" + Ala + "\n")
! cat polyala.fasta
>sp|Q6L6Q6|LYS_CRAGI Lysozyme OS=Crassostrea gigas OX=29159 GN=lysoz PE=2 SV=1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
In [16]:
alignm=modeller.alignment(env)
alignm.append(file='polyala.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'Lys_ALA'
alignm[1].code = '1LMP'
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [17]:
! cat align_ala.ali
>P1;Lys_ALA sequence:: : : : :::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA* >P1;1LMP structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY-----WCDDGRTP GAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
In [18]:
# добавим лиганд
with open("align_ala.ali", 'r') as align:
seq = align.read().split("*")
seq[0] = seq[0][:-2] + "..."
seq[1] = seq[1][:-3] + "-..."
new = "*".join(seq)
with open("align_ala_lig.ali", 'w') as out:
out.write(new)
In [19]:
# и начнем моделировать
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala_lig.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
Lys_ALA 1LMP
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: 1 135
atom names : C +N
atom indices : 674 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 135
atom names : C CA +N O
atom indices : 674 672 0 675
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: 10253 9585
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 138
Number of all, selected real atoms : 719 719
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9585 9585
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1365
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 : 681.4114
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 : 675 0 0 0.007 0.007 8.6014 1.000
2 Bond angle potential : 944 1 7 2.447 2.447 114.64 1.000
3 Stereochemical cosine torsion poten: 274 0 37 77.469 77.469 265.05 1.000
4 Stereochemical improper torsion pot: 270 0 0 1.026 1.026 7.4934 1.000
5 Soft-sphere overlap restraints : 1365 1 2 0.012 0.012 21.607 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.287 0.287 64.550 1.000
10 Distance restraints 2 (N-O) : 2564 0 1 0.359 0.359 101.09 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: 134 2 6 5.637 5.637 50.212 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 0.232 0.232 4.2039 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: 133 21 16 27.503 66.151 17.030 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.475 0.475 1.3514 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.046 0.046 25.578 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: Lys_ALA.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: 12140.2334
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 1146 68A 68A N CA 336 337 128.52 107.00 21.52 6.19 107.00 21.52 6.19
-------------------------------------------------------------------------------------------------
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 2363 67A 67A CA C 332 334 -157.36 -180.00 22.64 4.53 -180.00 22.64 4.53
-------------------------------------------------------------------------------------------------
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 2178 15A 16A C N 74 76 78.05 55.40 26.94 1.89 -62.50 154.66 31.41
1 16A 16A N CA 76 77 23.63 38.20 -40.90
2 2181 18A 19A C N 89 91 65.96 55.40 24.70 0.89 -62.50 140.44 28.51
2 19A 19A N CA 91 92 15.87 38.20 -40.90
3 2183 20A 21A C N 99 101 53.19 55.40 3.81 0.40 -62.50 138.42 28.11
3 21A 21A N CA 101 102 35.10 38.20 -40.90
4 2184 21A 22A C N 104 106 63.46 55.40 12.27 0.58 -62.50 144.03 29.29
4 22A 22A N CA 106 107 28.95 38.20 -40.90
5 2199 36A 37A C N 179 181 66.16 55.40 13.58 0.86 -62.50 146.85 29.87
5 37A 37A N CA 181 182 29.91 38.20 -40.90
6 2200 37A 38A C N 184 186 63.08 55.40 12.37 0.55 -62.50 143.49 29.18
6 38A 38A N CA 186 187 28.51 38.20 -40.90
7 2211 48A 49A C N 239 241 85.25 55.40 40.65 2.27 -62.50 156.46 31.62
7 49A 49A N CA 241 242 10.60 38.20 -40.90
8 2216 53A 54A C N 264 266 92.04 -134.00 139.00 3.41 -62.50 -154.80 32.22
8 54A 54A N CA 266 267 -175.90 147.00 -40.90
9 2219 56A 57A C N 279 281 59.16 55.40 13.30 1.11 -62.50 152.44 30.86
9 57A 57A N CA 281 282 50.96 38.20 -40.90
10 2225 62A 63A C N 309 311 -74.94 -68.20 61.09 5.16 -62.50 126.09 20.09
10 63A 63A N CA 311 312 84.58 145.30 -40.90
11 2226 63A 64A C N 314 316 150.06 -134.00 87.40 2.03 -62.50 -164.20 39.41
11 64A 64A N CA 316 317 -169.74 147.00 -40.90
12 2227 64A 65A C N 319 321 -60.10 -68.20 39.28 2.88 -62.50 147.78 24.34
12 65A 65A N CA 321 322 106.87 145.30 -40.90
13 2228 65A 66A C N 324 326 157.15 -134.00 70.59 1.81 -62.50 -149.76 41.68
13 66A 66A N CA 326 327 162.57 147.00 -40.90
14 2234 71A 72A C N 354 356 78.76 55.40 53.78 1.94 -62.50 144.55 28.84
14 72A 72A N CA 356 357 -10.24 38.20 -40.90
15 2238 75A 76A C N 374 376 46.00 55.40 37.23 1.55 -62.50 158.19 31.48
15 76A 76A N CA 376 377 74.22 38.20 -40.90
16 2241 78A 79A C N 389 391 45.12 55.40 33.36 1.30 -62.50 154.48 30.80
16 79A 79A N CA 391 392 69.93 38.20 -40.90
17 2244 81A 82A C N 404 406 67.54 55.40 12.14 1.32 -62.50 152.22 30.94
17 82A 82A N CA 406 407 38.22 38.20 -40.90
18 2271 108A 109A C N 539 541 81.33 -134.00 158.89 3.61 -62.50 178.91 28.70
18 109A 109A N CA 541 542 -147.30 147.00 -40.90
19 2284 121A 122A C N 604 606 49.33 55.40 11.92 0.45 -62.50 143.14 28.92
19 122A 122A N CA 606 607 48.46 38.20 -40.90
20 2292 129A 130A C N 644 646 -53.65 -62.50 11.23 1.79 -68.20 167.52 14.02
20 130A 130A N CA 646 647 -47.81 -40.90 145.30
21 2295 132A 133A C N 659 661 57.51 55.40 3.60 0.15 -62.50 142.14 28.88
21 133A 133A N CA 661 662 35.28 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 7 8 46 53 68 76 81 112 116 97
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 138
Number of all, selected real atoms : 719 719
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9585 9585
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1408
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 : 1103.1565
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 : 675 0 1 0.012 0.012 28.705 1.000
2 Bond angle potential : 944 9 21 3.594 3.594 230.76 1.000
3 Stereochemical cosine torsion poten: 274 0 37 77.229 77.229 263.32 1.000
4 Stereochemical improper torsion pot: 270 0 2 1.566 1.566 15.704 1.000
5 Soft-sphere overlap restraints : 1408 3 6 0.017 0.017 50.116 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 2 0.320 0.320 84.703 1.000
10 Distance restraints 2 (N-O) : 2564 1 16 0.489 0.489 192.58 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 134 0 4 5.171 5.171 42.255 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 0.315 0.315 5.9402 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: 133 26 24 36.652 71.676 129.29 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.803 0.803 3.0527 1.000
27 Distance restraints 5 (X-Y) : 1401 0 4 0.072 0.072 56.732 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: Lys_ALA.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: 13546.8213
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
1 971 43A 43A N CA 211 212 123.73 107.00 16.73 4.81 107.00 16.73 4.81
2 1129 65A 66A C N 324 326 147.07 120.00 27.07 6.15 120.00 27.07 6.15
3 1136 66A 67A C N 329 331 152.07 120.00 32.07 7.29 120.00 32.07 7.29
4 1149 68A 68A C CA 339 337 140.18 108.00 32.18 7.46 108.00 32.18 7.46
5 1230 80A 80A N CA 396 397 125.64 107.00 18.64 5.36 107.00 18.64 5.36
6 1234 80A 81A C N 399 401 151.64 120.00 31.64 7.19 120.00 31.64 7.19
7 1237 81A 81A N CA 401 402 127.63 107.00 20.63 5.93 107.00 20.63 5.93
-------------------------------------------------------------------------------------------------
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 6428 81A 68A N O 401 340 4.88 2.92 1.96 4.91 2.92 1.96 4.91
-------------------------------------------------------------------------------------------------
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 2178 15A 16A C N 74 76 78.39 55.40 26.59 1.96 -62.50 155.46 31.58
1 16A 16A N CA 76 77 24.83 38.20 -40.90
2 2181 18A 19A C N 89 91 66.20 55.40 24.94 0.90 -62.50 140.61 28.54
2 19A 19A N CA 91 92 15.72 38.20 -40.90
3 2183 20A 21A C N 99 101 54.22 55.40 5.24 0.41 -62.50 138.19 28.08
3 21A 21A N CA 101 102 33.10 38.20 -40.90
4 2184 21A 22A C N 104 106 63.67 55.40 13.20 0.59 -62.50 143.71 29.23
4 22A 22A N CA 106 107 27.91 38.20 -40.90
5 2199 36A 37A C N 179 181 65.84 55.40 12.10 0.89 -62.50 147.63 30.02
5 37A 37A N CA 181 182 32.08 38.20 -40.90
6 2200 37A 38A C N 184 186 63.34 55.40 12.68 0.57 -62.50 143.61 29.21
6 38A 38A N CA 186 187 28.31 38.20 -40.90
7 2205 42A 43A C N 209 211 -80.13 -62.50 17.65 3.36 -134.00 -178.98 11.09
7 43A 43A N CA 211 212 -40.19 -40.90 147.00
8 2211 48A 49A C N 239 241 87.47 55.40 46.08 2.37 -62.50 156.87 31.60
8 49A 49A N CA 241 242 5.11 38.20 -40.90
9 2216 53A 54A C N 264 266 90.89 -134.00 140.29 3.44 -62.50 -156.10 32.00
9 54A 54A N CA 266 267 -175.24 147.00 -40.90
10 2219 56A 57A C N 279 281 61.62 55.40 11.89 1.21 -62.50 152.86 30.99
10 57A 57A N CA 281 282 48.33 38.20 -40.90
11 2223 60A 61A C N 299 301 -60.43 -62.50 43.06 6.96 -62.50 43.06 6.96
11 61A 61A N CA 301 302 -83.91 -40.90 -40.90
12 2224 61A 62A C N 304 306 -91.28 -62.50 53.99 10.38 -62.50 53.99 10.38
12 62A 62A N CA 306 307 -86.58 -40.90 -40.90
13 2225 62A 63A C N 309 311 100.02 -134.00 146.41 3.43 -62.50 -170.48 31.27
13 63A 63A N CA 311 312 -138.40 147.00 -40.90
14 2226 63A 64A C N 314 316 -73.75 -68.20 63.32 4.91 -62.50 111.29 18.81
14 64A 64A N CA 316 317 -151.62 145.30 -40.90
15 2227 64A 65A C N 319 321 -114.23 -134.00 40.69 1.66 -62.50 160.87 24.41
15 65A 65A N CA 321 322 111.43 147.00 -40.90
16 2228 65A 66A C N 324 326 135.95 -62.50 164.02 32.55 -62.50 164.02 32.55
16 66A 66A N CA 326 327 -69.28 -40.90 -40.90
17 2229 66A 67A C N 329 331 -132.51 -134.00 58.87 3.31 -62.50 146.81 21.99
17 67A 67A N CA 331 332 88.14 147.00 -40.90
18 2234 71A 72A C N 354 356 77.57 55.40 58.15 2.12 -62.50 142.35 28.27
18 72A 72A N CA 356 357 -15.55 38.20 -40.90
19 2237 74A 75A C N 369 371 -62.69 -62.50 15.51 2.55 -68.20 158.39 12.97
19 75A 75A N CA 371 372 -56.40 -40.90 145.30
20 2238 75A 76A C N 374 376 -119.84 -134.00 47.44 2.29 -62.50 153.72 23.17
20 76A 76A N CA 376 377 101.72 147.00 -40.90
21 2241 78A 79A C N 389 391 52.51 55.40 26.66 1.37 -62.50 156.13 31.35
21 79A 79A N CA 391 392 64.70 38.20 -40.90
22 2244 81A 82A C N 404 406 94.42 55.40 44.03 3.41 -62.50 167.54 33.91
22 82A 82A N CA 406 407 17.81 38.20 -40.90
23 2271 108A 109A C N 539 541 80.88 -134.00 159.74 3.63 -62.50 177.92 28.56
23 109A 109A N CA 541 542 -146.26 147.00 -40.90
24 2284 121A 122A C N 604 606 48.78 55.40 14.93 0.54 -62.50 144.69 29.19
24 122A 122A N CA 606 607 51.58 38.20 -40.90
25 2293 130A 131A C N 649 651 149.60 -134.00 133.86 4.93 -62.50 160.44 32.55
25 131A 131A N CA 651 652 -103.09 147.00 -40.90
26 2295 132A 133A C N 659 661 165.24 -134.00 77.33 2.03 -62.50 -178.51 36.39
26 133A 133A N CA 661 662 -165.17 147.00 -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 1 3 6 8 48 54 81 75 95 112 108 107
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
Lys_ALA.B99990001.pdb 681.41138
Lys_ALA.B99990002.pdb 1103.15649
In [24]:
command = f"load Lys_ALA.B99990001.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
In [25]:
command = f"load Lys_ALA.B99990002.pdb, model_1; load 1lmp.pdb, model_2; " \
f"util.cbap model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set ray_opaque_background, 0; ray 600,700; "\
f"bg_color white; set antialias, 2; " \
f"png pct.png"
! pymol -Qcd "$command"
display(Image('pct.png'))
Теперь лучше
Lys_ALA.B99990001.pdb 681.41138
Lys_ALA.B99990002.pdb 1103.15649