Гомологичное моделирование комплекса белка с лигандом¶
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [2]:
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 kodomo 3.16.0-6-amd64 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): 2021/05/28 03:36:41
Готовим данные¶
Буду работать с белком LYS_BPAPS
In [3]:
# белок-заготовка
!wget http://www.pdb.org/pdb/files/1lmp.pdb
--2021-05-28 03:36:42-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.159.96
Connecting to www.pdb.org (www.pdb.org)|128.6.159.96|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2021-05-28 03:36:42-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 128.6.159.248
Connecting to www.rcsb.org (www.rcsb.org)|128.6.159.248|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://files.rcsb.org/download/1lmp.pdb [following]
--2021-05-28 03:36:43-- https://files.rcsb.org/download/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 128.6.158.49
Connecting to files.rcsb.org (files.rcsb.org)|128.6.158.49|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/octet-stream]
Saving to: `1lmp.pdb.1'
[ <=> ] 128 871 340K/s in 0,4s
2021-05-28 03:36:45 (340 KB/s) - `1lmp.pdb.1' saved [128871]
In [4]:
!wget http://www.uniprot.org/uniprot/Q9T1T5.fasta
--2021-05-28 03:36:45-- http://www.uniprot.org/uniprot/Q9T1T5.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.206, 193.62.193.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.206|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/Q9T1T5.fasta [following] --2021-05-28 03:36:45-- https://www.uniprot.org/uniprot/Q9T1T5.fasta Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.206|:443... connected. HTTP request sent, awaiting response... 200 Length: 261 [text/plain] Saving to: `Q9T1T5.fasta.1' 100%[======================================>] 261 --.-K/s in 0s 2021-05-28 03:36:46 (123 MB/s) - `Q9T1T5.fasta.1' saved [261/261]
In [5]:
# объект выравнивания
alignm = modeller.alignment(env)
In [6]:
alignm.append(file='Q9T1T5.fasta', align_codes='all',alignment_format='FASTA')
# Создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
# Добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
read_pd_459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [7]:
# Идентификаторы для удобстава
alignm[0].code = 'sequence'
alignm[1].code = 'model'
In [8]:
alignm.salign()
alignm.write(file='./all_in_one_new.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [10]:
!cat all_in_one_new.ali
>P1;sequence sequence:: : : : :::-1.00:-1.00 MHISEKGLVLIKRYEGLRLKAYQCRAGRWTLGYGHTHNLNIGDVITQEQAEAFLREDIAQVTALLNTQIKVPLTQ NQYDAICSLVFNIGMTAFTTSTLLKKLNVGDYSGASAEFMKWSKAKVNGKRTPLPGLIKRRQAEKALF-ESA* >P1;model structureX:1lmp.pdb: 1 :A:+132 :B:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQIN--SRYWCDDGRTPGAK NVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDL------------RSYVAGCGV/...*
Построение модели¶
In [11]:
# Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
sequence model
In [12]:
# Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one_new.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
# Проводим моделирование
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
transfe_404W> At least one template is aligned with model residue 144:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 145:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 146:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11428 10412
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 146
Number of all, selected real atoms : 1149 1149
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10412 10412
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2856
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 : 1252.5475
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 0 0 0.006 0.006 12.034 1.000
2 Bond angle potential : 1574 0 9 2.194 2.194 152.70 1.000
3 Stereochemical cosine torsion poten: 705 0 40 50.620 50.620 282.83 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.275 1.275 15.843 1.000
5 Soft-sphere overlap restraints : 2856 0 0 0.006 0.006 11.739 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 2 15 0.690 0.690 166.31 1.000
10 Distance restraints 2 (N-O) : 2566 0 29 0.779 0.779 278.77 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 0 2 4.729 4.729 38.241 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 80.133 80.133 35.819 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 90.821 90.821 44.862 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 2 78.338 78.338 34.508 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 103.419 103.419 12.920 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 838 0 0 0.479 0.479 14.359 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 33 28 37.565 81.395 142.23 1.000
26 Distance restraints 4 (SDCH-SDCH) : 112 0 1 0.896 0.896 9.3857 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: sequence.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20005.7949
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3942 18R 19L C N 148 150 66.87 60.20 11.75 0.47 -63.50 143.99 26.53
1 19L 19L N CA 150 151 19.93 29.60 -41.20
2 3944 20K 21A C N 165 167 54.30 55.40 3.64 0.31 -62.50 139.15 28.27
2 21A 21A N CA 167 168 34.73 38.20 -40.90
3 3945 21A 22Y C N 170 172 62.46 55.90 8.70 0.56 -63.50 147.73 27.92
3 22Y 22Y N CA 172 173 33.78 39.50 -43.40
4 3959 35H 36T C N 287 289 -135.44 -63.20 87.86 10.39 -63.20 87.86 10.39
4 36T 36T N CA 289 290 7.91 -42.10 -42.10
5 3960 36T 37H C N 294 296 60.15 56.30 7.62 0.58 -63.20 145.16 24.92
5 37H 37H N CA 296 297 34.23 40.80 -42.30
6 3964 40N 41I C N 328 330 -101.94 -120.60 72.20 3.43 -63.40 111.06 17.11
6 41I 41I N CA 330 331 60.56 130.30 -43.60
7 3972 48E 49Q C N 388 390 81.93 55.10 40.05 2.35 -121.10 -156.74 10.22
7 49Q 49Q N CA 390 391 10.57 40.30 139.70
8 3977 53F 54L C N 427 429 84.43 60.20 154.04 11.27 -108.50 174.17 7.82
8 54L 54L N CA 429 430 -178.28 29.60 132.50
9 3981 57D 58I C N 463 465 -60.49 -63.40 30.78 4.95 -120.60 166.67 11.74
9 58I 58I N CA 465 466 -74.24 -43.60 130.30
10 3982 58I 59A C N 471 473 57.58 -62.50 141.15 23.19 -68.20 160.44 15.82
10 59A 59A N CA 473 474 -115.09 -40.90 145.30
11 3983 59A 60Q C N 476 478 107.46 -63.80 171.58 28.10 -63.80 171.58 28.10
11 60Q 60Q N CA 478 479 -50.77 -40.30 -40.30
12 3991 67T 68Q C N 535 537 -113.10 -121.10 20.52 1.07 -63.80 168.47 27.40
12 68Q 68Q N CA 537 538 158.60 139.70 -40.30
13 3995 71V 72P C N 568 570 -56.88 -58.70 35.06 2.75 -64.50 147.48 11.41
13 72P 72P N CA 570 571 -65.52 -30.50 147.20
14 3996 72P 73L C N 575 577 -116.72 -108.50 43.23 2.41 -63.50 141.64 17.48
14 73L 73L N CA 577 578 90.06 132.50 -41.20
15 3998 74T 75Q C N 590 592 -119.90 -121.10 26.17 1.23 -63.80 163.76 21.60
15 75Q 75Q N CA 592 593 113.56 139.70 -40.30
16 3999 75Q 76N C N 599 601 -56.30 -63.20 6.99 1.10 55.90 137.48 16.81
16 76N 76N N CA 601 602 -39.95 -41.10 39.50
17 4000 76N 77Q C N 607 609 70.12 -63.80 143.99 21.21 -63.80 143.99 21.21
17 77Q 77Q N CA 609 610 -93.20 -40.30 -40.30
18 4027 103N 104V C N 815 817 -67.06 -125.40 58.86 2.06 -62.40 177.93 22.25
18 104V 104V N CA 817 818 135.47 143.30 -42.40
19 4028 104V 105G C N 822 824 113.85 82.20 44.15 1.40 -62.40 177.26 32.36
19 105G 105G N CA 824 825 -22.29 8.50 -41.20
20 4029 105G 106D C N 826 828 43.81 -70.90 139.25 11.62 -63.30 140.39 16.42
20 106D 106D N CA 828 829 -130.76 150.30 -40.00
21 4046 122V 123N C N 959 961 -45.69 -71.20 26.99 2.13 -63.20 168.21 20.11
21 123N 123N N CA 961 962 151.60 142.80 -41.10
22 4047 123N 124G C N 967 969 -113.89 -80.20 33.71 2.21 82.20 -126.21 17.90
22 124G 124G N CA 969 970 175.21 174.10 8.50
23 4048 124G 125K C N 971 973 -111.69 -118.00 49.97 2.50 -62.90 139.35 21.01
23 125K 125K N CA 973 974 -171.33 139.10 -40.80
24 4049 125K 126R C N 980 982 -67.88 -72.10 6.25 0.54 -63.00 172.46 23.63
24 126R 126R N CA 982 983 146.51 141.90 -41.10
25 4050 126R 127T C N 991 993 -137.40 -124.80 17.36 0.57 -63.20 178.60 27.76
25 127T 127T N CA 993 994 155.45 143.50 -42.10
26 4052 128P 129L C N 1005 1007 -58.41 -70.70 23.40 2.22 -63.50 157.36 21.56
26 129L 129L N CA 1007 1008 161.52 141.60 -41.20
27 4055 131G 132L C N 1024 1026 -69.59 -70.70 42.27 3.24 -63.50 135.08 19.11
27 132L 132L N CA 1026 1027 -176.15 141.60 -41.20
28 4057 133I 134K C N 1040 1042 -166.45 -118.00 52.70 2.38 -62.90 -170.11 21.95
28 134K 134K N CA 1042 1043 118.37 139.10 -40.80
29 4058 134K 135R C N 1049 1051 -129.68 -125.20 33.84 1.72 -63.00 162.46 18.59
29 135R 135R N CA 1051 1052 107.05 140.60 -41.10
30 4060 136R 137Q C N 1071 1073 172.56 -121.10 88.62 2.82 -63.80 173.16 31.19
30 137Q 137Q N CA 1073 1074 -161.54 139.70 -40.30
31 4063 139E 140K C N 1094 1096 66.39 56.60 30.61 1.60 -62.90 138.77 24.17
31 140K 140K N CA 1096 1097 9.59 38.60 -40.80
32 4065 141A 142L C N 1108 1110 60.87 60.20 5.34 0.26 -63.50 140.57 25.93
32 142L 142L N CA 1110 1111 24.31 29.60 -41.20
33 4067 143F 144E C N 1127 1129 -145.37 -117.80 29.72 0.88 -63.60 -169.72 29.95
33 144E 144E N CA 1129 1130 147.88 136.80 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 2 14 23 101 123 162 146 162 209 210 208
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 146
Number of all, selected real atoms : 1149 1149
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10412 10412
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2926
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 : 1287.7792
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 0 0 0.006 0.006 11.999 1.000
2 Bond angle potential : 1574 2 7 2.334 2.334 168.92 1.000
3 Stereochemical cosine torsion poten: 705 0 42 51.668 51.668 294.45 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.262 1.262 16.291 1.000
5 Soft-sphere overlap restraints : 2926 0 0 0.006 0.006 12.917 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 2 15 0.716 0.716 170.31 1.000
10 Distance restraints 2 (N-O) : 2566 0 17 0.804 0.804 253.10 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 0 3 5.365 5.365 49.215 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 77.720 77.720 36.269 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 77.320 77.320 35.757 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 75.293 75.293 24.396 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 86.608 86.608 13.642 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 838 0 0 0.419 0.419 11.329 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 37 31 41.065 82.905 179.76 1.000
26 Distance restraints 4 (SDCH-SDCH) : 112 0 0 0.842 0.842 9.4176 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: sequence.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 19353.1426
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1833 60Q 61V C N 485 487 143.72 120.00 23.72 5.39 120.00 23.72 5.39
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3942 18R 19L C N 148 150 65.62 60.20 14.10 0.49 -63.50 141.46 26.05
1 19L 19L N CA 150 151 16.58 29.60 -41.20
2 3944 20K 21A C N 165 167 63.16 -68.20 145.73 14.05 -62.50 167.45 26.26
2 21A 21A N CA 167 168 -151.58 145.30 -40.90
3 3945 21A 22Y C N 170 172 -111.34 -98.40 63.20 6.54 -63.50 119.89 16.94
3 22Y 22Y N CA 172 173 66.53 128.40 -43.40
4 3959 35H 36T C N 287 289 -131.80 -63.20 85.79 9.97 -63.20 85.79 9.97
4 36T 36T N CA 289 290 9.41 -42.10 -42.10
5 3960 36T 37H C N 294 296 58.44 56.30 5.74 0.41 -63.20 144.37 24.77
5 37H 37H N CA 296 297 35.47 40.80 -42.30
6 3972 48E 49Q C N 388 390 79.59 55.10 37.59 2.14 -121.10 -155.70 10.24
6 49Q 49Q N CA 390 391 11.79 40.30 139.70
7 3977 53F 54L C N 427 429 88.43 60.20 150.30 11.39 -108.50 169.09 7.61
7 54L 54L N CA 429 430 177.22 29.60 132.50
8 3984 60Q 61V C N 485 487 147.69 -125.40 145.04 8.34 -125.40 145.04 8.34
8 61V 61V N CA 487 488 27.18 143.30 143.30
9 3985 61V 62T C N 492 494 55.94 -63.20 124.37 20.95 -63.20 124.37 20.95
9 62T 62T N CA 494 495 -6.40 -42.10 -42.10
10 3991 67T 68Q C N 535 537 -113.47 -121.10 23.98 1.24 -63.80 164.93 26.90
10 68Q 68Q N CA 537 538 162.43 139.70 -40.30
11 3992 68Q 69I C N 544 546 -101.73 -97.30 46.30 4.78 -63.40 130.48 20.24
11 69I 69I N CA 546 547 81.12 127.20 -43.60
12 3993 69I 70K C N 552 554 166.91 -118.00 121.23 6.21 -62.90 155.34 20.49
12 70K 70K N CA 554 555 43.93 139.10 -40.80
13 3995 71V 72P C N 568 570 -44.08 -58.70 47.63 2.95 -64.50 138.48 11.44
13 72P 72P N CA 570 571 -75.83 -30.50 147.20
14 3996 72P 73L C N 575 577 -125.23 -108.50 31.76 1.81 -63.50 159.17 19.61
14 73L 73L N CA 577 578 105.51 132.50 -41.20
15 4001 77Q 78Y C N 616 618 -102.21 -98.40 64.97 6.88 -63.50 113.73 16.29
15 78Y 78Y N CA 618 619 63.54 128.40 -43.40
16 4002 78Y 79D C N 628 630 -19.30 -96.50 82.32 3.39 54.50 86.30 6.88
16 79D 79D N CA 630 631 85.64 114.20 40.90
17 4027 103N 104V C N 815 817 -67.07 -125.40 58.50 2.14 -62.40 178.87 22.91
17 104V 104V N CA 817 818 138.80 143.30 -42.40
18 4028 104V 105G C N 822 824 97.78 82.20 16.13 1.21 -62.40 169.00 31.75
18 105G 105G N CA 824 825 12.67 8.50 -41.20
19 4029 105G 106D C N 826 828 -5.74 -63.30 94.17 10.21 -63.30 94.17 10.21
19 106D 106D N CA 828 829 -114.53 -40.00 -40.00
20 4039 115M 116K C N 900 902 -122.37 -62.90 59.49 9.67 -62.90 59.49 9.67
20 116K 116K N CA 902 903 -39.10 -40.80 -40.80
21 4045 121K 122V C N 952 954 -103.37 -125.40 45.89 1.61 -62.40 151.10 17.14
21 122V 122V N CA 954 955 103.04 143.30 -42.40
22 4046 122V 123N C N 959 961 -146.19 -119.90 35.05 1.02 -63.20 179.12 27.05
22 123N 123N N CA 961 962 160.18 137.00 -41.10
23 4048 124G 125K C N 971 973 -85.28 -70.20 31.97 1.98 -62.90 152.26 21.06
23 125K 125K N CA 973 974 168.59 140.40 -40.80
24 4049 125K 126R C N 980 982 -118.20 -125.20 14.44 0.80 -63.00 174.63 27.40
24 126R 126R N CA 982 983 153.22 140.60 -41.10
25 4050 126R 127T C N 991 993 -118.95 -124.80 7.94 0.26 -63.20 -171.78 27.84
25 127T 127T N CA 993 994 138.13 143.50 -42.10
26 4052 128P 129L C N 1005 1007 -152.48 -108.50 59.46 2.66 -63.50 171.23 29.24
26 129L 129L N CA 1007 1008 172.51 132.50 -41.20
27 4053 129L 130P C N 1013 1015 -62.09 -58.70 3.39 0.43 -64.50 177.65 13.13
27 130P 130P N CA 1015 1016 -30.43 -30.50 147.20
28 4054 130P 131G C N 1020 1022 103.98 78.70 76.97 1.27 82.20 114.79 6.64
28 131G 131G N CA 1022 1023 121.20 -166.10 8.50
29 4055 131G 132L C N 1024 1026 -151.03 -108.50 81.92 3.88 -63.50 145.55 25.50
29 132L 132L N CA 1026 1027 -157.48 132.50 -41.20
30 4057 133I 134K C N 1040 1042 -168.62 -118.00 56.84 2.63 -62.90 -173.16 21.67
30 134K 134K N CA 1042 1043 113.25 139.10 -40.80
31 4058 134K 135R C N 1049 1051 -115.95 -125.20 16.72 0.57 -63.00 175.92 20.76
31 135R 135R N CA 1051 1052 126.67 140.60 -41.10
32 4059 135R 136R C N 1060 1062 -151.19 -125.20 50.89 2.82 -63.00 163.71 18.53
32 136R 136R N CA 1062 1063 96.84 140.60 -41.10
33 4060 136R 137Q C N 1071 1073 53.97 -121.10 177.15 7.24 -63.80 -166.99 24.78
33 137Q 137Q N CA 1073 1074 166.78 139.70 -40.30
34 4063 139E 140K C N 1094 1096 74.82 56.60 43.73 2.20 -62.90 143.31 24.76
34 140K 140K N CA 1096 1097 -1.16 38.60 -40.80
35 4064 140K 141A C N 1103 1105 -128.66 -134.00 40.77 2.18 -62.50 161.64 24.28
35 141A 141A N CA 1105 1106 106.58 147.00 -40.90
36 4065 141A 142L C N 1108 1110 -97.07 -108.50 27.34 1.33 -63.50 152.61 19.53
36 142L 142L N CA 1110 1111 107.67 132.50 -41.20
37 4067 143F 144E C N 1127 1129 -179.68 -117.80 69.11 2.02 -63.60 -168.63 31.73
37 144E 144E N CA 1129 1130 167.56 136.80 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 17 15 117 110 156 161 177 183 213 209
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sequence.B99990001.pdb 1252.54749
sequence.B99990002.pdb 1287.77917
Просмотр результата¶
In [13]:
import nglview
import ipywidgets
In [14]:
w1 = nglview.show_structure_file("sequence.B99990001.pdb")
w1
In [15]:
w2 = nglview.show_structure_file("sequence.B99990002.pdb")
w2
Неплохо выглядят, посмотрим на исходную модель лизоцима,
In [16]:
pre = nglview.show_structure_file('1lmp.pdb')
pre
Добавляем лиганд¶
In [17]:
new_seq = ''.join([i.code for i in alignm[0].residues])
new_seq += '/' + ''.join([i.code for i in [alignm[1].residues[-3],alignm[1].residues[-2],alignm[1].residues[-1]]])
alignm.append_sequence(new_seq)
del alignm[0]
alignm[1].code = 'newseq'
In [18]:
alignm.salign()
alignm.write(file='all_in_one_new.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [19]:
! cat all_in_one_new.ali
>P1;model structureX:1lmp.pdb: 1 :A:+132 :B:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQIN--SRYWCDDGRTPGAK NVCGIRCSQLLT---DDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGC------------GV/...* >P1;newseq sequence::1 :A:+149 :B:undefined:undefined:-1.00:-1.00 MHISEKGLVLIKRYEGLRLKAYQCRAGRWTLGYGHTHNLNIGDVITQEQAEAFLREDIAQVTALLNTQIKVPLTQ NQYDAICSLVFNIGMTAFTTSTLLKKLNVGDYSGASAEFMKWSKAKVNGKRTPLPGLIKRRQAEKALFESA/...*
лиганд вставлен, запускаем моделлирование вновь
In [20]:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one_new.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
newseq model
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12858 11842
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11842 11842
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2871
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 : 1078.2750
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 0 0 0.005 0.005 9.7826 1.000
2 Bond angle potential : 1574 1 6 2.149 2.149 141.70 1.000
3 Stereochemical cosine torsion poten: 705 0 38 51.480 51.480 283.73 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.284 1.284 16.048 1.000
5 Soft-sphere overlap restraints : 2871 2 2 0.008 0.008 23.073 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2407 0 0 0.266 0.266 51.384 1.000
10 Distance restraints 2 (N-O) : 2568 0 10 0.506 0.506 169.94 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 1 7 5.311 5.311 48.232 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 86.263 86.263 44.871 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 91.471 91.471 44.346 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 1 94.598 94.598 34.526 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 100.488 100.488 15.447 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 857 0 0 0.456 0.456 16.733 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 35 27 39.597 79.904 149.33 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 0 1.176 1.176 15.256 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.032 0.032 13.876 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: newseq.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20089.1582
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3942 18R 19L C N 148 150 62.63 60.20 4.30 0.17 -63.50 142.95 26.36
1 19L 19L N CA 150 151 26.06 29.60 -41.20
2 3944 20K 21A C N 165 167 56.52 55.40 4.96 0.21 -62.50 140.29 28.51
2 21A 21A N CA 167 168 33.37 38.20 -40.90
3 3945 21A 22Y C N 170 172 62.89 55.90 9.28 0.60 -63.50 147.89 27.95
3 22Y 22Y N CA 172 173 33.39 39.50 -43.40
4 3959 35H 36T C N 287 289 -142.77 -63.20 103.70 11.78 -63.20 103.70 11.78
4 36T 36T N CA 289 290 24.40 -42.10 -42.10
5 3960 36T 37H C N 294 296 56.91 56.30 7.97 0.66 -63.20 141.68 24.32
5 37H 37H N CA 296 297 32.86 40.80 -42.30
6 3964 40N 41I C N 328 330 -103.98 -120.60 73.66 3.58 -63.40 109.91 16.88
6 41I 41I N CA 330 331 58.54 130.30 -43.60
7 3972 48E 49Q C N 388 390 150.19 55.10 111.41 9.20 -121.10 -179.28 9.44
7 49Q 49Q N CA 390 391 -17.75 40.30 139.70
8 3977 53F 54L C N 427 429 92.05 60.20 145.47 11.41 -108.50 164.16 7.42
8 54L 54L N CA 429 430 171.54 29.60 132.50
9 3983 59A 60Q C N 476 478 -131.65 -63.80 79.52 11.04 -63.80 79.52 11.04
9 60Q 60Q N CA 478 479 1.17 -40.30 -40.30
10 3984 60Q 61V C N 485 487 -74.82 -62.40 13.18 1.84 -125.40 -174.27 10.25
10 61V 61V N CA 487 488 -37.98 -42.40 143.30
11 3985 61V 62T C N 492 494 91.45 -124.80 148.26 8.58 -63.20 -145.05 36.57
11 62T 62T N CA 494 495 107.19 143.50 -42.10
12 3992 68Q 69I C N 544 546 48.68 -97.30 149.90 7.41 -63.40 176.81 32.85
12 69I 69I N CA 546 547 93.15 127.20 -43.60
13 3993 69I 70K C N 552 554 178.91 -62.90 118.34 19.12 -62.90 118.34 19.12
13 70K 70K N CA 554 555 -34.78 -40.80 -40.80
14 3995 71V 72P C N 568 570 -66.10 -58.70 9.49 1.31 -64.50 176.37 13.08
14 72P 72P N CA 570 571 -36.44 -30.50 147.20
15 3998 74T 75Q C N 590 592 -142.29 -121.10 87.39 4.44 -63.80 123.40 15.88
15 75Q 75Q N CA 592 593 54.91 139.70 -40.30
16 3999 75Q 76N C N 599 601 -39.59 -71.20 63.36 3.38 55.90 107.05 8.86
16 76N 76N N CA 601 602 87.89 142.80 39.50
17 4009 85V 86F C N 676 678 -100.97 -124.20 60.91 2.21 -63.20 136.62 16.64
17 86F 86F N CA 678 679 87.00 143.30 -44.30
18 4012 88I 89G C N 703 705 68.38 78.70 47.52 0.95 82.20 128.96 6.95
18 89G 89G N CA 705 706 -119.71 -166.10 8.50
19 4013 89G 90M C N 707 709 -68.15 -73.00 4.87 0.37 -63.40 176.19 26.68
19 90M 90M N CA 709 710 143.37 143.00 -40.50
20 4014 90M 91T C N 715 717 -95.17 -124.80 55.06 1.71 -63.20 142.81 16.40
20 91T 91T N CA 717 718 97.08 143.50 -42.10
21 4027 103N 104V C N 815 817 -69.34 -125.40 56.37 2.39 -62.40 168.44 21.73
21 104V 104V N CA 817 818 149.30 143.30 -42.40
22 4028 104V 105G C N 822 824 111.87 82.20 44.25 1.31 -62.40 175.08 31.90
22 105G 105G N CA 824 825 -24.34 8.50 -41.20
23 4044 120A 121K C N 943 945 20.61 -70.20 118.92 9.94 -118.00 159.09 7.46
23 121K 121K N CA 945 946 -142.83 140.40 139.10
24 4048 124G 125K C N 971 973 -96.12 -62.90 88.14 10.18 -62.90 88.14 10.18
24 125K 125K N CA 973 974 40.85 -40.80 -40.80
25 4057 133I 134K C N 1040 1042 172.45 -118.00 79.58 2.64 -62.90 -171.49 31.69
25 134K 134K N CA 1042 1043 177.78 139.10 -40.80
26 4058 134K 135R C N 1049 1051 -75.78 -72.10 49.99 3.76 -63.00 127.79 18.14
26 135R 135R N CA 1051 1052 -168.24 141.90 -41.10
27 4060 136R 137Q C N 1071 1073 -101.16 -121.10 19.98 0.72 -63.80 -177.44 25.03
27 137Q 137Q N CA 1073 1074 138.40 139.70 -40.30
28 4061 137Q 138A C N 1080 1082 -127.45 -134.00 7.14 0.35 -62.50 -178.72 33.18
28 138A 138A N CA 1082 1083 149.86 147.00 -40.90
29 4062 138A 139E C N 1085 1087 -120.05 -117.80 2.42 0.11 -63.60 -174.95 22.09
29 139E 139E N CA 1087 1088 135.92 136.80 -40.30
30 4063 139E 140K C N 1094 1096 -75.74 -70.20 15.85 1.27 -62.90 166.85 21.00
30 140K 140K N CA 1096 1097 125.55 140.40 -40.80
31 4064 140K 141A C N 1103 1105 -173.00 -134.00 49.02 1.27 -62.50 -179.75 35.32
31 141A 141A N CA 1105 1106 176.70 147.00 -40.90
32 4065 141A 142L C N 1108 1110 -82.57 -108.50 37.32 1.69 -63.50 148.10 19.55
32 142L 142L N CA 1110 1111 105.67 132.50 -41.20
33 4066 142L 143F C N 1116 1118 -150.71 -124.20 47.72 1.47 -63.20 158.97 27.49
33 143F 143F N CA 1118 1119 -177.02 143.30 -44.30
34 4067 143F 144E C N 1127 1129 -62.29 -69.30 9.56 0.53 -63.60 176.31 23.58
34 144E 144E N CA 1129 1130 136.00 142.50 -40.30
35 4068 144E 145S C N 1136 1138 -157.16 -136.60 43.60 1.69 -64.10 164.26 18.62
35 145S 145S N CA 1138 1139 -170.36 151.20 -35.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 20 22 109 114 167 153 170 200 207 199
<< 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.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11842 11842
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2917
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 : 1155.1681
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 0 0 0.007 0.007 16.413 1.000
2 Bond angle potential : 1574 4 11 2.464 2.464 183.48 1.000
3 Stereochemical cosine torsion poten: 705 0 43 51.859 51.859 284.91 1.000
4 Stereochemical improper torsion pot: 477 0 1 1.430 1.430 21.584 1.000
5 Soft-sphere overlap restraints : 2917 1 5 0.010 0.010 35.633 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2407 0 0 0.282 0.282 63.090 1.000
10 Distance restraints 2 (N-O) : 2568 0 10 0.512 0.512 175.14 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 1 2 4.731 4.731 38.266 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 83.765 83.765 45.073 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 0 81.290 81.290 37.147 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 80.494 80.494 31.148 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 95.347 95.347 13.132 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 857 0 2 0.490 0.490 31.001 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 35 20 32.073 77.776 127.88 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 0 1.194 1.194 17.594 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.054 0.054 33.682 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: newseq.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 19878.1543
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 1758 54L 54L N CA 429 430 124.26 107.00 17.26 4.96 107.00 17.26 4.96
2 1833 60Q 61V C N 485 487 141.21 120.00 21.21 4.82 120.00 21.21 4.82
3 1843 61V 62T C N 492 494 150.14 120.00 30.14 6.85 120.00 30.14 6.85
-------------------------------------------------------------------------------------------------
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 4121 53F 53F CA C 419 427 -150.23 -180.00 29.77 5.95 -180.00 29.77 5.95
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3942 18R 19L C N 148 150 76.71 60.20 37.68 1.30 -63.50 144.99 26.33
1 19L 19L N CA 150 151 -4.28 29.60 -41.20
2 3944 20K 21A C N 165 167 58.86 55.40 11.49 0.45 -62.50 139.18 28.31
2 21A 21A N CA 167 168 27.25 38.20 -40.90
3 3945 21A 22Y C N 170 172 66.20 55.90 14.86 0.87 -63.50 148.44 27.99
3 22Y 22Y N CA 172 173 28.79 39.50 -43.40
4 3959 35H 36T C N 287 289 -135.12 -63.20 88.39 10.38 -63.20 88.39 10.38
4 36T 36T N CA 289 290 9.28 -42.10 -42.10
5 3960 36T 37H C N 294 296 58.53 56.30 7.28 0.52 -63.20 143.59 24.65
5 37H 37H N CA 296 297 33.87 40.80 -42.30
6 3964 40N 41I C N 328 330 -111.45 -120.60 69.95 3.65 -63.40 115.07 17.59
6 41I 41I N CA 330 331 60.95 130.30 -43.60
7 3972 48E 49Q C N 388 390 80.68 55.10 37.64 2.25 -121.10 -157.10 10.17
7 49Q 49Q N CA 390 391 12.68 40.30 139.70
8 3977 53F 54L C N 427 429 -48.72 -63.50 32.95 4.04 -108.50 167.86 9.51
8 54L 54L N CA 429 430 -70.64 -41.20 132.50
9 3983 59A 60Q C N 476 478 -106.29 -63.80 61.31 7.97 -63.80 61.31 7.97
9 60Q 60Q N CA 478 479 3.90 -40.30 -40.30
10 3985 61V 62T C N 492 494 -68.15 -63.20 75.21 9.33 -63.20 75.21 9.33
10 62T 62T N CA 494 495 32.95 -42.10 -42.10
11 3991 67T 68Q C N 535 537 -110.06 -121.10 22.81 1.19 -63.80 166.59 26.96
11 68Q 68Q N CA 537 538 159.66 139.70 -40.30
12 3992 68Q 69I C N 544 546 -100.96 -97.30 60.48 6.27 -63.40 116.64 18.02
12 69I 69I N CA 546 547 66.83 127.20 -43.60
13 3993 69I 70K C N 552 554 -162.50 -62.90 105.39 15.42 -62.90 105.39 15.42
13 70K 70K N CA 554 555 -6.36 -40.80 -40.80
14 3996 72P 73L C N 575 577 50.14 60.20 33.31 1.24 -63.50 153.08 27.78
14 73L 73L N CA 577 578 61.36 29.60 -41.20
15 4009 85V 86F C N 676 678 -81.42 -63.20 92.58 11.69 -63.20 92.58 11.69
15 86F 86F N CA 678 679 46.47 -44.30 -44.30
16 4012 88I 89G C N 703 705 70.84 78.70 35.70 0.71 82.20 140.24 7.38
16 89G 89G N CA 705 706 -131.27 -166.10 8.50
17 4013 89G 90M C N 707 709 -68.98 -73.00 26.55 1.73 -63.40 157.35 23.06
17 90M 90M N CA 709 710 116.75 143.00 -40.50
18 4014 90M 91T C N 715 717 -81.95 -124.80 70.49 2.19 -63.20 130.98 15.63
18 91T 91T N CA 717 718 87.53 143.50 -42.10
19 4016 92A 93F C N 727 729 -112.23 -63.20 84.17 9.50 -63.20 84.17 9.50
19 93F 93F N CA 729 730 24.11 -44.30 -44.30
20 4027 103N 104V C N 815 817 -68.43 -125.40 57.62 2.52 -62.40 165.73 21.33
20 104V 104V N CA 817 818 151.98 143.30 -42.40
21 4028 104V 105G C N 822 824 109.03 82.20 42.31 1.21 -62.40 172.27 31.41
21 105G 105G N CA 824 825 -24.21 8.50 -41.20
22 4042 118S 119K C N 929 931 -120.52 -62.90 60.43 8.94 -62.90 60.43 8.94
22 119K 119K N CA 931 932 -22.59 -40.80 -40.80
23 4047 123N 124G C N 967 969 -64.48 -62.40 3.96 0.70 -167.20 174.32 6.88
23 124G 124G N CA 969 970 -44.57 -41.20 174.60
24 4048 124G 125K C N 971 973 57.33 -62.90 134.75 23.54 -62.90 134.75 23.54
24 125K 125K N CA 973 974 20.06 -40.80 -40.80
25 4057 133I 134K C N 1040 1042 -118.44 -118.00 2.04 0.09 -62.90 -173.43 27.53
25 134K 134K N CA 1042 1043 141.09 139.10 -40.80
26 4058 134K 135R C N 1049 1051 -70.19 -72.10 1.99 0.14 -63.00 177.70 24.49
26 135R 135R N CA 1051 1052 141.35 141.90 -41.10
27 4059 135R 136R C N 1060 1062 -130.63 -125.20 79.60 3.72 -63.00 119.80 20.65
27 136R 136R N CA 1062 1063 -139.99 140.60 -41.10
28 4060 136R 137Q C N 1071 1073 -60.13 -73.00 13.98 0.89 -63.80 175.60 26.01
28 137Q 137Q N CA 1073 1074 135.26 140.70 -40.30
29 4061 137Q 138A C N 1080 1082 -59.28 -68.20 16.08 1.03 -62.50 172.85 28.49
29 138A 138A N CA 1082 1083 131.93 145.30 -40.90
30 4062 138A 139E C N 1085 1087 -136.43 -117.80 22.68 0.67 -63.60 -175.09 28.75
30 139E 139E N CA 1087 1088 149.74 136.80 -40.30
31 4063 139E 140K C N 1094 1096 -98.67 -118.00 34.27 1.31 -62.90 155.76 18.58
31 140K 140K N CA 1096 1097 110.80 139.10 -40.80
32 4064 140K 141A C N 1103 1105 177.70 -134.00 54.72 1.26 -62.50 -170.84 37.24
32 141A 141A N CA 1105 1106 172.71 147.00 -40.90
33 4065 141A 142L C N 1108 1110 -120.42 -108.50 18.54 1.05 -63.50 169.35 21.04
33 142L 142L N CA 1110 1111 118.29 132.50 -41.20
34 4066 142L 143F C N 1116 1118 -100.05 -124.20 24.85 0.80 -63.20 -177.99 27.75
34 143F 143F N CA 1118 1119 137.46 143.30 -44.30
35 4067 143F 144E C N 1127 1129 -65.86 -69.30 35.00 2.55 -63.60 147.99 19.61
35 144E 144E N CA 1129 1130 107.67 142.50 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 16 25 97 126 188 162 182 195 211 191
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
newseq.B99990001.pdb 1078.27502
newseq.B99990002.pdb 1155.16809
In [21]:
w1 = nglview.show_structure_file('newseq.B99990001.pdb')
w1
In [22]:
w2 = nglview.show_structure_file('newseq.B99990002.pdb')
w2
In [23]:
pre = nglview.show_structure_file('1lmp.pdb')
pre
Лиганд успешно попал в структуры
In [24]:
# Backup
! mv newseq.B99990001.pdb newseq.B99990001.1.pdb
! mv newseq.B99990002.pdb newseq.B99990002.1.pdb
In [25]:
! rm -rf newseq.rsr
Подвигаем лиганд
In [31]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:14:A','CA:42:A')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one_new.ali', knowns=pdb.code, sequence=s.code)
automodel__W> 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 [32]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12859 11843
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11843 11843
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3066
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 : 2510.0811
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 1 4 0.010 0.010 34.162 1.000
2 Bond angle potential : 1574 3 18 2.750 2.750 233.85 1.000
3 Stereochemical cosine torsion poten: 705 0 46 53.073 53.073 301.97 1.000
4 Stereochemical improper torsion pot: 477 0 0 1.509 1.509 23.854 1.000
5 Soft-sphere overlap restraints : 3066 2 4 0.009 0.009 32.593 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2407 14 69 0.878 0.878 642.12 1.000
10 Distance restraints 2 (N-O) : 2568 5 47 0.813 0.813 534.61 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 2 6 6.172 6.172 65.131 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 82.016 82.016 43.642 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 3 89.471 89.471 46.547 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 76.452 76.452 30.919 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 84.990 84.990 16.069 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 857 0 0 0.589 0.589 30.297 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 43 33 44.721 88.380 184.46 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 4 1.666 1.666 27.347 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.096 0.096 262.51 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: newseq.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 24572.9473
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 348 42G 42G C CA 340 339 1.65 1.49 0.16 4.65 1.49 0.16 4.65
-------------------------------------------------------------------------------------------------
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 1328 15E 15E N CA 118 119 127.71 107.00 20.71 5.95 107.00 20.71 5.95
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4792 10L 13R CA CA 71 96 7.86 5.10 2.76 5.05 5.10 2.76 5.05
2 4793 10L 14Y CA CA 71 107 9.03 5.99 3.04 4.52 5.99 3.04 4.52
3 4894 13R 18R CA CA 96 140 8.89 5.50 3.40 6.40 5.50 3.40 6.40
4 4919 13R 146A CA CA 96 1145 11.89 7.45 4.44 5.62 7.45 4.44 5.62
-------------------------------------------------------------------------------------------------
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 7153 14Y 9V N O 106 69 8.28 4.96 3.31 5.24 4.96 3.31 5.24
2 7154 14Y 10L N O 106 77 8.28 2.95 5.33 9.37 2.95 5.33 9.37
3 7163 14Y 146A N O 106 1148 14.45 9.07 5.38 4.98 9.07 5.38 4.98
4 7219 18R 13R N O 139 105 8.82 5.11 3.71 5.51 5.11 3.71 5.51
-------------------------------------------------------------------------------------------------
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 4082 14Y 14Y CA C 107 116 -156.90 -180.00 23.10 4.62 -180.00 23.10 4.62
-------------------------------------------------------------------------------------------------
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 3935 11I 12K C N 84 86 81.38 -62.90 161.31 28.18 -62.90 161.31 28.18
1 12K 12K N CA 86 87 31.34 -40.80 -40.80
2 3936 12K 13R C N 93 95 100.25 -125.20 144.84 4.57 -63.00 -154.59 25.62
2 13R 13R N CA 95 96 -165.76 140.60 -41.10
3 3942 18R 19L C N 148 150 61.96 60.20 4.37 0.15 -63.50 142.14 26.22
3 19L 19L N CA 150 151 25.60 29.60 -41.20
4 3944 20K 21A C N 165 167 57.70 55.40 9.58 0.41 -62.50 139.00 28.27
4 21A 21A N CA 167 168 28.90 38.20 -40.90
5 3945 21A 22Y C N 170 172 63.95 55.90 12.20 0.68 -63.50 147.24 27.80
5 22Y 22Y N CA 172 173 30.33 39.50 -43.40
6 3956 32G 33Y C N 261 263 -69.02 -98.40 36.87 2.50 -63.50 166.01 26.62
6 33Y 33Y N CA 263 264 150.68 128.40 -43.40
7 3957 33Y 34G C N 273 275 90.84 82.20 69.92 2.96 -62.40 154.50 26.73
7 34G 34G N CA 275 276 -60.88 8.50 -41.20
8 3959 35H 36T C N 287 289 -135.60 -63.20 91.34 10.56 -63.20 91.34 10.56
8 36T 36T N CA 289 290 13.59 -42.10 -42.10
9 3960 36T 37H C N 294 296 58.84 56.30 7.08 0.51 -63.20 144.03 24.72
9 37H 37H N CA 296 297 34.19 40.80 -42.30
10 3964 40N 41I C N 328 330 -88.28 -120.60 84.26 3.69 -63.40 99.26 15.50
10 41I 41I N CA 330 331 52.49 130.30 -43.60
11 3972 48E 49Q C N 388 390 77.63 55.10 30.80 2.01 -121.10 -158.74 10.00
11 49Q 49Q N CA 390 391 19.30 40.30 139.70
12 3977 53F 54L C N 427 429 78.52 60.20 134.64 9.61 -108.50 175.65 8.04
12 54L 54L N CA 429 430 162.99 29.60 132.50
13 3982 58I 59A C N 471 473 -175.08 -134.00 96.02 4.15 -68.20 138.75 8.87
13 59A 59A N CA 473 474 -126.22 147.00 145.30
14 3983 59A 60Q C N 476 478 99.39 -121.10 168.46 5.21 -63.80 -175.73 26.15
14 60Q 60Q N CA 478 479 -125.87 139.70 -40.30
15 3984 60Q 61V C N 485 487 -71.89 -62.40 23.70 2.61 -125.40 172.49 7.04
15 61V 61V N CA 487 488 -20.68 -42.40 143.30
16 3985 61V 62T C N 492 494 109.09 -124.80 174.46 10.49 -63.20 -175.85 31.34
16 62T 62T N CA 494 495 22.94 143.50 -42.10
17 3991 67T 68Q C N 535 537 -97.35 -121.10 41.36 2.16 -63.80 149.94 23.84
17 68Q 68Q N CA 537 538 173.56 139.70 -40.30
18 3992 68Q 69I C N 544 546 -107.28 -97.30 57.91 5.90 -63.40 121.93 18.75
18 69I 69I N CA 546 547 70.16 127.20 -43.60
19 3993 69I 70K C N 552 554 -175.90 -62.90 128.46 17.55 -62.90 128.46 17.55
19 70K 70K N CA 554 555 20.30 -40.80 -40.80
20 3995 71V 72P C N 568 570 -46.19 -58.70 45.02 2.85 -64.50 140.26 11.46
20 72P 72P N CA 570 571 -73.74 -30.50 147.20
21 3996 72P 73L C N 575 577 -108.94 -108.50 47.13 2.55 -63.50 134.48 16.70
21 73L 73L N CA 577 578 85.37 132.50 -41.20
22 3998 74T 75Q C N 590 592 -131.93 -121.10 56.78 2.86 -63.80 141.72 18.24
22 75Q 75Q N CA 592 593 83.97 139.70 -40.30
23 3999 75Q 76N C N 599 601 -65.00 -71.20 34.10 2.02 55.90 139.59 10.99
23 76N 76N N CA 601 602 109.27 142.80 39.50
24 4009 85V 86F C N 676 678 -123.23 -124.20 71.73 3.36 -63.20 130.50 14.93
24 86F 86F N CA 678 679 71.58 143.30 -44.30
25 4011 87N 88I C N 695 697 -33.97 -97.30 67.76 3.41 -120.60 89.14 6.76
25 88I 88I N CA 697 698 151.31 127.20 130.30
26 4012 88I 89G C N 703 705 -52.33 -62.40 10.30 1.74 82.20 144.17 11.05
26 89G 89G N CA 705 706 -43.34 -41.20 8.50
27 4013 89G 90M C N 707 709 -99.98 -125.60 59.83 2.23 -63.40 132.10 17.24
27 90M 90M N CA 709 710 86.43 140.50 -40.50
28 4014 90M 91T C N 715 717 -148.12 -124.80 27.14 1.03 -63.20 -178.40 28.78
28 91T 91T N CA 717 718 157.38 143.50 -42.10
29 4016 92A 93F C N 727 729 -119.78 -124.20 67.31 3.06 -63.20 133.06 15.36
29 93F 93F N CA 729 730 76.13 143.30 -44.30
30 4045 121K 122V C N 952 954 57.19 55.90 10.50 0.64 -125.40 -149.00 11.39
30 122V 122V N CA 954 955 29.08 39.50 143.30
31 4046 122V 123N C N 959 961 -75.51 -63.20 14.20 1.75 -119.90 176.68 6.93
31 123N 123N N CA 961 962 -34.02 -41.10 137.00
32 4048 124G 125K C N 971 973 -87.19 -62.90 89.89 10.60 -62.90 89.89 10.60
32 125K 125K N CA 973 974 45.74 -40.80 -40.80
33 4057 133I 134K C N 1040 1042 -107.07 -118.00 19.56 1.01 -62.90 169.73 24.65
33 134K 134K N CA 1042 1043 155.32 139.10 -40.80
34 4058 134K 135R C N 1049 1051 -76.36 -72.10 5.00 0.43 -63.00 -179.88 25.24
34 135R 135R N CA 1051 1052 139.27 141.90 -41.10
35 4059 135R 136R C N 1060 1062 -148.26 -125.20 57.37 2.18 -63.00 151.95 26.16
35 136R 136R N CA 1062 1063 -166.87 140.60 -41.10
36 4060 136R 137Q C N 1071 1073 -61.03 -73.00 12.96 0.82 -63.80 176.07 26.03
36 137Q 137Q N CA 1073 1074 135.75 140.70 -40.30
37 4061 137Q 138A C N 1080 1082 -100.32 -68.20 37.21 3.63 -62.50 171.62 26.54
37 138A 138A N CA 1082 1083 126.51 145.30 -40.90
38 4062 138A 139E C N 1085 1087 -105.09 -117.80 37.33 1.59 -63.60 147.94 17.79
38 139E 139E N CA 1087 1088 101.70 136.80 -40.30
39 4063 139E 140K C N 1094 1096 57.60 56.60 7.58 0.47 -62.90 140.31 24.49
39 140K 140K N CA 1096 1097 31.08 38.60 -40.80
40 4064 140K 141A C N 1103 1105 75.08 -68.20 144.37 12.81 -62.50 -151.92 31.78
40 141A 141A N CA 1105 1106 163.00 145.30 -40.90
41 4065 141A 142L C N 1108 1110 -122.17 -108.50 53.93 2.75 -63.50 146.40 23.96
41 142L 142L N CA 1110 1111 -175.33 132.50 -41.20
42 4066 142L 143F C N 1116 1118 -96.92 -71.40 28.93 1.64 -63.20 164.85 25.16
42 143F 143F N CA 1118 1119 154.34 140.70 -44.30
43 4068 144E 145S C N 1136 1138 -155.44 -136.60 51.63 2.15 -64.10 155.40 17.85
43 145S 145S N CA 1138 1139 -160.73 151.20 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11843 14Y 42G N CA 106 339 5.73 3.00 2.73 27.26 3.00 2.73 27.26
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 19 27 109 121 157 173 178 203 218 229
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 1192 1192
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11843 11843
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3120
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 : 2786.0540
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1168 1 5 0.011 0.011 41.561 1.000
2 Bond angle potential : 1574 4 21 2.987 2.987 277.73 1.000
3 Stereochemical cosine torsion poten: 705 0 45 52.707 52.707 297.48 1.000
4 Stereochemical improper torsion pot: 477 0 1 1.591 1.591 26.179 1.000
5 Soft-sphere overlap restraints : 3120 2 4 0.010 0.010 38.711 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2407 16 78 0.902 0.902 665.98 1.000
10 Distance restraints 2 (N-O) : 2568 12 67 0.874 0.874 665.38 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 2 9 6.748 6.748 77.867 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 88.744 88.744 56.911 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 3 81.818 81.818 48.354 1.000
16 Sidechain Chi_3 dihedral restraints: 42 0 0 76.944 76.944 30.390 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 107.122 107.122 12.026 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 857 0 0 0.512 0.512 22.542 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 48 33 45.143 93.799 248.16 1.000
26 Distance restraints 4 (SDCH-SDCH) : 119 0 2 1.302 1.302 17.833 1.000
27 Distance restraints 5 (X-Y) : 1402 1 1 0.095 0.095 258.94 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: newseq.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 26199.3770
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 348 42G 42G C CA 340 339 1.67 1.49 0.18 5.20 1.49 0.18 5.20
-------------------------------------------------------------------------------------------------
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 1328 15E 15E N CA 118 119 132.35 107.00 25.35 7.29 107.00 25.35 7.29
2 1339 16G 16G N CA 127 128 127.95 107.00 20.95 6.02 107.00 20.95 6.02
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4792 10L 13R CA CA 71 96 7.96 5.10 2.86 5.24 5.10 2.86 5.24
2 4793 10L 14Y CA CA 71 107 9.11 5.99 3.12 4.64 5.99 3.12 4.64
3 4894 13R 18R CA CA 96 140 8.64 5.50 3.15 5.93 5.50 3.15 5.93
4 4919 13R 146A CA CA 96 1145 11.73 7.45 4.28 5.42 7.45 4.28 5.42
-------------------------------------------------------------------------------------------------
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 7131 13R 9V N O 95 69 4.95 2.97 1.97 4.65 2.97 1.97 4.65
2 7153 14Y 9V N O 106 69 8.53 4.96 3.57 5.65 4.96 3.57 5.65
3 7154 14Y 10L N O 106 77 8.11 2.95 5.16 9.07 2.95 5.16 9.07
4 7161 14Y 132L N O 106 1033 17.04 10.60 6.44 5.53 10.60 6.44 5.53
5 7163 14Y 146A N O 106 1148 14.75 9.07 5.68 5.26 9.07 5.68 5.26
6 7170 15E 12K N O 118 94 5.49 3.16 2.33 5.03 3.16 2.33 5.03
7 7182 16G 13R N O 127 105 6.17 3.30 2.87 4.80 3.30 2.87 4.80
8 7198 17L 13R N O 131 105 7.21 4.49 2.72 4.88 4.49 2.72 4.88
9 7219 18R 13R N O 139 105 8.74 5.11 3.63 5.39 5.11 3.63 5.39
-------------------------------------------------------------------------------------------------
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 4084 16G 16G CA C 128 129 -153.21 -180.00 26.79 5.36 -180.00 26.79 5.36
-------------------------------------------------------------------------------------------------
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 3935 11I 12K C N 84 86 45.74 -62.90 119.64 20.89 -62.90 119.64 20.89
1 12K 12K N CA 86 87 9.32 -40.80 -40.80
2 3936 12K 13R C N 93 95 160.07 -125.20 84.58 2.55 -63.00 -165.10 34.86
2 13R 13R N CA 95 96 -179.79 140.60 -41.10
3 3938 14Y 15E C N 116 118 -69.17 -63.60 64.15 8.86 -63.60 64.15 8.86
3 15E 15E N CA 118 119 -104.21 -40.30 -40.30
4 3939 15E 16G C N 125 127 -101.73 -62.40 43.30 6.81 82.20 178.88 10.71
4 16G 16G N CA 127 128 -23.10 -41.20 8.50
5 3942 18R 19L C N 148 150 62.51 60.20 8.00 0.30 -63.50 140.94 25.99
5 19L 19L N CA 150 151 21.93 29.60 -41.20
6 3944 20K 21A C N 165 167 53.97 55.40 1.81 0.21 -62.50 140.17 28.46
6 21A 21A N CA 167 168 37.10 38.20 -40.90
7 3945 21A 22Y C N 170 172 65.06 55.90 15.28 0.79 -63.50 146.71 27.66
7 22Y 22Y N CA 172 173 27.28 39.50 -43.40
8 3956 32G 33Y C N 261 263 -70.33 -98.40 36.63 2.61 -63.50 164.80 26.50
8 33Y 33Y N CA 263 264 151.94 128.40 -43.40
9 3957 33Y 34G C N 273 275 92.97 82.20 73.63 3.03 -62.40 157.08 27.03
9 34G 34G N CA 275 276 -64.33 8.50 -41.20
10 3959 35H 36T C N 287 289 -131.95 -63.20 81.04 9.81 -63.20 81.04 9.81
10 36T 36T N CA 289 290 0.81 -42.10 -42.10
11 3960 36T 37H C N 294 296 58.10 56.30 7.82 0.58 -63.20 142.87 24.52
11 37H 37H N CA 296 297 33.19 40.80 -42.30
12 3972 48E 49Q C N 388 390 79.65 55.10 35.51 2.16 -121.10 -157.52 10.12
12 49Q 49Q N CA 390 391 14.65 40.30 139.70
13 3977 53F 54L C N 427 429 85.88 60.20 135.61 10.30 -108.50 168.36 7.70
13 54L 54L N CA 429 430 162.76 29.60 132.50
14 3982 58I 59A C N 471 473 -168.56 -134.00 89.40 4.01 -68.20 130.97 8.36
14 59A 59A N CA 473 474 -130.55 147.00 145.30
15 3983 59A 60Q C N 476 478 103.92 -121.10 160.07 4.94 -63.80 -167.75 27.02
15 60Q 60Q N CA 478 479 -134.27 139.70 -40.30
16 3984 60Q 61V C N 485 487 -65.86 -62.40 21.76 2.57 -125.40 174.68 6.95
16 61V 61V N CA 487 488 -20.92 -42.40 143.30
17 3985 61V 62T C N 492 494 121.12 -124.80 165.67 9.90 -63.20 -172.51 25.13
17 62T 62T N CA 494 495 23.37 143.50 -42.10
18 3991 67T 68Q C N 535 537 -132.70 -121.10 90.34 4.47 -63.80 113.68 14.59
18 68Q 68Q N CA 537 538 50.11 139.70 -40.30
19 3992 68Q 69I C N 544 546 -5.38 -97.30 94.01 4.56 -63.40 161.84 28.66
19 69I 69I N CA 546 547 107.49 127.20 -43.60
20 3993 69I 70K C N 552 554 160.54 -62.90 138.44 21.58 -62.90 138.44 21.58
20 70K 70K N CA 554 555 -18.11 -40.80 -40.80
21 3995 71V 72P C N 568 570 -56.04 -58.70 30.59 2.32 -64.50 152.07 11.80
21 72P 72P N CA 570 571 -60.97 -30.50 147.20
22 3996 72P 73L C N 575 577 -115.64 -108.50 48.02 2.66 -63.50 136.56 16.84
22 73L 73L N CA 577 578 85.02 132.50 -41.20
23 3998 74T 75Q C N 590 592 -140.45 -121.10 56.86 2.94 -63.80 147.94 18.98
23 75Q 75Q N CA 592 593 86.23 139.70 -40.30
24 3999 75Q 76N C N 599 601 -44.94 -63.20 18.40 2.68 55.90 130.51 15.77
24 76N 76N N CA 601 602 -43.35 -41.10 39.50
25 4000 76N 77Q C N 607 609 71.51 -63.80 145.09 21.43 -63.80 145.09 21.43
25 77Q 77Q N CA 609 610 -92.67 -40.30 -40.30
26 4001 77Q 78Y C N 616 618 -88.03 -98.40 52.30 5.51 -63.50 123.01 18.32
26 78Y 78Y N CA 618 619 77.14 128.40 -43.40
27 4002 78Y 79D C N 628 630 -42.98 -96.50 55.97 2.30 54.50 112.89 9.14
27 79D 79D N CA 630 631 97.84 114.20 40.90
28 4004 80A 81I C N 641 643 -67.46 -63.40 11.47 1.76 -120.60 171.62 7.88
28 81I 81I N CA 643 644 -32.88 -43.60 130.30
29 4005 81I 82C C N 649 651 88.09 -63.00 151.16 24.95 -63.00 151.16 24.95
29 82C 82C N CA 651 652 -45.89 -41.10 -41.10
30 4009 85V 86F C N 676 678 -86.82 -124.20 71.49 2.27 -63.20 128.85 16.37
30 86F 86F N CA 678 679 82.36 143.30 -44.30
31 4012 88I 89G C N 703 705 60.13 78.70 32.75 0.54 82.20 149.27 8.34
31 89G 89G N CA 705 706 -139.12 -166.10 8.50
32 4013 89G 90M C N 707 709 -97.48 -125.60 53.94 1.88 -63.40 139.21 18.42
32 90M 90M N CA 709 710 94.47 140.50 -40.50
33 4014 90M 91T C N 715 717 -129.85 -124.80 49.82 1.99 -63.20 141.52 22.45
33 91T 91T N CA 717 718 -166.94 143.50 -42.10
34 4027 103N 104V C N 815 817 -68.86 -125.40 57.12 2.48 -62.40 166.26 21.42
34 104V 104V N CA 817 818 151.47 143.30 -42.40
35 4028 104V 105G C N 822 824 109.07 82.20 44.03 1.23 -62.40 172.11 31.30
35 105G 105G N CA 824 825 -26.38 8.50 -41.20
36 4048 124G 125K C N 971 973 -106.55 -118.00 95.52 4.47 -62.90 95.61 10.98
36 125K 125K N CA 973 974 44.27 139.10 -40.80
37 4053 129L 130P C N 1013 1015 -54.46 -58.70 4.84 0.45 -64.50 -179.75 13.99
37 130P 130P N CA 1015 1016 -32.83 -30.50 147.20
38 4054 130P 131G C N 1020 1022 -61.05 -62.40 11.23 1.75 82.20 148.35 11.09
38 131G 131G N CA 1022 1023 -30.05 -41.20 8.50
39 4057 133I 134K C N 1040 1042 -123.12 -118.00 18.18 0.80 -62.90 173.45 26.12
39 134K 134K N CA 1042 1043 156.54 139.10 -40.80
40 4058 134K 135R C N 1049 1051 -145.01 -125.20 40.87 1.46 -63.00 164.46 27.73
40 135R 135R N CA 1051 1052 176.35 140.60 -41.10
41 4059 135R 136R C N 1060 1062 -123.24 -125.20 34.43 1.70 -63.00 156.03 25.21
41 136R 136R N CA 1062 1063 174.97 140.60 -41.10
42 4060 136R 137Q C N 1071 1073 -80.21 -73.00 64.61 4.37 -63.80 117.94 16.52
42 137Q 137Q N CA 1073 1074 76.49 140.70 -40.30
43 4061 137Q 138A C N 1080 1082 -175.95 -134.00 42.92 1.11 -62.50 -161.37 38.54
43 138A 138A N CA 1082 1083 156.06 147.00 -40.90
44 4062 138A 139E C N 1085 1087 -94.11 -117.80 38.24 1.32 -63.60 150.21 18.52
44 139E 139E N CA 1087 1088 106.77 136.80 -40.30
45 4064 140K 141A C N 1103 1105 177.97 -134.00 54.42 1.25 -62.50 -170.90 37.21
45 141A 141A N CA 1105 1106 172.57 147.00 -40.90
46 4066 142L 143F C N 1116 1118 -56.73 -71.40 17.11 0.96 -63.20 176.32 24.92
46 143F 143F N CA 1118 1119 131.90 140.70 -44.30
47 4067 143F 144E C N 1127 1129 -110.69 -117.80 64.17 3.34 -63.60 128.09 19.73
47 144E 144E N CA 1129 1130 -159.43 136.80 -40.30
48 4068 144E 145S C N 1136 1138 -56.55 -72.40 15.91 1.10 -64.10 174.13 12.19
48 145S 145S N CA 1138 1139 151.03 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11843 14Y 42G N CA 106 339 5.70 3.00 2.70 27.03 3.00 2.70 27.03
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 20 41 130 138 183 186 179 192 213 222
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
newseq.B99990001.pdb 2510.08105
newseq.B99990002.pdb 2786.05396
In [33]:
from IPython.display import Image
Наложение двух структур (с доп ограничениями (зеленая) и без). ВидноЮ что молекулы имеют несколько отличающуюся геометрию, особенно сильно отличается петля на C-конце. Немного отличаются положения спиралей ближе к реакциионному центру.
In [35]:
Image('super.png')
Out[35]:
Poly Ala¶
In [36]:
poly_a = 'A'*146 + '...' ; del alignm[1]
alignm.append_sequence(poly_a)
alignm[1].code = 'poly_a'
In [37]:
alignm.salign()
alignm.write(file='poly_a.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [38]:
! cat poly_a.ali
>P1;model structureX:1lmp.pdb: 1 :A:+132 :B:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------------- ----WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...* >P1;poly_a sequence::1 : :+149 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-...*
In [39]:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='poly_a.ali',
knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
poly_a model
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 146
atom names : C +N
atom indices : 729 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 146
atom names : C CA +N O
atom indices : 729 727 0 730
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10506 9783
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1364
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 : 858.7021
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 730 0 0 0.006 0.006 7.4887 1.000
2 Bond angle potential : 1021 0 5 2.157 2.157 96.563 1.000
3 Stereochemical cosine torsion poten: 296 0 39 77.201 77.201 289.38 1.000
4 Stereochemical improper torsion pot: 292 0 1 1.230 1.230 10.672 1.000
5 Soft-sphere overlap restraints : 1364 1 2 0.012 0.012 22.063 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 1 0.288 0.288 76.485 1.000
10 Distance restraints 2 (N-O) : 2564 0 11 0.434 0.434 179.98 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 0 6 5.364 5.364 49.206 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 0.272 0.272 6.4551 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 38 22 33.223 85.470 99.986 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.508 0.508 1.4179 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.039 0.039 18.998 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: poly_a.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15820.8330
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2354 15A 16A C N 74 76 78.91 55.40 26.13 2.08 -62.50 156.77 31.86
1 16A 16A N CA 76 77 26.78 38.20 -40.90
2 2356 17A 18A C N 84 86 -52.88 -62.50 9.66 1.89 -134.00 -168.90 11.79
2 18A 18A N CA 86 87 -39.97 -40.90 147.00
3 2357 18A 19A C N 89 91 -123.66 -134.00 53.09 2.74 -62.50 148.96 22.38
3 19A 19A N CA 91 92 94.92 147.00 -40.90
4 2360 21A 22A C N 104 106 -177.55 -134.00 107.77 6.65 -62.50 145.65 23.21
4 22A 22A N CA 106 107 48.42 147.00 -40.90
5 2375 36A 37A C N 179 181 66.77 55.40 15.52 0.86 -62.50 146.31 29.75
5 37A 37A N CA 181 182 27.63 38.20 -40.90
6 2376 37A 38A C N 184 186 63.13 55.40 11.44 0.57 -62.50 144.14 29.31
6 38A 38A N CA 186 187 29.76 38.20 -40.90
7 2387 48A 49A C N 239 241 83.68 55.40 38.16 2.16 -62.50 155.65 31.49
7 49A 49A N CA 241 242 12.57 38.20 -40.90
8 2392 53A 54A C N 264 266 96.30 -134.00 135.18 3.28 -62.50 -152.21 32.76
8 54A 54A N CA 266 267 -174.92 147.00 -40.90
9 2395 56A 57A C N 279 281 62.07 55.40 14.71 1.42 -62.50 154.98 31.39
9 57A 57A N CA 281 282 51.32 38.20 -40.90
10 2400 61A 62A C N 304 306 -47.90 -62.50 37.88 6.99 -62.50 37.88 6.99
10 62A 62A N CA 306 307 -5.94 -40.90 -40.90
11 2401 62A 63A C N 309 311 -54.37 -68.20 15.82 1.07 -62.50 178.69 29.69
11 63A 63A N CA 311 312 137.61 145.30 -40.90
12 2402 63A 64A C N 314 316 -162.51 -134.00 36.26 0.95 -62.50 -179.96 34.80
12 64A 64A N CA 316 317 169.39 147.00 -40.90
13 2403 64A 65A C N 319 321 -80.91 -68.20 47.24 4.24 -62.50 141.90 22.42
13 65A 65A N CA 321 322 99.80 145.30 -40.90
14 2404 65A 66A C N 324 326 -151.85 -134.00 18.38 0.46 -62.50 -169.95 35.92
14 66A 66A N CA 326 327 151.36 147.00 -40.90
15 2405 66A 67A C N 329 331 -121.30 -134.00 18.15 0.55 -62.50 -175.46 28.02
15 67A 67A N CA 331 332 134.02 147.00 -40.90
16 2406 67A 68A C N 334 336 -166.69 -134.00 38.44 0.91 -62.50 -175.81 35.69
16 68A 68A N CA 336 337 167.21 147.00 -40.90
17 2407 68A 69A C N 339 341 -170.03 -134.00 36.16 1.09 -62.50 -159.62 38.55
17 69A 69A N CA 341 342 150.02 147.00 -40.90
18 2408 69A 70A C N 344 346 -145.92 -134.00 21.62 1.32 -62.50 -170.75 28.38
18 70A 70A N CA 346 347 128.97 147.00 -40.90
19 2409 70A 71A C N 349 351 59.03 -68.20 128.99 11.61 -62.50 -164.96 29.56
19 71A 71A N CA 351 352 166.55 145.30 -40.90
20 2410 71A 72A C N 354 356 -104.18 -134.00 34.56 0.81 -62.50 175.46 27.03
20 72A 72A N CA 356 357 129.54 147.00 -40.90
21 2411 72A 73A C N 359 361 -160.09 -134.00 29.86 0.69 -62.50 -174.66 35.56
21 73A 73A N CA 361 362 161.53 147.00 -40.90
22 2412 73A 74A C N 364 366 -66.91 -68.20 1.36 0.10 -62.50 174.30 28.78
22 74A 74A N CA 366 367 144.86 145.30 -40.90
23 2413 74A 75A C N 369 371 -62.14 -68.20 6.48 0.47 -62.50 176.10 28.84
23 75A 75A N CA 371 372 143.00 145.30 -40.90
24 2414 75A 76A C N 374 376 -137.41 -134.00 9.35 0.43 -62.50 179.75 33.47
24 76A 76A N CA 376 377 155.71 147.00 -40.90
25 2415 76A 77A C N 379 381 -74.15 -68.20 7.37 0.73 -62.50 178.52 29.84
25 77A 77A N CA 381 382 140.96 145.30 -40.90
26 2416 77A 78A C N 384 386 -168.76 -134.00 54.79 1.85 -62.50 167.70 33.01
26 78A 78A N CA 386 387 -170.64 147.00 -40.90
27 2417 78A 79A C N 389 391 -155.15 -134.00 78.77 3.88 -62.50 133.59 26.62
27 79A 79A N CA 391 392 -137.13 147.00 -40.90
28 2422 83A 84A C N 414 416 79.54 55.40 57.74 2.09 -62.50 144.52 28.72
28 84A 84A N CA 416 417 -14.25 38.20 -40.90
29 2426 87A 88A C N 434 436 47.86 55.40 28.16 1.15 -62.50 153.18 30.67
29 88A 88A N CA 436 437 65.33 38.20 -40.90
30 2429 90A 91A C N 449 451 71.06 55.40 15.66 1.70 -62.50 155.19 31.56
30 91A 91A N CA 451 452 38.14 38.20 -40.90
31 2432 93A 94A C N 464 466 62.34 55.40 12.40 1.29 -62.50 153.53 31.13
31 94A 94A N CA 466 467 48.48 38.20 -40.90
32 2459 120A 121A C N 599 601 81.12 -134.00 159.09 3.61 -62.50 178.73 28.66
32 121A 121A N CA 601 602 -147.29 147.00 -40.90
33 2471 132A 133A C N 659 661 -55.89 -62.50 14.31 2.14 -68.20 161.58 13.47
33 133A 133A N CA 661 662 -53.59 -40.90 145.30
34 2472 133A 134A C N 664 666 -113.62 -134.00 55.03 2.51 -62.50 146.02 22.07
34 134A 134A N CA 666 667 95.88 147.00 -40.90
35 2473 134A 135A C N 669 671 -165.34 -134.00 36.06 0.84 -68.20 99.08 7.71
35 135A 135A N CA 671 672 164.84 147.00 145.30
36 2480 141A 142A C N 704 706 56.82 -68.20 132.58 12.52 -68.20 132.58 12.52
36 142A 142A N CA 706 707 -170.54 145.30 145.30
37 2481 142A 143A C N 709 711 -85.16 -68.20 75.29 6.65 -62.50 115.10 17.89
37 143A 143A N CA 711 712 71.95 145.30 -40.90
38 2483 144A 145A C N 719 721 61.05 55.40 6.02 0.71 -62.50 147.82 30.02
38 145A 145A N CA 721 722 40.25 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 6 33 58 75 62 89 110 112 94
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1426
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 : 788.5333
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 730 0 0 0.007 0.007 11.407 1.000
2 Bond angle potential : 1021 1 8 2.360 2.360 117.31 1.000
3 Stereochemical cosine torsion poten: 296 0 41 78.436 78.436 296.84 1.000
4 Stereochemical improper torsion pot: 292 0 0 1.271 1.271 11.722 1.000
5 Soft-sphere overlap restraints : 1426 2 2 0.012 0.012 25.359 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 1 0.274 0.274 71.173 1.000
10 Distance restraints 2 (N-O) : 2564 0 5 0.373 0.373 131.55 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 0 5 4.942 4.942 41.765 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 0.251 0.251 5.4107 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 37 21 29.626 84.908 44.568 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.521 0.521 1.3942 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.051 0.051 30.039 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: poly_a.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16133.7832
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2354 15A 16A C N 74 76 77.80 55.40 25.47 1.94 -62.50 155.47 31.59
1 16A 16A N CA 76 77 26.08 38.20 -40.90
2 2357 18A 19A C N 89 91 65.68 55.40 25.96 0.94 -62.50 139.58 28.33
2 19A 19A N CA 91 92 14.36 38.20 -40.90
3 2359 20A 21A C N 99 101 55.23 55.40 5.28 0.33 -62.50 138.96 28.24
3 21A 21A N CA 101 102 32.92 38.20 -40.90
4 2360 21A 22A C N 104 106 63.03 55.40 11.24 0.56 -62.50 144.14 29.32
4 22A 22A N CA 106 107 29.95 38.20 -40.90
5 2375 36A 37A C N 179 181 68.05 55.40 16.80 0.98 -62.50 147.21 29.94
5 37A 37A N CA 181 182 27.14 38.20 -40.90
6 2376 37A 38A C N 184 186 61.81 55.40 11.31 0.46 -62.50 142.55 28.99
6 38A 38A N CA 186 187 28.88 38.20 -40.90
7 2387 48A 49A C N 239 241 82.02 55.40 36.18 2.02 -62.50 154.48 31.27
7 49A 49A N CA 241 242 13.69 38.20 -40.90
8 2392 53A 54A C N 264 266 92.04 -134.00 138.78 3.42 -62.50 -154.25 32.28
8 54A 54A N CA 266 267 -176.74 147.00 -40.90
9 2395 56A 57A C N 279 281 60.40 55.40 14.53 1.28 -62.50 153.96 31.17
9 57A 57A N CA 281 282 51.85 38.20 -40.90
10 2401 62A 63A C N 309 311 -121.87 -134.00 26.16 1.09 -62.50 175.09 26.50
10 63A 63A N CA 311 312 123.82 147.00 -40.90
11 2402 63A 64A C N 314 316 179.30 -134.00 68.96 2.18 -62.50 169.41 33.78
11 64A 64A N CA 316 317 -162.25 147.00 -40.90
12 2403 64A 65A C N 319 321 -65.03 -68.20 6.69 0.44 -62.50 179.71 29.57
12 65A 65A N CA 321 322 139.41 145.30 -40.90
13 2404 65A 66A C N 324 326 -71.91 -68.20 4.77 0.47 -62.50 177.05 29.49
13 66A 66A N CA 326 327 142.31 145.30 -40.90
14 2405 66A 67A C N 329 331 -121.10 -134.00 14.06 0.32 -62.50 -172.89 33.79
14 67A 67A N CA 331 332 141.41 147.00 -40.90
15 2406 67A 68A C N 334 336 -143.80 -134.00 22.87 0.99 -62.50 171.89 32.52
15 68A 68A N CA 336 337 167.66 147.00 -40.90
16 2407 68A 69A C N 339 341 -64.54 -68.20 14.08 1.26 -62.50 160.22 26.36
16 69A 69A N CA 341 342 158.90 145.30 -40.90
17 2408 69A 70A C N 344 346 -58.37 -68.20 15.61 0.98 -62.50 174.12 28.74
17 70A 70A N CA 346 347 133.17 145.30 -40.90
18 2409 70A 71A C N 349 351 160.73 -134.00 70.80 1.61 -62.50 -160.91 39.62
18 71A 71A N CA 351 352 174.43 147.00 -40.90
19 2410 71A 72A C N 354 356 -84.18 -68.20 26.93 2.62 -62.50 165.94 26.21
19 72A 72A N CA 356 357 123.62 145.30 -40.90
20 2411 72A 73A C N 359 361 -142.70 -134.00 8.71 0.27 -62.50 -170.49 35.35
20 73A 73A N CA 361 362 147.39 147.00 -40.90
21 2412 73A 74A C N 364 366 -80.18 -68.20 15.33 0.98 -62.50 165.19 27.97
21 74A 74A N CA 366 367 154.86 145.30 -40.90
22 2413 74A 75A C N 369 371 -143.59 -134.00 15.11 0.51 -62.50 179.76 33.80
22 75A 75A N CA 371 372 158.67 147.00 -40.90
23 2414 75A 76A C N 374 376 -158.48 -134.00 28.38 0.66 -62.50 -175.34 35.37
23 76A 76A N CA 376 377 161.35 147.00 -40.90
24 2415 76A 77A C N 379 381 -70.88 -68.20 6.93 0.47 -62.50 167.62 27.89
24 77A 77A N CA 381 382 151.70 145.30 -40.90
25 2416 77A 78A C N 384 386 169.69 -134.00 67.37 1.63 -62.50 -174.01 37.02
25 78A 78A N CA 386 387 -176.02 147.00 -40.90
26 2417 78A 79A C N 389 391 179.95 -134.00 46.42 1.76 -62.50 -146.73 41.18
26 79A 79A N CA 391 392 141.16 147.00 -40.90
27 2422 83A 84A C N 414 416 78.47 55.40 53.42 1.93 -62.50 144.32 28.80
27 84A 84A N CA 416 417 -9.98 38.20 -40.90
28 2426 87A 88A C N 434 436 51.09 55.40 15.88 0.64 -62.50 147.68 29.79
28 88A 88A N CA 436 437 53.48 38.20 -40.90
29 2429 90A 91A C N 449 451 71.66 55.40 17.96 2.14 -62.50 159.75 32.45
29 91A 91A N CA 451 452 45.83 38.20 -40.90
30 2432 93A 94A C N 464 466 69.80 55.40 16.26 1.93 -62.50 158.14 32.12
30 94A 94A N CA 466 467 45.74 38.20 -40.90
31 2459 120A 121A C N 599 601 81.31 -134.00 159.40 3.62 -62.50 178.19 28.62
31 121A 121A N CA 601 602 -146.12 147.00 -40.90
32 2471 132A 133A C N 659 661 -53.65 -62.50 16.25 2.44 -68.20 160.83 13.48
32 133A 133A N CA 661 662 -54.52 -40.90 145.30
33 2472 133A 134A C N 664 666 -118.77 -134.00 53.31 2.59 -62.50 147.93 22.28
33 134A 134A N CA 666 667 95.91 147.00 -40.90
34 2473 134A 135A C N 669 671 -158.83 -134.00 28.74 0.67 -68.20 92.06 7.23
34 135A 135A N CA 671 672 161.46 147.00 145.30
35 2480 141A 142A C N 704 706 58.81 -68.20 132.54 12.36 -68.20 132.54 12.36
35 142A 142A N CA 706 707 -176.81 145.30 145.30
36 2481 142A 143A C N 709 711 -83.43 -68.20 79.57 6.94 -62.50 110.11 17.14
36 143A 143A N CA 711 712 67.20 145.30 -40.90
37 2483 144A 145A C N 719 721 67.01 55.40 21.28 0.84 -62.50 143.27 29.11
37 145A 145A N CA 721 722 20.36 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 8 45 64 76 77 83 122 109 91
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
poly_a.B99990001.pdb 858.70215
poly_a.B99990002.pdb 788.53333
In [42]:
poly_a = nglview.show_structure_file('poly_a.B99990001.pdb')
poly_a
ЦЕпочка сформировала хорошую структуру, лиганд находится в похожей на нативную полости в белке. Структура хороша, но бессмысленна.
Скоринг¶
In [45]:
import pandas as pd
ligand = [0, 0, 1, 1, 1, 1]
score = [1422.7, 1250.8, 1011.6, 1084.2, 913.6, 951.2]
struc = ['native', 'native', 'native', 'native', 'polyala', 'polyala']
model = ['model1', 'model2', 'model1', 'model2', 'model1', 'model2']
pd.DataFrame({'is_ligand_bound' : ligand, 'molpdf' : score, 'structure' : struc, 'model' : model})
Out[45]:
| is_ligand_bound | molpdf | structure | model | |
|---|---|---|---|---|
| 0 | 0 | 1422.7 | native | model1 |
| 1 | 0 | 1250.8 | native | model2 |
| 2 | 1 | 1011.6 | native | model1 |
| 3 | 1 | 1084.2 | native | model2 |
| 4 | 1 | 913.6 | polyala | model1 |
| 5 | 1 | 951.2 | polyala | model2 |
Структуры без лиганда имеют больший скор (меньше ограничений на структуру?). К счастью, PolyAla имеют скор меньший, чем у нормальных структур