import sys
import modeller
import _modeller
import modeller.automodel
Зададим некоторые параметры
Вытащим последовательность лизоцима Виргинской улитки
http://www.uniprot.org/uniprot/Q1XG90
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.19, 2017/07/19, r11078
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux shadbox 3.2.0-29-generic x86_64
Date and time of compilation : 2017/07/19 14:40:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/12/23 17:51:40
%%bash
wget http://www.pdb.org/pdb/files/1lmp.pdb
wget http://www.uniprot.org/uniprot/Q1XG90.fasta
--2017-12-23 17:51:41-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.244.52
Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-12-23 17:51:41-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 132.249.213.110
Connecting to www.rcsb.org (www.rcsb.org)|132.249.213.110|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-12-23 17:51:43-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 132.249.213.140
Connecting to files.rcsb.org (files.rcsb.org)|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb.5'
[ <=> ] 131,301 160K/s in 0.8s
2017-12-23 17:51:44 (160 KB/s) - `1lmp.pdb.5' saved [131301]
--2017-12-23 17:51:44-- http://www.uniprot.org/uniprot/Q1XG90.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.211, 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.211|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 216 [text/plain]
Saving to: `Q1XG90.fasta.3'
100%[======================================>] 216 --.-K/s in 0s
2017-12-23 17:51:45 (39.8 MB/s) - `Q1XG90.fasta.3' saved [216/216]
alignm = modeller.alignment(env)
alignm.append(file='Q1XG90.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'Q1XG90_id'
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
Q1XG90_id 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 1
transfe_404W> At least one template is aligned with model residue 133:
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 134:
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: 10955 10050
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 : 135
Number of all, selected real atoms : 1037 1037
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10050 10050
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2643
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1296.2905
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 : 1064 0 0 0.007 0.007 13.258 1.000
2 Bond angle potential : 1439 0 3 2.140 2.140 129.15 1.000
3 Stereochemical cosine torsion poten: 713 0 38 50.241 50.241 267.84 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.180 1.180 14.878 1.000
5 Soft-sphere overlap restraints : 2643 0 0 0.004 0.004 5.8549 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 3 13 0.660 0.660 228.17 1.000
10 Distance restraints 2 (N-O) : 2593 2 32 0.709 0.709 319.42 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 134 0 4 5.219 5.219 43.038 1.000
14 Sidechain Chi_1 dihedral restraints: 114 0 3 90.159 90.159 50.558 1.000
15 Sidechain Chi_2 dihedral restraints: 71 0 1 80.983 80.983 39.522 1.000
16 Sidechain Chi_3 dihedral restraints: 23 0 0 77.793 77.793 17.810 1.000
17 Sidechain Chi_4 dihedral restraints: 9 0 0 103.313 103.313 5.1624 1.000
18 Disulfide distance restraints : 1 0 0 0.006 0.006 0.56717E-02 1.000
19 Disulfide angle restraints : 2 0 0 2.503 2.503 0.27670 1.000
20 Disulfide dihedral angle restraints: 1 0 0 28.978 28.978 0.85187 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) : 766 0 0 0.408 0.408 13.294 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 133 37 26 35.891 93.528 137.80 1.000
26 Distance restraints 4 (SDCH-SDCH) : 101 0 0 0.934 0.934 9.4004 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: Q1XG90_id.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: 19362.0566
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8823 109G 106M N O 834 815 5.62 3.16 2.46 4.57 3.16 2.46 4.57
2 8948 115K 111P N O 867 848 5.58 2.99 2.60 4.52 2.99 2.60 4.52
-------------------------------------------------------------------------------------------------
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 3701 1M 2N C N 7 9 66.25 -71.20 146.70 11.62 -63.20 179.83 20.19
1 2N 2N N CA 9 10 -165.93 142.80 -41.10
2 3702 2N 3F C N 15 17 -69.19 -71.40 25.24 1.97 -63.20 159.97 21.81
2 3F 3F N CA 17 18 115.56 140.70 -44.30
3 3704 4L 5I C N 34 36 -6.36 -97.30 91.05 3.87 -120.60 114.49 7.70
3 5I 5I N CA 36 37 122.70 127.20 130.30
4 3717 17Y 18S C N 129 131 78.65 56.90 23.83 2.16 -64.10 155.51 20.75
4 18S 18S N CA 131 132 26.67 36.40 -35.00
5 3720 20I 21S C N 149 151 61.43 56.90 5.85 0.40 -64.10 142.62 18.87
5 21S 21S N CA 151 152 32.69 36.40 -35.00
6 3721 21S 22D C N 155 157 -57.08 -63.30 58.48 6.86 -63.30 58.48 6.86
6 22D 22D N CA 157 158 -98.15 -40.00 -40.00
7 3728 28I 29C C N 211 213 -64.78 -63.00 2.86 0.48 -117.90 -176.58 7.88
7 29C 29C N CA 213 214 -43.34 -41.10 141.10
8 3737 37A 38I C N 274 276 -129.09 -63.40 70.47 11.66 -63.40 70.47 11.66
8 38I 38I N CA 276 277 -18.11 -43.60 -43.60
9 3742 42W 43D C N 316 318 -102.57 -96.50 66.54 2.79 -63.30 96.31 10.26
9 43D 43D N CA 318 319 47.94 114.20 -40.00
10 3749 49C 50G C N 369 371 108.11 82.20 27.22 1.46 -62.40 175.45 32.68
10 50G 50G N CA 371 372 0.15 8.50 -41.20
11 3750 50G 51Y C N 373 375 70.18 55.90 23.14 1.22 -63.50 148.51 27.88
11 51Y 51Y N CA 375 376 21.29 39.50 -43.40
12 3762 62C 63G C N 482 484 -62.30 -62.40 14.06 2.09 82.20 157.95 12.20
12 63G 63G N CA 484 485 -55.26 -41.20 8.50
13 3767 67H 68S C N 513 515 -98.74 -72.40 36.68 1.75 -64.10 151.09 13.30
13 68S 68S N CA 515 516 177.93 152.40 -35.00
14 3768 68S 69M C N 519 521 -66.23 -63.40 5.40 1.02 56.30 146.28 26.48
14 69M 69M N CA 521 522 -45.10 -40.50 34.80
15 3769 69M 70E C N 527 529 -147.12 -117.80 47.49 2.58 -63.60 162.79 18.80
15 70E 70E N CA 529 530 99.43 136.80 -40.30
16 3772 72C 73A C N 548 550 49.75 55.40 20.96 0.85 -62.50 149.86 30.14
16 73A 73A N CA 550 551 58.38 38.20 -40.90
17 3773 73A 74D C N 553 555 -100.73 -96.50 11.00 0.46 -63.30 168.56 18.85
17 74D 74D N CA 555 556 124.35 114.20 -40.00
18 3775 75N 76Y C N 569 571 63.36 55.90 13.69 1.50 -124.30 -168.09 15.93
18 76Y 76Y N CA 571 572 50.98 39.50 135.40
19 3778 78C 79A C N 595 597 60.49 55.40 12.10 1.14 -62.50 152.44 30.89
19 79A 79A N CA 597 598 49.17 38.20 -40.90
20 3780 80S 81G C N 606 608 -80.29 -80.20 21.73 0.86 82.20 -142.97 7.28
20 81G 81G N CA 608 609 152.37 174.10 8.50
21 3795 95G 96C C N 731 733 -67.27 -63.00 4.46 0.66 -117.90 -173.87 7.97
21 96C 96C N CA 733 734 -39.78 -41.10 141.10
22 3803 103Y 104A C N 790 792 -55.58 -68.20 14.19 0.97 -62.50 179.84 29.82
22 104A 104A N CA 792 793 138.81 145.30 -40.90
23 3804 104A 105R C N 795 797 61.23 -63.00 151.22 27.53 -63.00 151.22 27.53
23 105R 105R N CA 797 798 45.12 -41.10 -41.10
24 3805 105R 106M C N 806 808 -88.55 -73.00 42.35 2.66 -63.40 139.40 22.82
24 106M 106M N CA 808 809 -177.62 143.00 -40.50
25 3806 106M 107H C N 814 816 72.38 56.30 66.58 4.90 -63.20 136.83 22.52
25 107H 107H N CA 816 817 -23.81 40.80 -42.30
26 3807 107H 108N C N 824 826 -85.91 -71.20 45.83 2.57 -63.20 134.62 18.12
26 108N 108N N CA 826 827 -173.79 142.80 -41.10
27 3810 110G 111P C N 840 842 -71.53 -64.50 19.58 1.17 -58.70 164.53 14.65
27 111P 111P N CA 842 843 165.48 147.20 -30.50
28 3811 111P 112N C N 847 849 75.00 55.90 78.24 4.21 -63.20 138.28 21.16
28 112N 112N N CA 849 850 -36.37 39.50 -41.10
29 3812 112N 113G C N 855 857 -72.43 -62.40 11.62 2.20 82.20 164.31 12.53
29 113G 113G N CA 857 858 -47.06 -41.20 8.50
30 3813 113G 114C C N 859 861 -66.34 -63.00 5.33 0.89 -117.90 -178.86 7.78
30 114C 114C N CA 861 862 -45.25 -41.10 141.10
31 3818 118H 119H C N 896 898 57.77 56.30 1.47 0.23 -63.20 146.77 25.14
31 119H 119H N CA 898 899 40.81 40.80 -42.30
32 3824 124N 125Y C N 944 946 -67.16 -98.40 37.43 2.63 -63.50 151.23 23.81
32 125Y 125Y N CA 946 947 107.78 128.40 -43.40
33 3825 125Y 126W C N 956 958 -68.04 -71.30 35.25 2.58 -63.00 148.18 18.23
33 126W 126W N CA 958 959 103.90 139.00 -44.20
34 3827 127R 128L C N 981 983 -61.81 -63.50 18.13 2.43 -70.70 159.40 12.42
34 128L 128L N CA 983 984 -59.25 -41.20 141.60
35 3829 129V 130Q C N 996 998 -46.53 -121.10 76.10 3.19 -63.80 165.74 23.49
35 130Q 130Q N CA 998 999 154.86 139.70 -40.30
36 3830 130Q 131A C N 1005 1007 -161.76 -134.00 30.60 0.69 -62.50 -172.34 36.03
36 131A 131A N CA 1007 1008 159.85 147.00 -40.90
37 3831 131A 132K C N 1010 1012 -179.14 -118.00 64.38 2.17 -62.90 -162.28 32.52
37 132K 132K N CA 1012 1013 159.26 139.10 -40.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 12 30 112 96 147 122 164 199 184 201
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 135
Number of all, selected real atoms : 1037 1037
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10050 10050
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2456
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 : 1092.2599
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 : 1064 0 0 0.006 0.006 11.252 1.000
2 Bond angle potential : 1439 0 2 2.041 2.041 116.27 1.000
3 Stereochemical cosine torsion poten: 713 0 41 50.321 50.321 267.17 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.071 1.071 11.383 1.000
5 Soft-sphere overlap restraints : 2456 0 0 0.004 0.004 3.8974 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 5 14 0.655 0.655 219.88 1.000
10 Distance restraints 2 (N-O) : 2593 0 22 0.639 0.639 225.51 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 134 0 1 4.297 4.297 29.173 1.000
14 Sidechain Chi_1 dihedral restraints: 114 0 2 83.924 83.924 38.112 1.000
15 Sidechain Chi_2 dihedral restraints: 71 0 1 80.917 80.917 34.355 1.000
16 Sidechain Chi_3 dihedral restraints: 23 0 0 75.377 75.377 18.415 1.000
17 Sidechain Chi_4 dihedral restraints: 9 0 0 107.398 107.398 7.5578 1.000
18 Disulfide distance restraints : 1 0 0 0.006 0.006 0.53702E-02 1.000
19 Disulfide angle restraints : 2 0 0 3.599 3.599 0.57208 1.000
20 Disulfide dihedral angle restraints: 1 0 0 9.043 9.043 0.99005E-01 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) : 766 0 0 0.388 0.388 12.160 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 133 35 17 32.881 95.419 84.460 1.000
26 Distance restraints 4 (SDCH-SDCH) : 101 0 0 1.026 1.026 11.995 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: Q1XG90_id.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: 18126.0898
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 3702 2N 3F C N 15 17 -64.41 -71.40 34.18 2.55 -63.20 151.55 20.96
1 3F 3F N CA 17 18 107.24 140.70 -44.30
2 3715 15V 16V C N 110 112 -74.41 -125.40 52.61 2.45 -62.40 161.76 21.18
2 16V 16V N CA 112 113 156.29 143.30 -42.40
3 3716 16V 17Y C N 117 119 73.58 55.90 31.18 1.57 -63.50 148.54 27.73
3 17Y 17Y N CA 119 120 13.82 39.50 -43.40
4 3717 17Y 18S C N 129 131 51.01 56.90 9.63 0.48 -64.10 139.63 18.13
4 18S 18S N CA 131 132 44.02 36.40 -35.00
5 3720 20I 21S C N 149 151 63.46 56.90 13.82 0.58 -64.10 140.64 18.73
5 21S 21S N CA 151 152 24.23 36.40 -35.00
6 3721 21S 22D C N 155 157 -76.96 -96.50 23.55 0.96 -63.30 167.91 19.93
6 22D 22D N CA 157 158 127.35 114.20 -40.00
7 3722 22D 23Q C N 163 165 49.32 55.10 7.64 0.52 -63.80 141.85 25.75
7 23Q 23Q N CA 165 166 45.29 40.30 -40.30
8 3728 28I 29C C N 211 213 -65.62 -63.00 4.83 0.78 -117.90 -178.56 7.79
8 29C 29C N CA 213 214 -45.15 -41.10 141.10
9 3737 37A 38I C N 274 276 -133.76 -63.40 79.89 12.88 -63.40 79.89 12.88
9 38I 38I N CA 276 277 -5.76 -43.60 -43.60
10 3742 42W 43D C N 316 318 -99.53 -96.50 80.73 3.39 -63.30 81.97 8.70
10 43D 43D N CA 318 319 33.53 114.20 -40.00
11 3749 49C 50G C N 369 371 106.17 82.20 25.59 1.31 -62.40 173.42 32.29
11 50G 50G N CA 371 372 -0.46 8.50 -41.20
12 3750 50G 51Y C N 373 375 69.52 55.90 24.78 1.23 -63.50 146.85 27.53
12 51Y 51Y N CA 375 376 18.80 39.50 -43.40
13 3762 62C 63G C N 482 484 -62.67 -62.40 13.95 2.10 82.20 158.24 12.22
13 63G 63G N CA 484 485 -55.15 -41.20 8.50
14 3767 67H 68S C N 513 515 -94.86 -72.40 30.56 1.47 -64.10 154.96 13.29
14 68S 68S N CA 515 516 173.13 152.40 -35.00
15 3768 68S 69M C N 519 521 -70.40 -63.40 7.15 1.22 56.30 146.67 26.87
15 69M 69M N CA 521 522 -39.09 -40.50 34.80
16 3769 69M 70E C N 527 529 -126.34 -117.80 51.45 2.72 -63.60 141.09 16.37
16 70E 70E N CA 529 530 86.07 136.80 -40.30
17 3772 72C 73A C N 548 550 51.01 55.40 16.45 0.67 -62.50 147.99 29.85
17 73A 73A N CA 550 551 54.06 38.20 -40.90
18 3773 73A 74D C N 553 555 -96.94 -96.50 12.33 0.52 -63.30 169.88 19.17
18 74D 74D N CA 555 556 126.52 114.20 -40.00
19 3775 75N 76Y C N 569 571 61.52 55.90 9.94 1.10 -124.30 -164.98 16.20
19 76Y 76Y N CA 571 572 47.70 39.50 135.40
20 3778 78C 79A C N 595 597 61.76 55.40 8.88 1.00 -62.50 150.72 30.59
20 79A 79A N CA 597 598 44.40 38.20 -40.90
21 3780 80S 81G C N 606 608 -79.68 -80.20 21.91 0.84 82.20 -143.54 7.25
21 81G 81G N CA 608 609 152.20 174.10 8.50
22 3803 103Y 104A C N 790 792 -54.96 -68.20 13.28 1.16 -62.50 173.03 28.00
22 104A 104A N CA 792 793 146.23 145.30 -40.90
23 3804 104A 105R C N 795 797 61.90 -72.10 154.97 10.27 -63.00 163.27 29.54
23 105R 105R N CA 797 798 64.05 141.90 -41.10
24 3808 108N 109G C N 832 834 -56.22 -62.40 8.36 1.56 82.20 145.27 10.99
24 109G 109G N CA 834 835 -35.57 -41.20 8.50
25 3812 112N 113G C N 855 857 -63.97 -62.40 1.61 0.27 82.20 154.27 11.72
25 113G 113G N CA 857 858 -40.83 -41.20 8.50
26 3813 113G 114C C N 859 861 -59.87 -63.00 10.42 1.10 -117.90 177.61 7.69
26 114C 114C N CA 861 862 -51.03 -41.10 141.10
27 3818 118H 119H C N 896 898 59.25 56.30 6.73 0.49 -63.20 144.68 24.83
27 119H 119H N CA 898 899 34.75 40.80 -42.30
28 3821 121A 122T C N 921 923 -107.02 -124.80 95.69 3.59 -63.20 101.52 10.84
28 122T 122T N CA 923 924 49.48 143.50 -42.10
29 3825 125Y 126W C N 956 958 -75.25 -71.30 45.72 3.56 -63.00 138.19 16.58
29 126W 126W N CA 958 959 93.45 139.00 -44.20
30 3826 126W 127R C N 970 972 -118.94 -125.20 21.33 1.14 -63.00 167.52 26.49
30 127R 127R N CA 972 973 160.99 140.60 -41.10
31 3827 127R 128L C N 981 983 -62.69 -63.50 0.98 0.18 -70.70 177.92 13.79
31 128L 128L N CA 983 984 -40.65 -41.20 141.60
32 3828 128L 129V C N 989 991 -61.12 -62.40 8.42 1.00 -125.40 177.98 10.02
32 129V 129V N CA 991 992 -50.72 -42.40 143.30
33 3829 129V 130Q C N 996 998 101.14 -121.10 141.70 4.71 -63.80 -139.20 29.15
33 130Q 130Q N CA 998 999 172.91 139.70 -40.30
34 3830 130Q 131A C N 1005 1007 173.63 -134.00 56.62 1.29 -62.50 -165.02 38.40
34 131A 131A N CA 1007 1008 168.52 147.00 -40.90
35 3831 131A 132K C N 1010 1012 -175.71 -118.00 60.71 2.04 -62.90 -163.21 32.22
35 132K 132K N CA 1012 1013 157.95 139.10 -40.80
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 11 18 82 79 135 126 152 171 194 180
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
Q1XG90_id.B99990001.pdb 1296.29053
Q1XG90_id.B99990002.pdb 1092.25989
import nglview
import ipywidgets
import IPython.display
from IPython.display import display,Image
w1 = nglview.show_structure_file('Q1XG90_id.B99990001.pdb')
display(w1)
Failed to display Jupyter Widget of type NGLWidget.
If you're reading this message in Jupyter Notebook or JupyterLab, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another notebook frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
print(alignm[0].residues[:])
[Residue MET, Residue ASN, Residue PHE, Residue LEU, Residue ILE, Residue LEU, Residue PHE, Residue CYS, Residue VAL, Residue VAL, Residue ALA, Residue SER, Residue ALA, Residue SER, Residue VAL, Residue VAL, Residue TYR, Residue SER, Residue SER, Residue ILE, Residue SER, Residue ASP, Residue GLN, Residue CYS, Residue LEU, Residue ARG, Residue CYS, Residue ILE, Residue CYS, Residue GLU, Residue VAL, Residue GLU, Residue SER, Residue GLY, Residue CYS, Residue ARG, Residue ALA, Residue ILE, Residue GLY, Residue CYS, Residue HIS, Residue TRP, Residue ASP, Residue VAL, Residue TYR, Residue SER, Residue ASN, Residue SER, Residue CYS, Residue GLY, Residue TYR, Residue PHE, Residue GLN, Residue ILE, Residue LYS, Residue GLN, Residue GLY, Residue TYR, Residue TRP, Residue THR, Residue ASP, Residue CYS, Residue GLY, Residue SER, Residue PRO, Residue GLY, Residue HIS, Residue SER, Residue MET, Residue GLU, Residue SER, Residue CYS, Residue ALA, Residue ASP, Residue ASN, Residue TYR, Residue ASN, Residue CYS, Residue ALA, Residue SER, Residue GLY, Residue CYS, Residue VAL, Residue ARG, Residue SER, Residue TYR, Residue MET, Residue ASP, Residue HIS, Residue TYR, Residue ILE, Residue LYS, Residue TYR, Residue ASN, Residue GLY, Residue CYS, Residue ALA, Residue ASP, Residue THR, Residue CYS, Residue GLU, Residue SER, Residue TYR, Residue ALA, Residue ARG, Residue MET, Residue HIS, Residue ASN, Residue GLY, Residue GLY, Residue PRO, Residue ASN, Residue GLY, Residue CYS, Residue LYS, Residue SER, Residue SER, Residue HIS, Residue HIS, Residue HIS, Residue ALA, Residue THR, Residue ASP, Residue ASN, Residue TYR, Residue TRP, Residue ARG, Residue LEU, Residue VAL, Residue GLN, Residue ALA, Residue LYS, Residue GLY, Residue CYS, Residue SER]
lig = ''
for i in alignm[0].residues:
lig += i.code
lig += '...'
alignm.append_sequence(lig)
alignm[2].code = 'ligand'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
## Выбираем объект для моделирования
s = alignm[2]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ligand 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 135
atom names : C +N
atom indices : 1035 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 135
atom names : C CA +N O
atom indices : 1035 1032 0 1036
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 1
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12329 11424
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 : 138
Number of all, selected real atoms : 1080 1080
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11424 11424
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2643
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 : 1067.3358
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 : 1064 0 0 0.007 0.007 14.233 1.000
2 Bond angle potential : 1439 0 4 2.227 2.227 134.93 1.000
3 Stereochemical cosine torsion poten: 713 0 37 50.022 50.022 267.84 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.350 1.350 19.100 1.000
5 Soft-sphere overlap restraints : 2643 1 2 0.010 0.010 28.366 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 0 2 0.327 0.327 85.251 1.000
10 Distance restraints 2 (N-O) : 2566 0 5 0.480 0.480 164.76 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 134 0 4 5.045 5.045 40.219 1.000
14 Sidechain Chi_1 dihedral restraints: 114 0 3 92.378 92.378 58.241 1.000
15 Sidechain Chi_2 dihedral restraints: 71 0 1 83.796 83.796 34.884 1.000
16 Sidechain Chi_3 dihedral restraints: 23 0 0 76.875 76.875 16.748 1.000
17 Sidechain Chi_4 dihedral restraints: 9 0 0 53.284 53.284 4.6222 1.000
18 Disulfide distance restraints : 1 0 0 0.004 0.004 0.23757E-02 1.000
19 Disulfide angle restraints : 2 0 0 2.105 2.105 0.19567 1.000
20 Disulfide dihedral angle restraints: 1 0 0 3.155 3.155 0.12251E-01 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) : 766 0 0 0.389 0.389 11.693 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 133 35 24 39.479 89.905 154.60 1.000
26 Distance restraints 4 (SDCH-SDCH) : 101 0 0 1.025 1.025 12.257 1.000
27 Distance restraints 5 (X-Y) : 1401 0 1 0.040 0.040 19.373 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: ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 18053.8398
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 3703 3F 4L C N 26 28 66.69 -63.50 154.04 21.56 -108.50 -156.28 11.03
1 4L 4L N CA 28 29 -123.53 -41.20 132.50
2 3716 16V 17Y C N 117 119 -102.34 -98.40 39.56 4.17 -63.50 138.02 20.07
2 17Y 17Y N CA 119 120 89.04 128.40 -43.40
3 3717 17Y 18S C N 129 131 -31.55 -72.40 82.02 3.77 -64.10 120.75 10.99
3 18S 18S N CA 131 132 81.28 152.40 -35.00
4 3719 19S 20I C N 141 143 -59.26 -63.40 4.90 0.78 -120.60 -173.11 8.47
4 20I 20I N CA 143 144 -46.23 -43.60 130.30
5 3721 21S 22D C N 155 157 -48.63 -70.90 41.00 1.40 -63.30 156.56 20.24
5 22D 22D N CA 157 158 115.87 150.30 -40.00
6 3722 22D 23Q C N 163 165 48.86 55.10 7.64 0.59 -63.80 141.13 25.62
6 23Q 23Q N CA 165 166 44.70 40.30 -40.30
7 3728 28I 29C C N 211 213 -59.94 -63.00 4.05 0.48 -117.90 -175.51 7.97
7 29C 29C N CA 213 214 -43.75 -41.10 141.10
8 3737 37A 38I C N 274 276 -131.50 -63.40 93.72 14.45 -63.40 93.72 14.45
8 38I 38I N CA 276 277 20.78 -43.60 -43.60
9 3742 42W 43D C N 316 318 -99.87 -96.50 70.48 2.96 -63.30 91.43 9.75
9 43D 43D N CA 318 319 43.80 114.20 -40.00
10 3749 49C 50G C N 369 371 111.31 82.20 36.52 1.35 -62.40 175.90 32.39
10 50G 50G N CA 371 372 -13.55 8.50 -41.20
11 3750 50G 51Y C N 373 375 64.48 55.90 15.97 0.78 -63.50 145.60 27.44
11 51Y 51Y N CA 375 376 26.04 39.50 -43.40
12 3757 57G 58Y C N 435 437 -109.08 -63.50 82.36 11.38 -63.50 82.36 11.38
12 58Y 58Y N CA 437 438 25.19 -43.40 -43.40
13 3762 62C 63G C N 482 484 -62.53 -62.40 9.08 1.36 82.20 156.21 12.01
13 63G 63G N CA 484 485 -50.28 -41.20 8.50
14 3769 69M 70E C N 527 529 -146.78 -117.80 97.66 5.29 -63.60 118.11 14.07
14 70E 70E N CA 529 530 43.54 136.80 -40.30
15 3772 72C 73A C N 548 550 52.43 55.40 11.21 0.46 -62.50 145.92 29.50
15 73A 73A N CA 550 551 49.01 38.20 -40.90
16 3773 73A 74D C N 553 555 -78.72 -70.90 22.65 1.50 -63.30 169.74 20.06
16 74D 74D N CA 555 556 129.04 150.30 -40.00
17 3774 74D 75N C N 561 563 -115.37 -119.90 52.92 2.30 -63.20 135.80 14.80
17 75N 75N N CA 563 564 84.27 137.00 -41.10
18 3778 78C 79A C N 595 597 71.99 55.40 21.78 1.29 -62.50 149.37 30.36
18 79A 79A N CA 597 598 24.10 38.20 -40.90
19 3780 80S 81G C N 606 608 -93.35 -80.20 22.83 1.51 82.20 -131.08 7.95
19 81G 81G N CA 608 609 155.43 174.10 8.50
20 3795 95G 96C C N 731 733 -66.56 -63.00 4.54 0.80 -117.90 -177.65 7.82
20 96C 96C N CA 733 734 -43.92 -41.10 141.10
21 3804 104A 105R C N 795 797 -91.78 -72.10 52.35 4.40 -63.00 137.53 16.83
21 105R 105R N CA 797 798 93.38 141.90 -41.10
22 3805 105R 106M C N 806 808 -52.58 -63.40 74.55 10.33 -63.40 74.55 10.33
22 106M 106M N CA 808 809 -114.26 -40.50 -40.50
23 3808 108N 109G C N 832 834 -59.21 -62.40 15.05 2.41 82.20 145.68 10.83
23 109G 109G N CA 834 835 -26.50 -41.20 8.50
24 3812 112N 113G C N 855 857 -62.95 -62.40 4.05 0.63 82.20 154.78 11.83
24 113G 113G N CA 857 858 -45.22 -41.20 8.50
25 3814 114C 115K C N 865 867 69.50 56.60 41.89 2.20 -62.90 138.18 23.90
25 115K 115K N CA 867 868 -1.26 38.60 -40.80
26 3815 115K 116S C N 874 876 -148.69 -64.10 92.34 12.32 -64.10 92.34 12.32
26 116S 116S N CA 876 877 -72.02 -35.00 -35.00
27 3818 118H 119H C N 896 898 58.15 56.30 5.94 0.43 -63.20 143.96 24.70
27 119H 119H N CA 898 899 35.15 40.80 -42.30
28 3821 121A 122T C N 921 923 -117.90 -124.80 95.96 3.91 -63.20 105.22 11.11
28 122T 122T N CA 923 924 47.78 143.50 -42.10
29 3824 124N 125Y C N 944 946 -58.07 -98.40 55.14 4.11 -63.50 150.70 23.63
29 125Y 125Y N CA 946 947 165.99 128.40 -43.40
30 3825 125Y 126W C N 956 958 -51.16 -71.30 30.94 1.83 -63.00 160.14 20.76
30 126W 126W N CA 958 959 115.51 139.00 -44.20
31 3826 126W 127R C N 970 972 -152.37 -125.20 112.76 4.79 -63.00 112.82 20.49
31 127R 127R N CA 972 973 -109.97 140.60 -41.10
32 3827 127R 128L C N 981 983 -56.35 -63.50 8.58 1.19 -70.70 173.05 13.67
32 128L 128L N CA 983 984 -45.95 -41.20 141.60
33 3829 129V 130Q C N 996 998 53.89 -63.80 174.85 31.31 -63.80 174.85 31.31
33 130Q 130Q N CA 998 999 89.01 -40.30 -40.30
34 3830 130Q 131A C N 1005 1007 -66.50 -68.20 16.45 1.27 -62.50 169.88 27.65
34 131A 131A N CA 1007 1008 128.94 145.30 -40.90
35 3831 131A 132K C N 1010 1012 -114.53 -118.00 11.49 0.50 -62.90 176.66 20.72
35 132K 132K N CA 1012 1013 128.15 139.10 -40.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 18 24 87 117 153 139 154 186 200 169
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90: -90.2092
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 : 138
Number of all, selected real atoms : 1080 1080
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11424 11424
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2666
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 : 1060.0707
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 : 1064 0 0 0.006 0.006 9.7159 1.000
2 Bond angle potential : 1439 0 2 2.089 2.089 121.02 1.000
3 Stereochemical cosine torsion poten: 713 0 44 51.834 51.834 284.78 1.000
4 Stereochemical improper torsion pot: 480 0 0 1.329 1.329 17.442 1.000
5 Soft-sphere overlap restraints : 2666 2 2 0.009 0.009 27.611 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2406 0 1 0.281 0.281 72.242 1.000
10 Distance restraints 2 (N-O) : 2566 0 7 0.417 0.417 147.80 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 134 0 3 4.747 4.747 35.614 1.000
14 Sidechain Chi_1 dihedral restraints: 114 0 5 88.239 88.239 58.734 1.000
15 Sidechain Chi_2 dihedral restraints: 71 0 3 98.712 98.712 45.429 1.000
16 Sidechain Chi_3 dihedral restraints: 23 0 0 93.503 93.503 18.985 1.000
17 Sidechain Chi_4 dihedral restraints: 9 0 0 93.856 93.856 6.8221 1.000
18 Disulfide distance restraints : 1 0 0 0.003 0.003 0.18120E-02 1.000
19 Disulfide angle restraints : 2 0 0 2.653 2.653 0.31092 1.000
20 Disulfide dihedral angle restraints: 1 0 0 14.746 14.746 0.25520 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) : 766 0 0 0.419 0.419 15.719 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 133 34 25 42.929 89.714 169.12 1.000
26 Distance restraints 4 (SDCH-SDCH) : 101 0 0 0.976 0.976 10.739 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.037 0.037 17.730 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: ligand.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 18138.4922
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 3701 1M 2N C N 7 9 -59.65 -71.20 21.88 1.70 -63.20 157.57 19.51
1 2N 2N N CA 9 10 161.37 142.80 -41.10
2 3702 2N 3F C N 15 17 -0.23 -71.40 104.89 6.16 -63.20 124.98 21.32
2 3F 3F N CA 17 18 63.66 140.70 -44.30
3 3703 3F 4L C N 26 28 86.29 -70.70 156.99 14.33 -108.50 165.57 7.76
3 4L 4L N CA 28 29 143.40 141.60 132.50
4 3717 17Y 18S C N 129 131 77.26 56.90 20.90 2.19 -64.10 156.30 20.81
4 18S 18S N CA 131 132 31.67 36.40 -35.00
5 3720 20I 21S C N 149 151 66.14 56.90 21.71 0.89 -64.10 140.16 18.73
5 21S 21S N CA 151 152 16.76 36.40 -35.00
6 3721 21S 22D C N 155 157 -67.48 -70.90 13.71 0.52 -63.30 177.06 21.61
6 22D 22D N CA 157 158 137.02 150.30 -40.00
7 3722 22D 23Q C N 163 165 65.04 55.10 138.85 9.09 -63.80 141.25 20.47
7 23Q 23Q N CA 165 166 -98.19 40.30 -40.30
8 3737 37A 38I C N 274 276 -126.36 -63.40 85.41 13.20 -63.40 85.41 13.20
8 38I 38I N CA 276 277 14.11 -43.60 -43.60
9 3742 42W 43D C N 316 318 -93.95 -96.50 78.70 3.31 -63.30 81.52 8.72
9 43D 43D N CA 318 319 35.54 114.20 -40.00
10 3749 49C 50G C N 369 371 115.97 82.20 37.67 1.74 -62.40 -178.60 33.53
10 50G 50G N CA 371 372 -8.20 8.50 -41.20
11 3750 50G 51Y C N 373 375 56.64 55.90 7.67 0.48 -63.50 141.77 26.81
11 51Y 51Y N CA 375 376 31.87 39.50 -43.40
12 3757 57G 58Y C N 435 437 -105.47 -63.50 80.07 11.09 -63.50 80.07 11.09
12 58Y 58Y N CA 437 438 24.79 -43.40 -43.40
13 3762 62C 63G C N 482 484 -62.57 -62.40 12.95 1.94 82.20 157.75 12.17
13 63G 63G N CA 484 485 -54.15 -41.20 8.50
14 3769 69M 70E C N 527 529 -134.29 -63.60 97.18 11.68 -63.60 97.18 11.68
14 70E 70E N CA 529 530 26.38 -40.30 -40.30
15 3772 72C 73A C N 548 550 58.20 55.40 9.47 0.80 -62.50 149.45 30.29
15 73A 73A N CA 550 551 47.24 38.20 -40.90
16 3773 73A 74D C N 553 555 -93.66 -96.50 14.15 0.59 -63.30 170.79 19.43
16 74D 74D N CA 555 556 128.07 114.20 -40.00
17 3774 74D 75N C N 561 563 -121.11 -119.90 56.48 2.59 -63.20 134.72 14.56
17 75N 75N N CA 563 564 80.54 137.00 -41.10
18 3778 78C 79A C N 595 597 52.37 55.40 26.72 1.37 -62.50 156.06 31.33
18 79A 79A N CA 597 598 64.75 38.20 -40.90
19 3780 80S 81G C N 606 608 -134.92 -167.20 39.95 0.74 82.20 -158.17 15.48
19 81G 81G N CA 608 609 151.06 174.60 8.50
20 3795 95G 96C C N 731 733 -62.77 -63.00 5.57 0.66 -117.90 -179.16 7.80
20 96C 96C N CA 733 734 -46.67 -41.10 141.10
21 3803 103Y 104A C N 790 792 -59.29 -68.20 31.11 2.20 -62.50 156.43 25.79
21 104A 104A N CA 792 793 115.49 145.30 -40.90
22 3804 104A 105R C N 795 797 153.23 -63.00 143.78 23.86 -63.00 143.78 23.86
22 105R 105R N CA 797 798 -39.21 -41.10 -41.10
23 3805 105R 106M C N 806 808 72.52 -73.00 160.88 12.87 -63.40 173.55 23.53
23 106M 106M N CA 808 809 -148.41 143.00 -40.50
24 3808 108N 109G C N 832 834 -58.32 -62.40 15.99 2.60 82.20 144.63 10.74
24 109G 109G N CA 834 835 -25.74 -41.20 8.50
25 3812 112N 113G C N 855 857 -65.14 -62.40 3.97 0.73 82.20 156.44 11.93
25 113G 113G N CA 857 858 -44.08 -41.20 8.50
26 3814 114C 115K C N 865 867 -108.28 -62.90 90.96 10.46 -62.90 90.96 10.46
26 115K 115K N CA 867 868 38.03 -40.80 -40.80
27 3815 115K 116S C N 874 876 -154.86 -64.10 96.78 12.95 -64.10 96.78 12.95
27 116S 116S N CA 876 877 -68.62 -35.00 -35.00
28 3818 118H 119H C N 896 898 55.52 56.30 4.74 0.49 -63.20 142.28 24.40
28 119H 119H N CA 898 899 36.13 40.80 -42.30
29 3821 121A 122T C N 921 923 -126.78 -124.80 97.51 4.24 -63.20 108.65 11.51
29 122T 122T N CA 923 924 46.01 143.50 -42.10
30 3826 126W 127R C N 970 972 -108.35 -125.20 32.80 1.15 -63.00 160.11 19.02
30 127R 127R N CA 972 973 112.46 140.60 -41.10
31 3827 127R 128L C N 981 983 -150.26 -108.50 53.62 2.97 -70.70 90.32 9.09
31 128L 128L N CA 983 984 98.87 132.50 141.60
32 3828 128L 129V C N 989 991 56.49 55.90 4.34 0.26 -125.40 -151.64 11.15
32 129V 129V N CA 991 992 35.20 39.50 143.30
33 3830 130Q 131A C N 1005 1007 50.95 55.40 8.92 0.33 -62.50 142.86 28.91
33 131A 131A N CA 1007 1008 45.93 38.20 -40.90
34 3831 131A 132K C N 1010 1012 -56.07 -70.20 35.23 2.23 -62.90 149.08 19.74
34 132K 132K N CA 1012 1013 108.13 140.40 -40.80
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 22 100 106 164 150 158 205 193 179
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ligand.B99990001.pdb 1067.33582
ligand.B99990002.pdb 1060.07068
w2 = nglview.show_structure_file('ligand.B99990001.pdb')
display(w2)
Failed to display Jupyter Widget of type NGLWidget.
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import IPython.display
from IPython.display import display,display_svg,SVG,Image, HTML
import subprocess
converted = subprocess.call(["jupyter-nbconvert", '--to', 'html',"SB. HW6. Tevanyan.ipynb"], shell=False)
if converted==0:
print 'Your ipynb-file was sucessfully converted!'
else:
print 'Smth went wrong. for instance, check the filename...'
show_link = '<a href="%s" target="_blank">You can download it here!</a>'%('SB. HW6. Tevanyan.html')
display(HTML(show_link))
Your ipynb-file was sucessfully converted!