In [1]:
import sys
sys.path.append('/usr/lib/modeller9v7/modlib/')
sys.path.append('/usr/lib/modeller9v7/lib/x86_64-intel8/python2.5/')
import modeller
import _modeller
import modeller.automodel
Задание: построить модель выбранного лизоцима (LYS_LAMBD)по последовательности белка и по известной структуре белка лизоцима форели (PDB:1lmp).
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, 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.fbb.msu.ru 3.8-2-amd64 x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/05/25 15:13:07
In [14]:
## известная структура лизоцима форели
! wget http://www.pdb.org/pdb/files/1lmp.pdb
## выбранная последовательность
! wget http://www.uniprot.org/uniprot/P05105.fasta
--2017-05-25 15:36:25-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 132.249.231.77
Connecting to www.pdb.org|132.249.231.77|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-05-25 15:36:25-- http://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 132.249.231.10
Connecting to www.rcsb.org|132.249.231.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-05-25 15:36:26-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 128.6.244.231
Connecting to files.rcsb.org|128.6.244.231|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb.1'
[ <=> ] 131,301 251K/s in 0.5s
2017-05-25 15:36:27 (251 KB/s) - `1lmp.pdb.1' saved [131301]
--2017-05-25 15:36:27-- http://www.uniprot.org/uniprot/P05105.fasta
Resolving www.uniprot.org... 128.175.240.211, 193.62.193.81
Connecting to www.uniprot.org|128.175.240.211|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 205 [text/plain]
Saving to: `P05105.fasta'
100%[======================================>] 205 --.-K/s in 0s
2017-05-25 15:36:27 (22.9 MB/s) - `P05105.fasta' saved [205/205]
In [15]:
alignm=modeller.alignment(env)
In [16]:
alignm.append(file='P05105.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 = 'LMP'
In [17]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [18]:
## 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()
LMP 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C +N
atom indices : 1110 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C CA +N O
atom indices : 1110 1107 0 1111
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM 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: 11694 10727
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 : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2388
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 : 913.5706
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 : 1136 0 1 0.007 0.007 17.822 1.000
2 Bond angle potential : 1532 1 7 2.065 2.065 131.63 1.000
3 Stereochemical cosine torsion poten: 734 0 25 47.287 47.287 253.07 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.146 1.146 14.083 1.000
5 Soft-sphere overlap restraints : 2388 0 0 0.003 0.003 2.0322 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) : 2217 0 2 0.344 0.344 96.432 1.000
10 Distance restraints 2 (N-O) : 2375 0 5 0.387 0.387 133.35 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: 138 0 1 4.690 4.690 35.792 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 70.637 70.637 36.752 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 1 81.202 81.202 34.676 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 75.207 75.207 21.789 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 94.727 94.727 12.608 1.000
18 Disulfide distance restraints : 3 0 0 0.021 0.021 0.23264 1.000
19 Disulfide angle restraints : 6 0 0 2.577 2.577 0.87999 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.731 22.731 1.5829 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) : 1240 0 0 0.415 0.415 18.139 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: 137 18 19 29.927 67.299 83.124 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.525 0.525 19.573 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: LMP.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: 15504.1484
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 2119 90D 90D N CA 713 714 123.23 107.00 16.23 4.67 107.00 16.23 4.67
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -66.64 -68.20 6.28 0.56 -62.50 167.77 27.70
1 19A 19A N CA 141 142 151.38 145.30 -40.90
2 3911 19A 20K C N 144 146 -76.61 -70.20 14.63 1.19 -62.90 168.61 21.18
2 20K 20K N CA 146 147 127.25 140.40 -40.80
3 3914 22F 23T C N 175 177 -53.19 -78.10 27.20 1.32 -63.20 179.32 22.35
3 23T 23T N CA 177 178 138.86 149.80 -42.10
4 3915 23T 24R C N 182 184 -65.99 -72.10 8.00 0.69 -63.00 171.86 23.42
4 24R 24R N CA 184 185 147.06 141.90 -41.10
5 3918 26G 27L C N 203 205 -63.64 -70.70 7.07 0.63 -63.50 177.70 24.68
5 27L 27L N CA 205 206 141.10 141.60 -41.20
6 3920 28V 29Q C N 218 220 -133.00 -121.10 31.30 1.25 -63.80 166.15 28.06
6 29Q 29Q N CA 220 221 168.64 139.70 -40.30
7 3921 29Q 30E C N 227 229 -128.80 -117.80 19.33 0.70 -63.60 179.27 27.58
7 30E 30E N CA 229 230 152.70 136.80 -40.30
8 3922 30E 31L C N 236 238 -100.23 -108.50 15.27 0.87 -63.50 177.30 26.86
8 31L 31L N CA 238 239 145.34 132.50 -41.20
9 3924 32R 33R C N 255 257 -93.53 -72.10 22.58 1.57 -63.00 172.62 25.42
9 33R 33R N CA 257 258 149.01 141.90 -41.10
10 3925 33R 34L C N 266 268 -131.80 -108.50 33.76 1.53 -63.50 175.68 28.62
10 34L 34L N CA 268 269 156.94 132.50 -41.20
11 3926 34L 35G C N 274 276 107.99 78.70 56.61 0.87 82.20 139.36 8.03
11 35G 35G N CA 276 277 145.46 -166.10 8.50
12 3929 37D 38E C N 297 299 58.36 54.60 5.55 0.33 -63.60 145.10 24.97
12 38E 38E N CA 299 300 38.31 42.40 -40.30
13 3943 51E 52S C N 411 413 -137.67 -64.10 81.54 8.56 -64.10 81.54 8.56
13 52S 52S N CA 413 414 0.16 -35.00 -35.00
14 3952 60G 61K C N 479 481 -69.34 -62.90 11.42 1.32 -70.20 171.77 12.42
14 61K 61K N CA 481 482 -31.37 -40.80 140.40
15 3981 89K 90D C N 711 713 169.54 -96.50 97.30 3.96 -63.30 -178.92 20.40
15 90D 90D N CA 713 714 88.92 114.20 -40.00
16 4007 115K 116R C N 905 907 -28.92 -125.20 96.29 3.86 -63.00 -178.32 22.44
16 116R 116R N CA 907 908 140.45 140.60 -41.10
17 4008 116R 117H C N 916 918 52.13 -63.20 157.13 26.53 -63.20 157.13 26.53
17 117H 117H N CA 918 919 64.42 -42.30 -42.30
18 4009 117H 118K C N 926 928 -63.20 -62.90 23.62 3.08 -118.00 165.80 8.55
18 118K 118K N CA 928 929 -64.42 -40.80 139.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 14 51 79 135 126 125 155 174 181
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 139
Number of all, selected real atoms : 1112 1112
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10727 10727
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2374
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 : 921.7354
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 : 1136 0 1 0.007 0.007 18.090 1.000
2 Bond angle potential : 1532 1 7 2.041 2.041 127.70 1.000
3 Stereochemical cosine torsion poten: 734 0 26 46.820 46.820 248.49 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.214 1.214 15.677 1.000
5 Soft-sphere overlap restraints : 2374 0 0 0.003 0.003 1.8951 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) : 2217 0 2 0.339 0.339 93.711 1.000
10 Distance restraints 2 (N-O) : 2375 0 5 0.417 0.417 144.10 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: 138 0 1 4.630 4.630 34.881 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 74.326 74.326 32.413 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 72.658 72.658 32.125 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 73.940 73.940 20.377 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 121.627 121.627 15.943 1.000
18 Disulfide distance restraints : 3 0 0 0.020 0.020 0.21795 1.000
19 Disulfide angle restraints : 6 0 0 2.124 2.124 0.59784 1.000
20 Disulfide dihedral angle restraints: 3 0 0 29.478 29.478 2.5588 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) : 1240 0 0 0.386 0.386 22.246 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: 137 21 21 31.672 68.708 82.604 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.601 0.601 28.116 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: LMP.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: 15528.9258
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 2119 90D 90D N CA 713 714 122.80 107.00 15.80 4.54 107.00 15.80 4.54
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3910 18D 19A C N 139 141 -84.90 -68.20 28.82 1.83 -62.50 151.97 26.06
1 19A 19A N CA 141 142 168.79 145.30 -40.90
2 3911 19A 20K C N 144 146 -89.48 -70.20 26.25 2.20 -62.90 165.54 20.19
2 20K 20K N CA 146 147 122.59 140.40 -40.80
3 3914 22F 23T C N 175 177 -76.34 -78.10 9.47 0.35 -63.20 177.89 23.68
3 23T 23T N CA 177 178 140.49 149.80 -42.10
4 3915 23T 24R C N 182 184 -81.49 -72.10 13.62 1.18 -63.00 174.11 22.33
4 24R 24R N CA 184 185 132.03 141.90 -41.10
5 3917 25C 26G C N 199 201 -85.04 -80.20 6.60 0.22 82.20 -121.47 7.39
5 26G 26G N CA 201 202 178.59 174.10 8.50
6 3918 26G 27L C N 203 205 -93.50 -108.50 20.34 0.91 -63.50 162.75 21.07
6 27L 27L N CA 205 206 118.76 132.50 -41.20
7 3922 30E 31L C N 236 238 -59.70 -70.70 11.64 0.92 -63.50 179.05 25.08
7 31L 31L N CA 238 239 137.81 141.60 -41.20
8 3923 31L 32R C N 244 246 -72.40 -72.10 11.63 0.89 -63.00 165.64 23.01
8 32R 32R N CA 246 247 153.53 141.90 -41.10
9 3924 32R 33R C N 255 257 -106.54 -125.20 30.73 1.70 -63.00 159.93 24.62
9 33R 33R N CA 257 258 165.01 140.60 -41.10
10 3925 33R 34L C N 266 268 -90.54 -70.70 89.97 6.11 -63.50 93.44 14.64
10 34L 34L N CA 268 269 -130.64 141.60 -41.20
11 3926 34L 35G C N 274 276 117.57 78.70 71.59 1.14 82.20 130.17 8.02
11 35G 35G N CA 276 277 133.77 -166.10 8.50
12 3929 37D 38E C N 297 299 54.61 54.60 1.14 0.09 -63.60 143.62 24.69
12 38E 38E N CA 299 300 41.26 42.40 -40.30
13 3952 60G 61K C N 479 481 -95.21 -118.00 92.53 4.13 -70.20 94.35 7.39
13 61K 61K N CA 481 482 49.42 139.10 140.40
14 3953 61K 62V C N 488 490 -64.14 -62.40 6.80 0.78 -125.40 -170.69 7.64
14 62V 62V N CA 490 491 -35.82 -42.40 143.30
15 3956 64K 65N C N 512 514 -73.94 -119.90 63.89 3.46 -63.20 137.94 17.84
15 65N 65N N CA 514 515 -178.62 137.00 -41.10
16 3957 65N 66G C N 520 522 -61.17 -62.40 14.31 2.20 82.20 147.69 10.97
16 66G 66G N CA 522 523 -26.95 -41.20 8.50
17 3981 89K 90D C N 711 713 166.98 -96.50 97.81 3.98 -63.30 -170.34 21.17
17 90D 90D N CA 713 714 98.36 114.20 -40.00
18 4005 113I 114Y C N 884 886 -34.08 -98.40 66.36 3.20 -63.50 158.22 26.62
18 114Y 114Y N CA 886 887 112.06 128.40 -43.40
19 4007 115K 116R C N 905 907 -64.58 -125.20 60.72 2.35 -63.00 178.32 23.98
19 116R 116R N CA 907 908 137.22 140.60 -41.10
20 4008 116R 117H C N 916 918 59.89 -63.20 166.62 28.16 -63.20 166.62 28.16
20 117H 117H N CA 918 919 70.01 -42.30 -42.30
21 4009 117H 118K C N 926 928 -60.75 -62.90 29.00 3.65 -118.00 161.66 8.35
21 118K 118K N CA 928 929 -69.72 -40.80 139.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 9 64 88 112 111 141 174 175 193
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LMP.B99990001.pdb 913.57062
LMP.B99990002.pdb 921.73541
In [19]:
# визуализация результата
import nglview
import ipywidgets
w1 = nglview.show_structure_file('LMP.B99990001.pdb')
w1
Мы получили модель, однако лиганд был полностью проигнорирован. Чтобы это исправить, нужно к последовательности нашего лизоцима добавить "...", что позволит считать три дополнительных остатка лиганда, которые есть в структуре лизоцима форели.
In [20]:
string=""
for i in alignm[0].residues:
string=string+i.code
string=string+"..."
out=open("With.fasta","w")
out.write(">WithLigand\n"+string)
out.close()
In [21]:
alignm.append(file='With.fasta', align_codes='all',alignment_format='FASTA')
Out[21]:
1
In [22]:
alignm.salign()
alignm.write(file='all_in_one(2).ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [23]:
## 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(2).ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
WithLigand 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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C +N
atom indices : 1110 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C CA +N O
atom indices : 1110 1107 0 1111
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM 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: 13083 12116
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2538
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 : 1111.7734
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 : 1136 0 1 0.009 0.009 25.447 1.000
2 Bond angle potential : 1532 4 13 3.020 3.020 191.62 1.000
3 Stereochemical cosine torsion poten: 734 0 25 47.346 47.346 253.27 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.427 1.427 20.749 1.000
5 Soft-sphere overlap restraints : 2538 1 2 0.007 0.007 15.931 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) : 2217 0 3 0.329 0.329 93.662 1.000
10 Distance restraints 2 (N-O) : 2375 0 7 0.384 0.384 149.87 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: 138 0 3 4.535 4.535 33.475 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 74.598 74.598 48.006 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 1 72.490 72.490 40.974 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 78.105 78.105 20.359 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 97.365 97.365 11.284 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.38530 1.000
19 Disulfide angle restraints : 6 0 0 2.973 2.973 1.1712 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.146 21.146 1.2684 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) : 1240 0 0 0.491 0.491 32.266 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: 137 16 23 31.661 57.616 98.564 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 1 0.789 0.789 47.409 1.000
27 Distance restraints 5 (X-Y) : 1389 0 0 0.049 0.049 26.057 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: WithLigand.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: 15849.0117
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 1970 76N 76N ND2 CG 608 606 139.41 122.50 16.91 4.71 122.50 16.91 4.71
2 2119 90D 90D N CA 713 714 125.32 107.00 18.32 5.27 107.00 18.32 5.27
-------------------------------------------------------------------------------------------------
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 3909 17C 18D C N 131 133 -125.12 -63.30 61.82 9.78 -96.50 156.32 6.54
1 18D 18D N CA 133 134 -39.48 -40.00 114.20
2 3910 18D 19A C N 139 141 -65.65 -68.20 10.72 0.95 -62.50 163.42 26.94
2 19A 19A N CA 141 142 155.72 145.30 -40.90
3 3911 19A 20K C N 144 146 -120.10 -118.00 36.14 1.73 -62.90 154.96 23.54
3 20K 20K N CA 146 147 175.18 139.10 -40.80
4 3912 20K 21R C N 153 155 -72.85 -72.10 22.26 1.70 -63.00 155.07 21.62
4 21R 21R N CA 155 156 164.15 141.90 -41.10
5 3913 21R 22F C N 164 166 -72.53 -71.40 44.08 3.58 -63.20 141.25 18.99
5 22F 22F N CA 166 167 96.64 140.70 -44.30
6 3914 22F 23T C N 175 177 -165.44 -124.80 117.44 3.95 -63.20 120.74 20.81
6 23T 23T N CA 177 178 -106.32 143.50 -42.10
7 3915 23T 24R C N 182 184 -51.71 -72.10 20.40 1.54 -63.00 178.02 23.31
7 24R 24R N CA 184 185 141.24 141.90 -41.10
8 3917 25C 26G C N 199 201 105.16 78.70 72.19 1.13 82.20 120.44 6.97
8 26G 26G N CA 201 202 126.74 -166.10 8.50
9 3920 28V 29Q C N 218 220 -127.30 -121.10 22.63 0.96 -63.80 170.50 28.42
9 29Q 29Q N CA 220 221 161.47 139.70 -40.30
10 3922 30E 31L C N 236 238 -106.70 -108.50 8.79 0.49 -63.50 -177.14 28.04
10 31L 31L N CA 238 239 141.11 132.50 -41.20
11 3923 31L 32R C N 244 246 -82.64 -72.10 65.71 5.28 -63.00 119.76 14.95
11 32R 32R N CA 246 247 77.04 141.90 -41.10
12 3925 33R 34L C N 266 268 -59.53 -70.70 11.72 0.93 -63.50 179.29 25.12
12 34L 34L N CA 268 269 138.05 141.60 -41.20
13 3926 34L 35G C N 274 276 95.38 78.70 51.02 0.84 82.20 137.82 7.35
13 35G 35G N CA 276 277 145.69 -166.10 8.50
14 3929 37D 38E C N 297 299 57.61 54.60 4.17 0.26 -63.60 145.12 24.97
14 38E 38E N CA 299 300 39.51 42.40 -40.30
15 3952 60G 61K C N 479 481 -100.45 -118.00 86.86 3.95 -70.20 91.51 7.28
15 61K 61K N CA 481 482 54.03 139.10 140.40
16 3981 89K 90D C N 711 713 -147.27 -63.30 91.22 15.54 -63.30 91.22 15.54
16 90D 90D N CA 713 714 -75.63 -40.00 -40.00
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 15 16 76 92 130 153 130 169 172 176
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2546
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 : 1095.9680
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 : 1136 0 1 0.009 0.009 24.736 1.000
2 Bond angle potential : 1532 1 7 2.252 2.252 154.69 1.000
3 Stereochemical cosine torsion poten: 734 0 29 47.857 47.857 267.53 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.392 1.392 19.692 1.000
5 Soft-sphere overlap restraints : 2546 1 2 0.007 0.007 16.457 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) : 2217 0 3 0.362 0.362 106.24 1.000
10 Distance restraints 2 (N-O) : 2375 0 8 0.407 0.407 153.51 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: 138 0 3 4.830 4.830 37.962 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 79.011 79.011 50.505 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 68.337 68.337 38.113 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 80.625 80.625 20.017 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 84.230 84.230 10.987 1.000
18 Disulfide distance restraints : 3 0 0 0.026 0.026 0.34329 1.000
19 Disulfide angle restraints : 6 0 0 2.298 2.298 0.69960 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.371 22.371 1.5847 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) : 1240 0 0 0.422 0.422 22.659 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: 137 23 20 31.722 72.673 101.14 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.844 0.844 34.012 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.056 0.056 35.094 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: WithLigand.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: 17609.4668
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 2119 90D 90D N CA 713 714 128.15 107.00 21.15 6.08 107.00 21.15 6.08
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -159.91 -134.00 30.85 0.74 -62.50 -176.61 35.23
1 19A 19A N CA 141 142 163.73 147.00 -40.90
2 3911 19A 20K C N 144 146 -112.97 -118.00 5.60 0.26 -62.90 -175.45 26.93
2 20K 20K N CA 146 147 141.57 139.10 -40.80
3 3912 20K 21R C N 153 155 -147.22 -125.20 31.39 0.96 -63.00 177.21 29.63
3 21R 21R N CA 155 156 162.98 140.60 -41.10
4 3913 21R 22F C N 164 166 -99.96 -124.20 37.79 1.07 -63.20 162.82 20.28
4 22F 22F N CA 166 167 114.32 143.30 -44.30
5 3914 22F 23T C N 175 177 -153.14 -124.80 33.69 1.24 -63.20 -179.78 28.88
5 23T 23T N CA 177 178 161.72 143.50 -42.10
6 3915 23T 24R C N 182 184 -130.62 -125.20 12.36 0.46 -63.00 -179.65 29.01
6 24R 24R N CA 184 185 151.70 140.60 -41.10
7 3917 25C 26G C N 199 201 -131.58 -167.20 92.16 2.97 82.20 167.20 13.03
7 26G 26G N CA 201 202 89.60 174.60 8.50
8 3918 26G 27L C N 203 205 -123.84 -108.50 33.40 1.61 -63.50 167.85 27.04
8 27L 27L N CA 205 206 162.17 132.50 -41.20
9 3919 27L 28V C N 211 213 -59.34 -62.40 5.14 0.83 -125.40 -169.73 10.69
9 28V 28V N CA 213 214 -38.27 -42.40 143.30
10 3920 28V 29Q C N 218 220 -112.49 -121.10 10.13 0.49 -63.80 -178.67 29.26
10 29Q 29Q N CA 220 221 145.03 139.70 -40.30
11 3921 29Q 30E C N 227 229 -88.36 -69.30 22.07 1.99 -63.60 173.45 21.86
11 30E 30E N CA 229 230 131.37 142.50 -40.30
12 3922 30E 31L C N 236 238 -121.41 -108.50 16.70 0.74 -63.50 -175.01 29.26
12 31L 31L N CA 238 239 143.10 132.50 -41.20
13 3923 31L 32R C N 244 246 -122.96 -125.20 4.47 0.25 -63.00 -175.54 29.06
13 32R 32R N CA 246 247 144.46 140.60 -41.10
14 3924 32R 33R C N 255 257 -76.53 -72.10 6.73 0.44 -63.00 172.46 24.22
14 33R 33R N CA 257 258 146.97 141.90 -41.10
15 3925 33R 34L C N 266 268 -149.14 -108.50 55.54 2.49 -63.50 171.37 29.06
15 34L 34L N CA 268 269 170.37 132.50 -41.20
16 3926 34L 35G C N 274 276 88.13 78.70 16.72 0.27 82.20 171.69 8.63
16 35G 35G N CA 276 277 -179.91 -166.10 8.50
17 3929 37D 38E C N 297 299 64.30 54.60 16.36 0.87 -63.60 145.57 25.03
17 38E 38E N CA 299 300 29.23 42.40 -40.30
18 3943 51E 52S C N 411 413 -139.91 -64.10 84.94 8.79 -64.10 84.94 8.79
18 52S 52S N CA 413 414 3.31 -35.00 -35.00
19 3981 89K 90D C N 711 713 171.89 -96.50 94.94 3.86 -63.30 179.68 20.16
19 90D 90D N CA 713 714 89.26 114.20 -40.00
20 4007 115K 116R C N 905 907 -55.74 -125.20 77.61 2.36 -63.00 147.26 20.38
20 116R 116R N CA 907 908 105.98 140.60 -41.10
21 4008 116R 117H C N 916 918 170.35 -63.20 127.13 19.48 -63.20 127.13 19.48
21 117H 117H N CA 918 919 -29.13 -42.30 -42.30
22 4009 117H 118K C N 926 928 59.63 -70.20 151.30 12.49 -118.00 -165.60 8.82
22 118K 118K N CA 928 929 -141.92 140.40 139.10
23 4020 128H 129C C N 1030 1032 -126.63 -63.00 75.86 9.68 -63.00 75.86 9.68
23 129C 129C N CA 1032 1033 0.22 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 11 15 71 104 132 110 151 171 173 214
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
WithLigand.B99990001.pdb 1111.77344
WithLigand.B99990002.pdb 1095.96802
In [25]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('WithLigand.B99990002.pdb')
w1
Структура с лигандом.