In [3]:
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
from IPython.display import display,Image
Задаем некторые параметры:
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): 2017/05/18 18:02:06
Загружаем белок-заготовку и последовательность LYS_HYPCU (идентификатор P50717):
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-05-18 18:02:06-- 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]
--2017-05-18 18:02:07-- 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]
--2017-05-18 18:02:07-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 132.249.213.140
Connecting to files.rcsb.org|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb.1'
[ <=> ] 131,301 160K/s in 0.8s
2017-05-18 18:02:09 (160 KB/s) - `1lmp.pdb.1' saved [131301]
In [4]:
#LYS_HYPCU
! wget http://www.uniprot.org/uniprot/P50717.fasta
--2017-05-18 18:02:09-- http://www.uniprot.org/uniprot/P50717.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: `P50717.fasta.1' 100%[======================================>] 205 --.-K/s in 0s 2017-05-18 18:02:09 (12.1 MB/s) - `P50717.fasta.1' saved [205/205]
Создаем объект выравнивание и добавим в него последовательность и структуру:
In [5]:
alignm=modeller.alignment(env)
In [6]:
alignm.append(file='P50717.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')
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.
read_pd_459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [7]:
alignm[0].code=alignm[0].code[3:9] #переименовываем идентификатор
Делаем выравнивание и сохраняем:
In [8]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Строим модель:
In [9]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
P50717 1lmp
In [10]:
## 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()
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
----------------------------------------------
92 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C +N
atom indices : 1134 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C CA +N O
atom indices : 1134 1131 0 1135
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: 11929 10925
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 : 1136 1136
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10925 10925
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2446
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 : 1142.8545
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 : 1161 0 1 0.008 0.008 19.168 1.000
2 Bond angle potential : 1566 1 6 2.298 2.298 161.26 1.000
3 Stereochemical cosine torsion poten: 750 0 26 47.095 47.095 263.85 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.363 1.363 18.720 1.000
5 Soft-sphere overlap restraints : 2446 0 0 0.003 0.003 2.4075 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) : 2232 0 4 0.395 0.395 125.49 1.000
10 Distance restraints 2 (N-O) : 2390 0 16 0.471 0.471 194.26 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: 141 0 2 4.781 4.781 38.006 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 80.639 80.639 35.520 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 1 68.224 68.224 42.219 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 80.856 80.856 26.881 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 95.819 95.819 15.758 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27281 1.000
19 Disulfide angle restraints : 6 0 0 2.541 2.541 0.85534 1.000
20 Disulfide dihedral angle restraints: 3 0 0 27.007 27.007 2.1550 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) : 1269 0 0 0.409 0.409 25.906 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: 140 25 22 34.792 67.862 137.56 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 0 0.664 0.664 32.565 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: P50717.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: 17391.6660
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 2170 92D 92D N CA 729 730 124.37 107.00 17.37 5.00 107.00 17.37 5.00
-------------------------------------------------------------------------------------------------
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 3979 9F 10A C N 75 77 -120.55 -134.00 54.99 3.34 -62.50 132.21 24.78
1 10A 10A N CA 77 78 -159.68 147.00 -40.90
2 3980 10A 11I C N 80 82 -66.54 -63.40 5.71 0.87 -120.60 177.56 8.18
2 11I 11I N CA 82 83 -38.83 -43.60 130.30
3 3981 11I 12A C N 88 90 -44.73 -68.20 33.77 2.13 -62.50 162.89 27.60
3 12A 12A N CA 90 91 121.02 145.30 -40.90
4 3982 12A 13A C N 93 95 -143.46 -134.00 9.84 0.43 -62.50 -167.33 35.91
4 13A 13A N CA 95 96 144.27 147.00 -40.90
5 3985 15C 16I C N 111 113 -63.74 -63.40 1.78 0.28 -120.60 -178.69 8.30
5 16I 16I N CA 113 114 -41.86 -43.60 130.30
6 3986 16I 17H C N 119 121 62.07 56.30 16.19 1.16 -63.20 142.52 24.48
6 17H 17H N CA 121 122 25.67 40.80 -42.30
7 3988 18C 19E C N 135 137 -153.45 -117.80 40.81 1.19 -63.60 -173.84 29.80
7 19E 19E N CA 137 138 156.66 136.80 -40.30
8 3990 20A 21K C N 149 151 -102.18 -118.00 17.36 0.58 -62.90 177.15 21.18
8 21K 21K N CA 151 152 131.94 139.10 -40.80
9 3991 21K 22Y C N 158 160 -66.76 -98.40 36.93 2.24 -63.50 169.19 27.01
9 22Y 22Y N CA 160 161 147.44 128.40 -43.40
10 3992 22Y 23Y C N 170 172 -134.17 -124.30 62.60 2.91 -63.50 138.73 25.38
10 23Y 23Y N CA 172 173 -162.78 135.40 -43.40
11 3993 23Y 24S C N 182 184 -55.72 -72.40 32.24 1.48 -64.10 160.03 12.11
11 24S 24S N CA 184 185 124.81 152.40 -35.00
12 3994 24S 25T C N 188 190 -99.44 -78.10 46.49 1.52 -63.20 131.88 19.33
12 25T 25T N CA 190 191 -168.90 149.80 -42.10
13 3995 25T 26R C N 195 197 -76.27 -72.10 53.88 4.23 -63.00 129.95 16.70
13 26R 26R N CA 197 198 88.18 141.90 -41.10
14 3997 27C 28D C N 212 214 -66.98 -70.90 18.50 0.73 -63.30 172.25 21.04
14 28D 28D N CA 214 215 132.21 150.30 -40.00
15 4007 37G 38F C N 296 298 -61.58 -63.20 22.15 2.97 -124.20 162.83 8.83
15 38F 38F N CA 298 299 -66.39 -44.30 143.30
16 4008 38F 39P C N 307 309 -83.62 -58.70 63.76 3.77 -64.50 120.54 10.03
16 39P 39P N CA 309 310 28.19 -30.50 147.20
17 4023 53E 54S C N 428 430 -134.92 -64.10 77.98 8.26 -64.10 77.98 8.26
17 54S 54S N CA 430 431 -2.36 -35.00 -35.00
18 4054 84S 85N C N 674 676 -117.51 -63.20 71.00 8.15 -63.20 71.00 8.15
18 85N 85N N CA 676 677 4.62 -41.10 -41.10
19 4061 91K 92D C N 727 729 -135.23 -63.30 82.02 14.01 -63.30 82.02 14.01
19 92D 92D N CA 729 730 -79.41 -40.00 -40.00
20 4063 93C 94N C N 741 743 -179.44 -63.20 119.18 19.04 55.90 164.22 10.66
20 94N 94N N CA 743 744 -67.39 -41.10 39.50
21 4085 115I 116F C N 901 903 -46.41 -124.20 87.21 2.37 -63.20 149.13 21.84
21 116F 116F N CA 903 904 103.89 143.30 -44.30
22 4089 119H 120N C N 942 944 56.54 -71.20 146.33 11.79 -119.90 -167.42 9.71
22 120N 120N N CA 944 945 -145.82 142.80 137.00
23 4100 130H 131C C N 1050 1052 -113.02 -63.00 51.58 7.83 -63.00 51.58 7.83
23 131C 131C N CA 1052 1053 -28.52 -41.10 -41.10
24 4106 136L 137P C N 1092 1094 -61.36 -64.50 6.72 0.67 -58.70 176.39 14.79
24 137P 137P N CA 1094 1095 153.14 147.20 -30.50
25 4107 137P 138D C N 1099 1101 104.91 -63.30 168.27 26.90 -63.30 168.27 26.90
25 138D 138D N CA 1101 1102 -35.64 -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 10 21 81 81 107 118 125 151 181 206
<< 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 : 142
Number of all, selected real atoms : 1136 1136
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10925 10925
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2427
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 : 1002.8312
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 : 1161 0 1 0.007 0.007 17.203 1.000
2 Bond angle potential : 1566 1 6 2.145 2.145 143.09 1.000
3 Stereochemical cosine torsion poten: 750 0 25 46.301 46.301 252.45 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.131 1.131 13.806 1.000
5 Soft-sphere overlap restraints : 2427 0 0 0.003 0.003 2.2040 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) : 2232 0 1 0.377 0.377 101.42 1.000
10 Distance restraints 2 (N-O) : 2390 0 9 0.451 0.451 160.04 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: 141 1 2 4.743 4.743 37.412 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 74.639 74.639 34.342 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 0 75.037 75.037 36.831 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 84.601 84.601 26.072 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 101.364 101.364 14.603 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27579 1.000
19 Disulfide angle restraints : 6 0 0 2.219 2.219 0.65212 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.321 25.321 1.9333 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) : 1269 0 0 0.357 0.357 25.037 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: 140 18 22 32.073 60.088 106.44 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 0 0.579 0.579 29.012 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: P50717.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: 15960.9502
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 2170 92D 92D N CA 729 730 124.09 107.00 17.09 4.91 107.00 17.09 4.91
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 38F 38F CA C 299 307 -156.26 -180.00 23.74 4.75 -180.00 23.74 4.75
-------------------------------------------------------------------------------------------------
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 3979 9F 10A C N 75 77 -137.49 -134.00 61.68 3.42 -62.50 133.56 25.86
1 10A 10A N CA 77 78 -151.42 147.00 -40.90
2 3981 11I 12A C N 88 90 -68.78 -68.20 15.30 1.21 -62.50 158.63 26.31
2 12A 12A N CA 90 91 160.59 145.30 -40.90
3 3982 12A 13A C N 93 95 -111.18 -134.00 25.80 1.31 -62.50 167.30 30.01
3 13A 13A N CA 95 96 159.04 147.00 -40.90
4 3986 16I 17H C N 119 121 -177.54 -125.60 90.64 2.39 -63.20 154.98 26.19
4 17H 17H N CA 121 122 -146.91 138.80 -42.30
5 3988 18C 19E C N 135 137 -65.82 -69.30 4.39 0.25 -63.60 179.89 24.11
5 19E 19E N CA 137 138 139.82 142.50 -40.30
6 3990 20A 21K C N 149 151 97.20 56.60 103.55 10.53 -62.90 -123.07 39.99
6 21K 21K N CA 151 152 133.86 38.60 -40.80
7 3993 23Y 24S C N 182 184 -130.45 -136.60 18.08 0.77 -64.10 -178.26 11.24
7 24S 24S N CA 184 185 134.20 151.20 -35.00
8 3994 24S 25T C N 188 190 -90.32 -78.10 43.20 1.50 -63.20 129.53 18.42
8 25T 25T N CA 190 191 -168.76 149.80 -42.10
9 3995 25T 26R C N 195 197 -65.45 -72.10 9.65 0.63 -63.00 176.03 23.62
9 26R 26R N CA 197 198 134.92 141.90 -41.10
10 3997 27C 28D C N 212 214 -56.01 -70.90 32.54 1.09 -63.30 161.53 20.39
10 28D 28D N CA 214 215 121.37 150.30 -40.00
11 4023 53E 54S C N 428 430 -138.64 -64.10 82.81 8.67 -64.10 82.81 8.67
11 54S 54S N CA 430 431 1.07 -35.00 -35.00
12 4054 84S 85N C N 674 676 -115.16 -119.90 28.50 1.40 -63.20 162.34 23.25
12 85N 85N N CA 676 677 165.11 137.00 -41.10
13 4055 85N 86T C N 682 684 -72.76 -63.20 10.43 1.36 55.90 150.16 18.49
13 86T 86T N CA 684 685 -37.93 -42.10 39.50
14 4061 91K 92D C N 727 729 -135.22 -63.30 79.77 13.61 -63.30 79.77 13.61
14 92D 92D N CA 729 730 -74.49 -40.00 -40.00
15 4074 104D 105I C N 822 824 -107.01 -63.40 78.52 11.94 -63.40 78.52 11.94
15 105I 105I N CA 824 825 21.70 -43.60 -43.60
16 4085 115I 116F C N 901 903 -51.13 -124.20 82.55 2.23 -63.20 149.68 21.60
16 116F 116F N CA 903 904 104.89 143.30 -44.30
17 4099 129N 130H C N 1040 1042 -120.59 -63.20 71.95 8.59 -63.20 71.95 8.59
17 130H 130H N CA 1042 1043 1.10 -42.30 -42.30
18 4100 130H 131C C N 1050 1052 -122.44 -63.00 60.10 9.51 -63.00 60.10 9.51
18 131C 131C N CA 1052 1053 -32.21 -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 10 23 64 70 127 116 144 151 170 191
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P50717.B99990001.pdb 1142.85449
P50717.B99990002.pdb 1002.83118
Проверяем все ли в порядке:
In [4]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('P50717.B99990001.pdb')
w2 = nglview.show_structure_file('P50717.B99990002.pdb')
#изобразим первую модель
Image(url="model1.png")
Out[4]:
Понимаем, что лиганда в выравнивании нет. Приписываем к последовательности "..." (обозначение лиганда):
In [12]:
seq=''
for i in alignm[0].residues:
seq=seq+i.code
seq_with_ligand=seq+"..."
seq_with_ligand
Out[12]:
'MQKLAVFLFAIAAVCIHCEAKYYSTRCDLVRELRKQGFPENQMGDWVCLVENESGRKTDKVGPVNKNGSKDYGLFQINDKYWCSNTRTPGKDCNVTCADLLLDDITKASTCAKKIFKRHNFRAWYGWRNHCDGKTLPDTSNC...'
Добавляем в выравнивание:
In [13]:
alignm.append_sequence(seq_with_ligand)
In [14]:
alignm[2].code = "P50717_with_ligand"
In [15]:
s_with_ligand=alignm[2]
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
b = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s_with_ligand.code)
b.name='mod'+s_with_ligand.code
b.starting_model = 1
b.ending_model = 2
b.make()
SALIGN_____> adding the next group to the alignment; iteration 1
SALIGN_____> adding the next group to the alignment; iteration 2
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
----------------------------------------------
92 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C +N
atom indices : 1134 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C CA +N O
atom indices : 1134 1131 0 1135
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: 13318 12314
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.
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 : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12314 12314
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2439
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 : 1346.7565
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 : 1161 0 1 0.009 0.009 24.278 1.000
2 Bond angle potential : 1566 3 13 3.203 3.203 225.22 1.000
3 Stereochemical cosine torsion poten: 750 0 27 46.855 46.855 261.04 1.000
4 Stereochemical improper torsion pot: 481 0 1 1.433 1.433 21.549 1.000
5 Soft-sphere overlap restraints : 2439 1 2 0.008 0.008 18.572 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) : 2232 0 4 0.373 0.373 118.52 1.000
10 Distance restraints 2 (N-O) : 2390 3 26 0.512 0.512 292.04 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: 141 0 9 5.705 5.705 54.127 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 3 75.764 75.764 35.302 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 0 71.791 71.791 34.780 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 1 70.723 70.723 24.032 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 91.897 91.897 13.582 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.36737 1.000
19 Disulfide angle restraints : 6 0 0 3.861 3.861 1.9752 1.000
20 Disulfide dihedral angle restraints: 3 0 0 16.619 16.619 0.90564 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) : 1269 0 0 0.496 0.496 38.507 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: 140 24 24 31.848 68.241 122.82 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 1 0.627 0.627 32.433 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.049 0.049 26.705 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: P50717_with_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: 17973.4746
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 2170 92D 92D N CA 729 730 125.53 107.00 18.53 5.33 107.00 18.53 5.33
-------------------------------------------------------------------------------------------------
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 3979 9F 10A C N 75 77 -162.85 -134.00 75.78 3.42 -62.50 143.11 28.56
1 10A 10A N CA 77 78 -142.93 147.00 -40.90
2 3981 11I 12A C N 88 90 -59.32 -68.20 14.39 0.91 -62.50 174.90 28.82
2 12A 12A N CA 90 91 133.97 145.30 -40.90
3 3986 16I 17H C N 119 121 -125.00 -125.60 22.26 0.86 -63.20 168.40 25.10
3 17H 17H N CA 121 122 161.05 138.80 -42.30
4 3988 18C 19E C N 135 137 -100.01 -117.80 31.40 1.13 -63.60 155.55 18.98
4 19E 19E N CA 137 138 110.93 136.80 -40.30
5 3989 19E 20A C N 144 146 -155.47 -134.00 27.07 0.70 -62.50 -178.73 34.66
5 20A 20A N CA 146 147 163.49 147.00 -40.90
6 3990 20A 21K C N 149 151 -141.54 -118.00 34.19 1.73 -62.90 173.91 19.98
6 21K 21K N CA 151 152 114.31 139.10 -40.80
7 3991 21K 22Y C N 158 160 -148.40 -124.30 48.30 1.90 -63.50 163.17 29.92
7 22Y 22Y N CA 160 161 177.25 135.40 -43.40
8 3992 22Y 23Y C N 170 172 -126.80 -124.30 23.27 1.13 -63.50 170.27 30.18
8 23Y 23Y N CA 172 173 158.53 135.40 -43.40
9 3993 23Y 24S C N 182 184 -177.80 -136.60 47.57 1.45 -64.10 -171.76 21.84
9 24S 24S N CA 184 185 174.97 151.20 -35.00
10 3994 24S 25T C N 188 190 -104.59 -124.80 35.25 1.09 -63.20 162.09 18.36
10 25T 25T N CA 190 191 114.62 143.50 -42.10
11 3995 25T 26R C N 195 197 -136.38 -125.20 60.48 3.14 -63.00 142.59 16.13
11 26R 26R N CA 197 198 81.16 140.60 -41.10
12 3997 27C 28D C N 212 214 -96.31 -70.90 77.58 2.76 -63.30 101.89 14.71
12 28D 28D N CA 214 215 -136.40 150.30 -40.00
13 4007 37G 38F C N 296 298 -60.00 -63.20 26.20 3.43 -124.20 159.85 8.70
13 38F 38F N CA 298 299 -70.31 -44.30 143.30
14 4008 38F 39P C N 307 309 -85.35 -58.70 65.55 3.85 -64.50 119.64 10.06
14 39P 39P N CA 309 310 29.39 -30.50 147.20
15 4023 53E 54S C N 428 430 -147.87 -136.60 26.13 1.48 -64.10 -177.07 11.72
15 54S 54S N CA 430 431 127.62 151.20 -35.00
16 4024 54S 55G C N 434 436 -44.37 -62.40 23.45 4.39 82.20 131.24 9.82
16 55G 55G N CA 436 437 -26.20 -41.20 8.50
17 4025 55G 56R C N 438 440 156.15 57.30 99.14 11.19 57.30 99.14 11.19
17 56R 56R N CA 440 441 30.39 38.00 38.00
18 4054 84S 85N C N 674 676 -111.65 -119.90 37.97 1.90 -63.20 152.73 21.85
18 85N 85N N CA 676 677 174.07 137.00 -41.10
19 4055 85N 86T C N 682 684 -75.03 -63.20 15.00 1.73 55.90 149.60 18.46
19 86T 86T N CA 684 685 -32.88 -42.10 39.50
20 4061 91K 92D C N 727 729 -135.36 -63.30 78.79 13.43 -63.30 78.79 13.43
20 92D 92D N CA 729 730 -71.85 -40.00 -40.00
21 4085 115I 116F C N 901 903 -43.15 -124.20 93.04 2.48 -63.20 143.31 21.25
21 116F 116F N CA 903 904 97.60 143.30 -44.30
22 4100 130H 131C C N 1050 1052 -121.79 -63.00 64.39 8.97 -63.00 64.39 8.97
22 131C 131C N CA 1052 1053 -14.83 -41.10 -41.10
23 4101 131C 132D C N 1056 1058 -55.90 -63.30 23.99 2.61 -70.90 147.65 8.03
23 132D 132D N CA 1058 1059 -62.82 -40.00 150.30
24 4102 132D 133G C N 1064 1066 -73.57 -62.40 14.03 2.05 82.20 161.13 12.03
24 133G 133G N CA 1066 1067 -32.70 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 15 21 75 84 123 105 124 160 169 187
<< 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 : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12314 12314
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2531
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 : 1349.6533
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 : 1161 0 1 0.008 0.008 23.469 1.000
2 Bond angle potential : 1566 2 12 2.451 2.451 184.61 1.000
3 Stereochemical cosine torsion poten: 750 0 31 48.955 48.955 281.21 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.380 1.380 20.582 1.000
5 Soft-sphere overlap restraints : 2531 1 2 0.008 0.008 19.104 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) : 2232 0 9 0.413 0.413 157.98 1.000
10 Distance restraints 2 (N-O) : 2390 1 22 0.514 0.514 228.50 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: 141 1 5 6.107 6.107 62.018 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 4 79.428 79.428 46.535 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 1 65.040 65.040 34.221 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 69.743 69.743 22.291 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 88.036 88.036 15.843 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32521 1.000
19 Disulfide angle restraints : 6 0 0 3.458 3.458 1.5841 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.892 21.892 1.4169 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) : 1269 0 0 0.402 0.402 25.830 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: 140 26 24 37.473 74.108 157.82 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 1 0.680 0.680 36.482 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.052 0.052 29.831 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: P50717_with_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: 18640.8125
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 1492 31R 31R N CA 237 238 122.76 107.00 15.76 4.53 107.00 15.76 4.53
2 2170 92D 92D N CA 729 730 124.64 107.00 17.64 5.07 107.00 17.64 5.07
-------------------------------------------------------------------------------------------------
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 7034 35K 10A N O 276 81 11.74 7.94 3.81 4.53 7.94 3.81 4.53
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3979 9F 10A C N 75 77 -153.92 -134.00 20.03 0.74 -62.50 -163.28 37.13
1 10A 10A N CA 77 78 144.92 147.00 -40.90
2 3981 11I 12A C N 88 90 -112.91 -134.00 25.65 0.63 -62.50 -179.52 27.58
2 12A 12A N CA 90 91 132.39 147.00 -40.90
3 3982 12A 13A C N 93 95 -105.13 -134.00 29.18 0.82 -62.50 -178.57 31.98
3 13A 13A N CA 95 96 142.75 147.00 -40.90
4 3986 16I 17H C N 119 121 -170.75 -125.60 66.72 1.67 -63.20 168.55 27.77
4 17H 17H N CA 121 122 -172.08 138.80 -42.30
5 3988 18C 19E C N 135 137 -62.11 -69.30 9.38 0.53 -63.60 176.78 23.65
5 19E 19E N CA 137 138 136.47 142.50 -40.30
6 3989 19E 20A C N 144 146 -129.83 -134.00 26.38 1.39 -62.50 175.29 26.39
6 20A 20A N CA 146 147 120.95 147.00 -40.90
7 3990 20A 21K C N 149 151 -104.86 -118.00 24.09 0.93 -62.90 165.13 19.56
7 21K 21K N CA 151 152 118.91 139.10 -40.80
8 3991 21K 22Y C N 158 160 -106.99 -98.40 13.07 1.06 -63.50 167.69 24.54
8 22Y 22Y N CA 160 161 118.55 128.40 -43.40
9 3992 22Y 23Y C N 170 172 -108.80 -98.40 16.28 1.34 -63.50 165.59 24.14
9 23Y 23Y N CA 172 173 115.88 128.40 -43.40
10 3993 23Y 24S C N 182 184 159.17 -136.60 90.23 2.90 -64.10 175.75 22.38
10 24S 24S N CA 184 185 -145.43 151.20 -35.00
11 3994 24S 25T C N 188 190 -60.99 -78.10 17.71 1.15 -63.20 163.55 20.83
11 25T 25T N CA 190 191 154.37 149.80 -42.10
12 3995 25T 26R C N 195 197 -102.12 -125.20 29.34 1.58 -63.00 164.90 24.98
12 26R 26R N CA 197 198 158.71 140.60 -41.10
13 3997 27C 28D C N 212 214 -132.12 -96.50 57.20 2.40 -63.30 175.13 26.06
13 28D 28D N CA 214 215 158.96 114.20 -40.00
14 4000 30V 31R C N 235 237 108.66 -125.20 128.74 4.52 -63.00 -130.32 27.75
14 31R 31R N CA 237 238 166.31 140.60 -41.10
15 4007 37G 38F C N 296 298 -60.50 -63.20 26.96 3.57 -124.20 158.90 8.64
15 38F 38F N CA 298 299 -71.13 -44.30 143.30
16 4008 38F 39P C N 307 309 -85.50 -58.70 67.17 3.96 -64.50 117.99 9.94
16 39P 39P N CA 309 310 31.09 -30.50 147.20
17 4032 62G 63P C N 493 495 -72.37 -58.70 31.61 1.85 -64.50 149.40 11.57
17 63P 63P N CA 495 496 -1.99 -30.50 147.20
18 4033 63P 64V C N 500 502 -57.61 -62.40 10.60 1.64 -73.50 172.87 14.55
18 64V 64V N CA 502 503 -32.94 -42.40 139.20
19 4054 84S 85N C N 674 676 -119.15 -63.20 69.25 8.17 -63.20 69.25 8.17
19 85N 85N N CA 676 677 -0.30 -41.10 -41.10
20 4061 91K 92D C N 727 729 -141.83 -63.30 84.93 14.46 -63.30 84.93 14.46
20 92D 92D N CA 729 730 -72.34 -40.00 -40.00
21 4085 115I 116F C N 901 903 -40.95 -124.20 95.52 2.54 -63.20 142.52 21.29
21 116F 116F N CA 903 904 96.47 143.30 -44.30
22 4087 117K 118R C N 921 923 -79.46 -125.20 78.10 2.59 -63.00 119.54 15.10
22 118R 118R N CA 923 924 77.30 140.60 -41.10
23 4088 118R 119H C N 932 934 -167.37 -63.20 104.34 16.25 -63.20 104.34 16.25
23 119H 119H N CA 934 935 -36.30 -42.30 -42.30
24 4099 129N 130H C N 1040 1042 -115.72 -63.20 53.53 7.92 -63.20 53.53 7.92
24 130H 130H N CA 1042 1043 -31.96 -42.30 -42.30
25 4106 136L 137P C N 1092 1094 -60.85 -64.50 7.63 0.76 -58.70 175.62 14.69
25 137P 137P N CA 1094 1095 153.89 147.20 -30.50
26 4107 137P 138D C N 1099 1101 101.53 -63.30 164.91 26.39 -63.30 164.91 26.39
26 138D 138D N CA 1101 1102 -35.05 -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 13 26 86 88 129 125 133 159 194 185
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P50717_with_ligand.B99990001.pdb 1346.75647
P50717_with_ligand.B99990002.pdb 1349.65332
Получили 2 модели комплекса белка с лигандом:
In [5]:
w3=nglview.show_structure_file('P50717_with_ligand.B99990001.pdb')
w4=nglview.show_structure_file('P50717_with_ligand.B99990002.pdb')
#изобразим первую модель
Image(url="model1_ligand.png")
Out[5]:
