Гомологичное моделирование комплекса белка с лигандом
Используя известную структуру лизоцима форели как образец, будем строить модель комплекса лизоцима двустворчатого моллюска LYS_MERLU с лигандом.
Импортируем модуль modeller.
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
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): 2017/09/06 13:43:09
In [3]:
#создаем объект выравнивания
alignm=modeller.alignment(env)
In [4]:
alignm.append(file='P86383.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 идентификатор
alignm[0].code = 'MERLU'
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.
В pdb-файле есть сахара NAG и NDG:
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM NDG 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
In [6]:
#Делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Получили файл с выравниванием all_in_one.ali. Теперь строим модель:
In [7]:
## 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()
MERLU 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 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
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 122
atom names : C +N
atom indices : 924 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 122
atom names : C CA +N O
atom indices : 924 918 0 925
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 122:
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.
irestab_402W> ires, irestp: 130 69
irestab_402W> ires, irestp: 130 69
irestab_402W> ires, irestp: 130 69
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: 9863 9030
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 : 122
Number of all, selected real atoms : 926 926
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9030 9030
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1920
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 : 717.8771
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 : 947 0 0 0.005 0.005 6.0416 1.000
2 Bond angle potential : 1266 0 3 2.014 2.014 99.681 1.000
3 Stereochemical cosine torsion poten: 591 0 31 48.649 48.649 204.79 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.034 1.034 8.6559 1.000
5 Soft-sphere overlap restraints : 1920 0 0 0.002 0.002 1.1142 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) : 2204 0 0 0.326 0.326 65.794 1.000
10 Distance restraints 2 (N-O) : 2337 0 9 0.434 0.434 134.98 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 0 2 4.271 4.271 26.032 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 3 79.915 79.915 28.480 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 1 82.538 82.538 29.478 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 78.898 78.898 23.994 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 73.542 73.542 9.7172 1.000
18 Disulfide distance restraints : 1 0 0 0.004 0.004 0.32185E-02 1.000
19 Disulfide angle restraints : 2 0 0 0.929 0.929 0.38121E-01 1.000
20 Disulfide dihedral angle restraints: 1 0 0 18.934 18.934 0.40722 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) : 752 0 0 0.357 0.357 8.8332 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: 120 22 15 32.954 74.324 65.737 1.000
26 Distance restraints 4 (SDCH-SDCH) : 95 0 0 0.717 0.717 4.1050 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: MERLU.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: 13185.1895
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 3190 1F 2A C N 10 12 -64.11 -62.50 3.49 0.52 -134.00 -171.38 11.63
1 2A 2A N CA 12 13 -37.81 -40.90 147.00
2 3191 2A 3G C N 15 17 70.01 78.70 75.18 2.50 -80.20 159.92 8.50
2 3G 3G N CA 17 18 119.23 -166.10 174.10
3 3192 3G 4G C N 19 21 -86.26 -80.20 16.46 0.95 82.20 -134.24 7.54
3 4G 4G N CA 21 22 158.79 174.10 8.50
4 3203 14I 15C C N 98 100 -87.98 -63.00 74.32 7.80 -63.00 74.32 7.80
4 15C 15C N CA 100 101 28.90 -41.10 -41.10
5 3204 15C 16K C N 104 106 59.28 56.60 10.97 0.61 -62.90 140.20 24.49
5 16K 16K N CA 106 107 27.97 38.60 -40.80
6 3207 18E 19S C N 130 132 51.23 56.90 23.58 1.08 -64.10 148.97 18.94
6 19S 19S N CA 132 133 59.29 36.40 -35.00
7 3219 30M 31G C N 215 217 -63.73 -62.40 3.27 0.45 82.20 153.22 11.60
7 31G 31G N CA 217 218 -38.21 -41.20 8.50
8 3224 35C 36G C N 245 247 -176.29 82.20 101.54 6.72 -62.40 123.28 19.65
8 36G 36G N CA 247 248 6.01 8.50 -41.20
9 3225 36G 37Y C N 249 251 57.10 55.90 7.91 0.64 -63.50 150.91 28.59
9 37Y 37Y N CA 251 252 47.32 39.50 -43.40
10 3226 37Y 38F C N 261 263 68.28 58.10 17.86 0.97 -63.20 145.59 26.05
10 38F 38F N CA 263 264 18.22 32.90 -44.30
11 3231 42E 43A C N 307 309 -77.24 -62.50 15.04 3.00 -134.00 178.38 10.95
11 43A 43A N CA 309 310 -43.90 -40.90 147.00
12 3232 43A 44Y C N 312 314 18.93 -98.40 117.35 4.57 -124.30 143.54 10.49
12 44Y 44Y N CA 314 315 125.90 128.40 135.40
13 3242 53S 54S C N 392 394 89.00 -136.60 137.50 4.75 -64.10 -149.29 17.47
13 54S 54S N CA 394 395 -179.77 151.20 -35.00
14 3245 56K 57S C N 421 423 55.98 56.90 12.98 0.75 -64.10 146.75 19.01
14 57S 57S N CA 423 424 49.35 36.40 -35.00
15 3252 63Y 64C C N 467 469 -67.72 -63.00 6.15 1.08 -117.90 -179.05 7.75
15 64C 64C N CA 469 470 -45.04 -41.10 141.10
16 3254 65A 66S C N 478 480 -100.21 -72.40 88.96 4.37 -64.10 95.21 9.46
16 66S 66S N CA 480 481 -123.10 152.40 -35.00
17 3256 67L 68C C N 492 494 -79.06 -117.90 66.77 1.96 -63.00 128.89 14.70
17 68C 68C N CA 494 495 86.79 141.10 -41.10
18 3291 102K 103G C N 770 772 -63.30 -62.40 1.15 0.22 82.20 153.99 11.72
18 103G 103G N CA 772 773 -41.92 -41.20 8.50
19 3294 105T 106I C N 787 789 -130.92 -120.60 60.67 3.86 -63.40 132.60 20.17
19 106I 106I N CA 789 790 70.52 130.30 -43.60
20 3297 108Y 109W C N 811 813 54.95 58.80 5.23 0.22 -63.00 142.94 25.13
20 109W 109W N CA 813 814 36.54 33.00 -44.20
21 3300 111R 112L C N 844 846 -109.68 -108.50 91.84 4.98 -63.50 93.99 11.52
21 112L 112L N CA 846 847 40.67 132.50 -41.20
22 3306 117G 118C C N 888 890 65.74 57.40 28.05 0.95 -117.90 -139.77 9.53
22 118C 118C N CA 890 891 9.21 36.00 141.10
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 9 11 48 72 100 104 144 147 159 128
<< 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 : 122
Number of all, selected real atoms : 926 926
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9030 9030
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1925
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 : 627.7158
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 : 947 0 0 0.005 0.005 6.1474 1.000
2 Bond angle potential : 1266 0 2 1.830 1.830 83.513 1.000
3 Stereochemical cosine torsion poten: 591 0 31 49.769 49.769 212.96 1.000
4 Stereochemical improper torsion pot: 381 0 0 0.997 0.997 8.3117 1.000
5 Soft-sphere overlap restraints : 1925 0 0 0.003 0.003 1.9446 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) : 2204 0 0 0.290 0.290 52.825 1.000
10 Distance restraints 2 (N-O) : 2337 0 1 0.384 0.384 95.890 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: 121 0 1 4.050 4.050 23.406 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 80.233 80.233 23.559 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 93.638 93.638 29.210 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 62.048 62.048 17.993 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 98.999 98.999 12.381 1.000
18 Disulfide distance restraints : 1 0 0 0.010 0.010 0.17969E-01 1.000
19 Disulfide angle restraints : 2 0 0 3.001 3.001 0.39763 1.000
20 Disulfide dihedral angle restraints: 1 0 0 14.252 14.252 0.23918 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) : 752 0 0 0.319 0.319 8.6182 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: 120 19 15 28.652 71.288 44.322 1.000
26 Distance restraints 4 (SDCH-SDCH) : 95 0 0 0.847 0.847 5.9790 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: MERLU.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: 12981.2520
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 3192 3G 4G C N 19 21 -80.86 -80.20 13.67 0.57 82.20 -137.12 7.26
1 4G 4G N CA 21 22 160.45 174.10 8.50
2 3203 14I 15C C N 98 100 -81.25 -63.00 62.25 6.61 -63.00 62.25 6.61
2 15C 15C N CA 100 101 18.42 -41.10 -41.10
3 3204 15C 16K C N 104 106 61.13 56.60 8.03 0.43 -62.90 143.80 25.11
3 16K 16K N CA 106 107 31.97 38.60 -40.80
4 3207 18E 19S C N 130 132 66.91 56.90 24.34 0.99 -64.10 139.95 18.72
4 19S 19S N CA 132 133 14.21 36.40 -35.00
5 3219 30M 31G C N 215 217 -64.55 -62.40 2.73 0.40 82.20 154.41 11.70
5 31G 31G N CA 217 218 -39.51 -41.20 8.50
6 3225 36G 37Y C N 249 251 65.45 55.90 10.13 0.94 -63.50 151.51 28.64
6 37Y 37Y N CA 251 252 36.14 39.50 -43.40
7 3226 37Y 38F C N 261 263 61.38 58.10 3.72 0.36 -63.20 145.64 26.25
7 38F 38F N CA 263 264 31.14 32.90 -44.30
8 3242 53S 54S C N 392 394 97.05 -136.60 132.04 4.35 -64.10 -149.47 18.33
8 54S 54S N CA 394 395 -170.48 151.20 -35.00
9 3245 56K 57S C N 421 423 58.60 56.90 14.14 1.05 -64.10 149.52 19.39
9 57S 57S N CA 423 424 50.43 36.40 -35.00
10 3254 65A 66S C N 478 480 84.92 56.90 29.99 2.84 -64.10 160.92 21.50
10 66S 66S N CA 480 481 25.71 36.40 -35.00
11 3257 68C 69V C N 498 500 59.83 55.90 4.24 0.52 -125.40 -157.53 10.77
11 69V 69V N CA 500 501 41.08 39.50 143.30
12 3268 79W 80A C N 602 604 -108.13 -62.50 98.05 14.69 -62.50 98.05 14.69
12 80A 80A N CA 604 605 45.89 -40.90 -40.90
13 3286 97P 98R C N 731 733 -65.46 -72.10 51.56 4.11 -63.00 125.90 17.17
13 98R 98R N CA 733 734 -166.98 141.90 -41.10
14 3287 98R 99G C N 742 744 88.49 82.20 46.52 1.94 -62.40 150.93 27.11
14 99G 99G N CA 744 745 -37.59 8.50 -41.20
15 3291 102K 103G C N 770 772 -63.32 -62.40 1.19 0.22 82.20 154.03 11.72
15 103G 103G N CA 772 773 -41.96 -41.20 8.50
16 3295 106I 107G C N 795 797 -73.50 -62.40 11.12 2.01 82.20 163.66 12.40
16 107G 107G N CA 797 798 -41.92 -41.20 8.50
17 3297 108Y 109W C N 811 813 59.35 58.80 1.72 0.13 -63.00 145.55 25.65
17 109W 109W N CA 813 814 34.63 33.00 -44.20
18 3300 111R 112L C N 844 846 -108.55 -108.50 88.60 4.79 -63.50 96.29 11.80
18 112L 112L N CA 846 847 43.90 132.50 -41.20
19 3304 115I 116S C N 878 880 -114.88 -136.60 92.03 4.16 -64.10 109.28 7.03
19 116S 116S N CA 880 881 61.77 151.20 -35.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 3 12 44 76 101 90 110 138 148 146
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
MERLU.B99990001.pdb 717.87714
MERLU.B99990002.pdb 627.71582
Программа рассчитала две pdb-структуры (MERLU.B99990001.pdb и MERLU.B99990002.pdb). Выбираем структуру с меньшим значением MODELLER objective function (см. Model evaluation). Это MERLU.B99990002.pdb.
In [12]:
#можно посмотреть структуру прямо в notebook!
import nglview
import ipywidgets
w1 = nglview.show_structure_file('MERLU.B99990002.pdb')
w1
In [13]:
from IPython.display import Image
Image(filename='02.png')
Out[13]:
Оказалось, что в этой полученной структуре MERLU лиганда нет.
Надо переделать работу, добавив три остатка лиганда к последовательности MERLU.
Если посмотреть в файл с выравниванием all_in_one.ali, то можно увидеть, что в конце последовательности 1lmp стоят три точки, но их нет в MERLU. Видимо, это лиганды, они и правда находятся в конце pdb-файла 1lmp:
HET NAG A 130 14
HET NAG A 131 14
HET NDG A 132 15
Добавляем три точки к последовательности MERLU и проделываем все шаги заново.
In [16]:
## Получить список остаков
s = ''
for res in alignm[0].residues:
s += res.code
s += '...'
print s
## Добавить в объект выравнивание последовательность из строки
alignm.append_sequence(s)
FAGGIVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKRYAKWAGCPLRCEGFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ...
In [18]:
alignm.salign()
alignm.write(file='all_in_one1.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 [19]:
## Выбираем объект для моделирования
s_lig = alignm[2]
pdb = alignm[1]
s_lig.code = 'MERLU-lig'
print s_lig.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one1.ali', knowns= pdb.code , sequence = s_lig.code )
a.name='mod'+s_lig.code
a.starting_model = 1
a.ending_model = 2
a.make()
MERLU-lig 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
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 122
atom names : C +N
atom indices : 924 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 122
atom names : C CA +N O
atom indices : 924 918 0 925
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 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: 11264 10431
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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10431 10431
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2164
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 : 828.8471
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 : 947 0 0 0.005 0.005 6.2059 1.000
2 Bond angle potential : 1266 0 1 1.915 1.915 91.789 1.000
3 Stereochemical cosine torsion poten: 591 0 25 49.368 49.368 217.05 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.177 1.177 11.128 1.000
5 Soft-sphere overlap restraints : 2164 1 2 0.008 0.008 15.627 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) : 2204 0 0 0.313 0.313 60.626 1.000
10 Distance restraints 2 (N-O) : 2337 0 8 0.444 0.444 137.52 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 121 0 1 4.387 4.387 27.463 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 1 89.534 89.534 40.434 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 92.626 92.626 28.249 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 78.850 78.850 19.648 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 109.458 109.458 13.814 1.000
18 Disulfide distance restraints : 1 0 0 0.013 0.013 0.28467E-01 1.000
19 Disulfide angle restraints : 2 0 0 2.114 2.114 0.19735 1.000
20 Disulfide dihedral angle restraints: 1 0 0 15.386 15.386 0.27660 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) : 752 0 0 0.484 0.484 18.838 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: 120 26 21 37.986 79.827 114.00 1.000
26 Distance restraints 4 (SDCH-SDCH) : 95 0 0 1.018 1.018 8.0610 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.039 0.039 17.903 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: MERLU-lig.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: 15415.5391
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 3192 3G 4G C N 19 21 -83.42 -80.20 14.38 0.73 82.20 -135.48 7.39
1 4G 4G N CA 21 22 160.09 174.10 8.50
2 3204 15C 16K C N 104 106 78.09 56.60 25.14 2.06 -62.90 155.82 27.21
2 16K 16K N CA 106 107 25.55 38.60 -40.80
3 3207 18E 19S C N 130 132 64.40 56.90 17.71 0.72 -64.10 139.92 18.67
3 19S 19S N CA 132 133 20.35 36.40 -35.00
4 3209 20G 21C C N 140 142 59.01 -69.10 144.50 13.45 -117.90 -170.64 7.60
4 21C 21C N CA 142 143 -151.35 141.80 141.10
5 3210 21C 22R C N 146 148 -78.64 -63.00 23.50 2.73 57.30 149.23 18.58
5 22R 22R N CA 148 149 -23.56 -41.10 38.00
6 3213 24V 25G C N 172 174 24.00 -62.40 93.76 14.91 -62.40 93.76 14.91
6 25G 25G N CA 174 175 -77.63 -41.20 -41.20
7 3219 30M 31G C N 215 217 -64.47 -62.40 2.17 0.36 82.20 154.65 11.74
7 31G 31G N CA 217 218 -40.52 -41.20 8.50
8 3224 35C 36G C N 245 247 -170.90 82.20 107.09 6.94 -62.40 116.81 18.70
8 36G 36G N CA 247 248 2.08 8.50 -41.20
9 3225 36G 37Y C N 249 251 62.61 55.90 7.16 0.65 -63.50 149.56 28.29
9 37Y 37Y N CA 251 252 37.01 39.50 -43.40
10 3226 37Y 38F C N 261 263 60.94 58.10 5.11 0.27 -63.20 143.99 25.93
10 38F 38F N CA 263 264 28.65 32.90 -44.30
11 3229 40I 41K C N 289 291 -91.50 -118.00 91.29 4.00 -62.90 96.86 11.35
11 41K 41K N CA 291 292 51.74 139.10 -40.80
12 3242 53S 54S C N 392 394 85.92 -136.60 143.30 4.74 -64.10 -159.27 17.08
12 54S 54S N CA 394 395 -168.37 151.20 -35.00
13 3245 56K 57S C N 421 423 56.74 56.90 16.35 1.03 -64.10 149.35 19.28
13 57S 57S N CA 423 424 52.75 36.40 -35.00
14 3254 65A 66S C N 478 480 81.13 56.90 26.07 2.44 -64.10 157.82 21.07
14 66S 66S N CA 480 481 26.77 36.40 -35.00
15 3256 67L 68C C N 492 494 -99.47 -117.90 47.87 1.57 -63.00 142.75 15.36
15 68C 68C N CA 494 495 96.92 141.10 -41.10
16 3264 75R 76Y C N 562 564 -101.13 -98.40 80.87 8.58 -63.50 98.45 13.96
16 76Y 76Y N CA 564 565 47.57 128.40 -43.40
17 3268 79W 80A C N 602 604 -108.97 -62.50 94.30 14.13 -62.50 94.30 14.13
17 80A 80A N CA 604 605 41.16 -40.90 -40.90
18 3282 93H 94N C N 708 710 -60.72 -119.90 59.24 2.52 -63.20 179.24 22.28
18 94N 94N N CA 710 711 139.67 137.00 -41.10
19 3283 94N 95G C N 716 718 121.97 82.20 58.78 1.76 -62.40 175.75 31.13
19 95G 95G N CA 718 719 -34.78 8.50 -41.20
20 3291 102K 103G C N 770 772 -62.60 -62.40 2.32 0.36 82.20 153.86 11.74
20 103G 103G N CA 772 773 -43.52 -41.20 8.50
21 3294 105T 106I C N 787 789 -125.23 -120.60 4.66 0.34 -63.40 -175.89 28.40
21 106I 106I N CA 789 790 129.82 130.30 -43.60
22 3297 108Y 109W C N 811 813 62.66 58.80 6.85 0.20 -63.00 144.60 25.57
22 109W 109W N CA 813 814 27.34 33.00 -44.20
23 3299 110N 111R C N 833 835 -68.69 -63.00 6.36 0.87 -125.20 -172.43 7.66
23 111R 111R N CA 835 836 -38.25 -41.10 140.60
24 3300 111R 112L C N 844 846 22.51 -63.50 118.26 21.40 -63.50 118.26 21.40
24 112L 112L N CA 846 847 39.97 -41.20 -41.20
25 3307 118C 119H C N 894 896 -138.20 -125.60 15.57 0.39 -63.20 -174.41 28.10
25 119H 119H N CA 896 897 147.93 138.80 -42.30
26 3308 119H 120G C N 904 906 63.79 78.70 36.51 0.55 82.20 142.48 7.83
26 120G 120G N CA 906 907 -132.78 -166.10 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 7 9 68 76 122 123 126 140 158 158
<< 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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 125
Number of all, selected real atoms : 969 969
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10431 10431
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2205
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 : 910.2463
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 : 947 0 0 0.005 0.005 7.2082 1.000
2 Bond angle potential : 1266 2 5 3.028 3.028 137.76 1.000
3 Stereochemical cosine torsion poten: 591 0 33 50.974 50.974 228.04 1.000
4 Stereochemical improper torsion pot: 381 0 0 1.175 1.175 11.513 1.000
5 Soft-sphere overlap restraints : 2205 1 2 0.008 0.008 15.979 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) : 2204 0 0 0.284 0.284 56.545 1.000
10 Distance restraints 2 (N-O) : 2337 1 12 0.436 0.436 165.03 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: 121 0 0 4.158 4.158 24.668 1.000
14 Sidechain Chi_1 dihedral restraints: 97 0 0 85.473 85.473 34.871 1.000
15 Sidechain Chi_2 dihedral restraints: 65 0 0 95.534 95.534 27.765 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 75.014 75.014 20.847 1.000
17 Sidechain Chi_4 dihedral restraints: 17 0 0 97.754 97.754 10.163 1.000
18 Disulfide distance restraints : 1 0 0 0.002 0.002 0.10558E-02 1.000
19 Disulfide angle restraints : 2 0 0 2.424 2.424 0.25959 1.000
20 Disulfide dihedral angle restraints: 1 0 0 24.870 24.870 0.66115 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) : 752 0 0 0.368 0.368 10.041 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: 120 29 19 34.861 82.867 130.94 1.000
26 Distance restraints 4 (SDCH-SDCH) : 95 0 0 0.925 0.925 7.3419 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.042 0.042 20.606 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: MERLU-lig.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: 15660.5410
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 6014 10C 6V N O 66 39 5.36 2.86 2.50 4.51 2.86 2.50 4.51
-------------------------------------------------------------------------------------------------
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 3192 3G 4G C N 19 21 -86.82 -80.20 8.73 0.63 82.20 -127.33 7.51
1 4G 4G N CA 21 22 168.40 174.10 8.50
2 3194 5I 6V C N 31 33 -78.15 -125.40 52.88 2.75 -62.40 151.36 20.10
2 6V 6V N CA 33 34 167.06 143.30 -42.40
3 3195 6V 7S C N 38 40 73.06 56.90 72.04 3.37 -64.10 137.16 17.63
3 7S 7S N CA 40 41 -33.80 36.40 -35.00
4 3204 15C 16K C N 104 106 75.41 56.60 19.99 1.94 -62.90 156.22 27.29
4 16K 16K N CA 106 107 31.83 38.60 -40.80
5 3207 18E 19S C N 130 132 63.51 56.90 17.09 0.70 -64.10 139.22 18.57
5 19S 19S N CA 132 133 20.64 36.40 -35.00
6 3214 25G 26C C N 176 178 -56.15 -63.00 6.89 1.18 -117.90 -171.19 8.18
6 26C 26C N CA 178 179 -40.47 -41.10 141.10
7 3219 30M 31G C N 215 217 -65.18 -62.40 4.45 0.61 82.20 154.46 11.67
7 31G 31G N CA 217 218 -37.72 -41.20 8.50
8 3221 32S 33L C N 225 227 -71.39 -70.70 18.55 1.38 -63.50 158.85 22.52
8 33L 33L N CA 227 228 160.14 141.60 -41.20
9 3222 33L 34S C N 233 235 76.23 56.90 77.09 3.49 -64.10 140.37 17.89
9 34S 34S N CA 235 236 -38.23 36.40 -35.00
10 3224 35C 36G C N 245 247 -175.61 82.20 102.64 6.51 -62.40 120.10 19.48
10 36G 36G N CA 247 248 -1.11 8.50 -41.20
11 3225 36G 37Y C N 249 251 62.18 55.90 6.43 0.65 -63.50 149.83 28.35
11 37Y 37Y N CA 251 252 38.16 39.50 -43.40
12 3226 37Y 38F C N 261 263 62.08 58.10 6.45 0.37 -63.20 144.55 26.02
12 38F 38F N CA 263 264 27.82 32.90 -44.30
13 3242 53S 54S C N 392 394 90.32 -136.60 137.13 4.65 -64.10 -151.09 17.59
13 54S 54S N CA 394 395 -175.71 151.20 -35.00
14 3245 56K 57S C N 421 423 56.27 56.90 16.16 0.98 -64.10 148.85 19.21
14 57S 57S N CA 423 424 52.54 36.40 -35.00
15 3254 65A 66S C N 478 480 152.10 56.90 98.04 10.17 -64.10 151.59 17.12
15 66S 66S N CA 480 481 12.96 36.40 -35.00
16 3257 68C 69V C N 498 500 63.29 55.90 7.91 0.97 -125.40 -161.13 10.59
16 69V 69V N CA 500 501 42.29 39.50 143.30
17 3264 75R 76Y C N 562 564 -101.55 -98.40 81.19 8.61 -63.50 98.33 13.93
17 76Y 76Y N CA 564 565 47.27 128.40 -43.40
18 3269 80A 81G C N 607 609 18.05 78.70 90.33 1.86 -62.40 99.15 14.63
18 81G 81G N CA 609 610 -99.15 -166.10 -41.20
19 3282 93H 94N C N 708 710 -60.87 -119.90 59.18 2.56 -63.20 177.67 22.09
19 94N 94N N CA 710 711 141.25 137.00 -41.10
20 3283 94N 95G C N 716 718 118.03 82.20 55.13 1.60 -62.40 179.74 31.78
20 95G 95G N CA 718 719 -33.40 8.50 -41.20
21 3286 97P 98R C N 731 733 -65.66 -72.10 16.41 1.38 -63.00 161.93 22.05
21 98R 98R N CA 733 734 157.00 141.90 -41.10
22 3287 98R 99G C N 742 744 121.91 82.20 60.32 1.77 -62.40 175.74 31.22
22 99G 99G N CA 744 745 -36.90 8.50 -41.20
23 3291 102K 103G C N 770 772 -64.90 -62.40 5.47 0.95 82.20 156.90 11.99
23 103G 103G N CA 772 773 -46.06 -41.20 8.50
24 3294 105T 106I C N 787 789 -131.18 -120.60 70.14 4.42 -63.40 124.61 18.94
24 106I 106I N CA 789 790 60.96 130.30 -43.60
25 3297 108Y 109W C N 811 813 75.47 58.80 30.13 0.85 -63.00 147.95 26.15
25 109W 109W N CA 813 814 7.90 33.00 -44.20
26 3300 111R 112L C N 844 846 -109.98 -108.50 70.10 3.80 -63.50 113.57 13.96
26 112L 112L N CA 846 847 62.42 132.50 -41.20
27 3303 114K 115I C N 870 872 -88.23 -63.40 76.47 11.81 -63.40 76.47 11.81
27 115I 115I N CA 872 873 28.72 -43.60 -43.60
28 3304 115I 116S C N 878 880 -141.02 -64.10 83.67 9.01 -64.10 83.67 9.01
28 116S 116S N CA 880 881 -2.07 -35.00 -35.00
29 3306 117G 118C C N 888 890 65.60 57.40 29.28 1.02 -117.90 -138.88 9.57
29 118C 118C N CA 890 891 7.90 36.00 141.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 15 12 62 105 124 123 128 156 156 164
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
MERLU-lig.B99990001.pdb 828.84711
MERLU-lig.B99990002.pdb 910.24634
Программа построила две структуры теперь уже с лигандом: MERLU-lig.B99990001.pdb и MERLU-lig.B99990002.pdb.
У первой значение MODELLER OBJECTIVE FUNCTION меньше, поэтому выбираем ее:
In [20]:
from IPython.display import Image
Image(filename='lig.png')
Out[20]:
Дата последнего обновления: 25.08.17
© Ксения Березина
© Ксения Березина