Загружаем модуль
In [1]:
import modeller
import _modeller
import modeller.automodel
Задаем параметры
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Darwin Air-Ekaterina.Dlink 17.7.0 x86_64
Date and time of compilation : 2020/04/06 12:04:46
MODELLER executable type : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2020/05/21 00:57:29
Скачиваем белок заготовку
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-05-21 01:00:56-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-05-21 01:00:57-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: http://files.rcsb.org/view/1lmp.pdb [following] --2020-05-21 01:00:57-- http://files.rcsb.org/view/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 128.6.244.12 Connecting to files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb’ 1lmp.pdb [ <=> ] 127,35K 339KB/s in 0,4s 2020-05-21 01:00:58 (339 KB/s) - ‘1lmp.pdb’ saved [130410]
Скачиваем белок последовательность
In [5]:
! wget http://www.uniprot.org/uniprot/LYS_GALME.fasta
--2020-05-21 01:02:59-- http://www.uniprot.org/uniprot/LYS_GALME.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org:443/uniprot/LYS_GALME.fasta [following] --2020-05-21 01:03:00-- https://www.uniprot.org/uniprot/LYS_GALME.fasta Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected. HTTP request sent, awaiting response... 302 Location: /uniprot/P82174.fasta [following] --2020-05-21 01:03:00-- https://www.uniprot.org/uniprot/P82174.fasta Reusing existing connection to www.uniprot.org:443. HTTP request sent, awaiting response... 200 Length: 195 [text/plain] Saving to: ‘LYS_GALME.fasta’ LYS_GALME.fasta 100%[===================>] 195 --.-KB/s in 0s 2020-05-21 01:03:00 (4,89 MB/s) - ‘LYS_GALME.fasta’ saved [195/195]
Создаем объект выравнивание, добавляем последовательность и структуру
In [6]:
alignm=modeller.alignment(env)
In [8]:
alignm.append(file='LYS_GALME.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')
## добавим идентификаторы
alignm[0].code = 'LYS_GALME'
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Делаем выравнивание и сохраняем
In [9]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [10]:
! cat all_in_one.ali #смотрим
>P1;LYS_GALME sequence:: : : : :::-1.00:-1.00 KTFTRCELVQALRRQGFD---EAKLRDWVCLVENESRGRTDIVGKPNKNGSRDYGLFQINDKYWCSN--TSKAGK DCNITCSQLLTDDITVASKCAKKVYKRHNFM-AWYGWRNHCQNKPLPDISKC------* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQINSRYWCDDGRTPGAKN VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Построим модель
In [13]:
## 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()
LYS_GALME 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
18 1 18 22 D E 8.206
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 11256 10395
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 : 121
Number of all, selected real atoms : 982 982
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10395 10395
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2023
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 : 875.7149
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 : 1002 0 0 0.006 0.006 11.454 1.000
2 Bond angle potential : 1348 0 7 2.201 2.201 129.34 1.000
3 Stereochemical cosine torsion poten: 641 0 20 46.017 46.017 208.67 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.334 1.334 16.639 1.000
5 Soft-sphere overlap restraints : 2023 0 0 0.003 0.003 1.6882 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) : 2163 0 3 0.334 0.334 86.813 1.000
10 Distance restraints 2 (N-O) : 2304 0 3 0.415 0.415 118.97 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: 120 0 1 5.171 5.171 37.836 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 1 66.274 66.274 24.398 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 66.409 66.409 28.083 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 76.140 76.140 19.944 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 87.676 87.676 18.072 1.000
18 Disulfide distance restraints : 3 0 0 0.009 0.009 0.45735E-01 1.000
19 Disulfide angle restraints : 6 0 0 2.093 2.093 0.58053 1.000
20 Disulfide dihedral angle restraints: 3 0 0 31.234 31.234 2.8250 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) : 1405 0 0 0.425 0.425 30.905 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: 119 8 17 31.885 45.303 101.29 1.000
26 Distance restraints 4 (SDCH-SDCH) : 629 0 0 0.681 0.681 38.162 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: LYS_GALME.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: 12228.4443
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 3442 32E 33S C N 268 270 -137.93 -64.10 83.38 8.54 -64.10 83.38 8.54
1 33S 33S N CA 270 271 3.75 -35.00 -35.00
2 3452 42K 43P C N 343 345 -76.55 -58.70 30.11 1.86 -64.50 153.92 12.13
2 43P 43P N CA 345 346 -6.25 -30.50 147.20
3 3473 63S 64N C N 519 521 -150.58 -63.20 99.93 16.43 -63.20 99.93 16.43
3 64N 64N N CA 521 522 -89.58 -41.10 -41.10
4 3475 65T 66S C N 534 536 -52.08 -64.10 56.17 3.54 -72.40 119.47 7.73
4 66S 66S N CA 536 537 -89.87 -35.00 152.40
5 3476 66S 67K C N 540 542 -56.46 -62.90 64.63 8.06 56.60 -177.14 21.40
5 67K 67K N CA 542 543 -105.11 -40.80 38.60
6 3477 67K 68A C N 549 551 105.74 -134.00 133.35 3.03 -68.20 -176.22 17.31
6 68A 68A N CA 551 552 -155.39 147.00 145.30
7 3478 68A 69G C N 554 556 159.04 82.20 86.30 3.93 -62.40 138.95 24.38
7 69G 69G N CA 556 557 -30.78 8.50 -41.20
8 3510 100F 101M C N 803 805 -68.38 -63.40 54.76 7.80 -63.40 54.76 7.80
8 101M 101M N CA 805 806 14.03 -40.50 -40.50
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 8 9 39 69 100 110 108 139 158 155
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 121
Number of all, selected real atoms : 982 982
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10395 10395
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2005
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 : 846.7451
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 : 1002 0 0 0.006 0.006 10.180 1.000
2 Bond angle potential : 1348 0 9 2.202 2.202 130.01 1.000
3 Stereochemical cosine torsion poten: 641 0 18 45.996 45.996 207.51 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.166 1.166 13.195 1.000
5 Soft-sphere overlap restraints : 2005 0 0 0.002 0.002 1.2139 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) : 2163 0 3 0.375 0.375 95.271 1.000
10 Distance restraints 2 (N-O) : 2304 0 6 0.419 0.419 131.94 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 120 0 4 4.973 4.973 35.002 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 60.203 60.203 20.019 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 2 64.824 64.824 31.517 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 83.617 83.617 24.114 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 81.512 81.512 13.552 1.000
18 Disulfide distance restraints : 3 0 0 0.005 0.005 0.14440E-01 1.000
19 Disulfide angle restraints : 6 0 0 2.030 2.030 0.54578 1.000
20 Disulfide dihedral angle restraints: 3 0 0 30.959 30.959 2.7539 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) : 1405 0 0 0.451 0.451 25.758 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: 119 7 17 26.947 43.108 76.890 1.000
26 Distance restraints 4 (SDCH-SDCH) : 629 0 0 0.676 0.676 27.266 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: LYS_GALME.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: 11538.8086
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 3442 32E 33S C N 268 270 -138.65 -64.10 85.81 8.58 -64.10 85.81 8.58
1 33S 33S N CA 270 271 7.49 -35.00 -35.00
2 3473 63S 64N C N 519 521 -145.45 -63.20 94.55 15.54 -63.20 94.55 15.54
2 64N 64N N CA 521 522 -87.74 -41.10 -41.10
3 3478 68A 69G C N 554 556 169.62 82.20 95.14 4.65 -62.40 128.55 22.44
3 69G 69G N CA 556 557 -29.04 8.50 -41.20
4 3508 98H 99N C N 784 786 -80.72 -119.90 73.37 2.35 -63.20 117.38 13.78
4 99N 99N N CA 786 787 74.97 137.00 -41.10
5 3509 99N 100F C N 792 794 -56.52 -63.20 8.14 1.00 -124.20 -179.13 9.78
5 100F 100F N CA 794 795 -48.97 -44.30 143.30
6 3520 110C 111Q C N 895 897 -53.70 -63.80 17.17 2.20 -73.00 166.24 11.26
6 111Q 111Q N CA 897 898 -54.19 -40.30 140.70
7 3521 111Q 112N C N 904 906 -121.88 -119.90 71.23 3.28 55.90 179.71 18.81
7 112N 112N N CA 906 907 65.80 137.00 39.50
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 5 11 43 64 101 80 116 131 159 174
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_GALME.B99990001.pdb 875.71490
LYS_GALME.B99990002.pdb 846.74512
In [16]:
from xmlrpc.client import ServerProxy
import time
from IPython.display import Image
from pymol import stored, cmd
import numpy as np
In [19]:
cmd = ServerProxy(uri="http://localhost:9123/RPC2")
Image(filename='LYS.png')
Out[19]:
Добавление лиганда
In [25]:
## Получить список остаков
str_res=""
for res in alignm[0].residues:
str_res=str_res+res.code
str_res=str_res+"."
print(str_res)
alignm[0].code="LYS"
## Добавить в объект выравнивание последовательность из строки
alignm.append_sequence(str_res)
alignm[2].code="with_lig"
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
KTFTRCELVQALRRQGFDEAKLRDWVCLVENESRGRTDIVGKPNKNGSRDYGLFQINDKYWCSNTSKAGKDCNITCSQLLTDDITVASKCAKKVYKRHNFMAWYGWRNHCQNKPLPDISKC. SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2 SALIGN_____> adding the next group to the alignment; iteration 3
In [26]:
## Выбираем объект для моделирования
s1 = alignm[2]
pdb = alignm[1]
print(pdb.code,s1.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code, sequence = s1.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
1lmp with_lig
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
18 1 18 22 D E 8.206
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 121
atom names : C +N
atom indices : 980 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 121
atom names : C CA +N O
atom indices : 980 977 0 981
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.
15 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
15 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: 11691 10830
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 : 997 997
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10830 10830
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2100
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 : 946.5279
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 : 1002 0 0 0.007 0.007 13.363 1.000
2 Bond angle potential : 1348 0 7 2.315 2.315 142.02 1.000
3 Stereochemical cosine torsion poten: 641 0 19 46.284 46.284 215.12 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.399 1.399 17.459 1.000
5 Soft-sphere overlap restraints : 2100 0 0 0.003 0.003 1.9420 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) : 2163 0 4 0.384 0.384 112.78 1.000
10 Distance restraints 2 (N-O) : 2304 0 4 0.455 0.455 137.63 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: 120 0 4 5.264 5.264 39.210 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 73.037 73.037 31.465 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 73.045 73.045 30.174 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 65.354 65.354 20.954 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 83.126 83.126 16.572 1.000
18 Disulfide distance restraints : 3 0 0 0.005 0.005 0.13421E-01 1.000
19 Disulfide angle restraints : 6 0 0 2.970 2.970 1.1687 1.000
20 Disulfide dihedral angle restraints: 3 0 0 28.272 28.272 2.0923 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) : 1405 0 0 0.519 0.519 35.775 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: 119 8 15 25.932 41.378 74.569 1.000
26 Distance restraints 4 (SDCH-SDCH) : 629 0 0 0.768 0.768 43.049 1.000
27 Distance restraints 5 (X-Y) : 435 0 1 0.059 0.059 11.170 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: with_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: 12976.8799
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 3442 32E 33S C N 268 270 -136.78 -64.10 80.12 8.47 -64.10 80.12 8.47
1 33S 33S N CA 270 271 -1.28 -35.00 -35.00
2 3473 63S 64N C N 519 521 -148.65 -63.20 86.15 13.50 -63.20 86.15 13.50
2 64N 64N N CA 521 522 -52.03 -41.10 -41.10
3 3475 65T 66S C N 534 536 -53.93 -64.10 57.87 3.71 -72.40 117.09 7.53
3 66S 66S N CA 536 537 -91.97 -35.00 152.40
4 3476 66S 67K C N 540 542 -59.81 -70.20 14.01 1.17 56.60 160.98 10.52
4 67K 67K N CA 542 543 149.79 140.40 38.60
5 3477 67K 68A C N 549 551 -165.77 -134.00 71.51 3.04 -68.20 117.66 7.73
5 68A 68A N CA 551 552 -148.94 147.00 145.30
6 3478 68A 69G C N 554 556 167.49 82.20 96.22 4.34 -62.40 130.21 23.05
6 69G 69G N CA 556 557 -36.05 8.50 -41.20
7 3508 98H 99N C N 784 786 -86.51 -119.90 76.54 2.63 -63.20 111.69 12.81
7 99N 99N N CA 786 787 68.13 137.00 -41.10
8 3509 99N 100F C N 792 794 -60.16 -63.20 4.70 0.83 -124.20 -172.73 10.06
8 100F 100F N CA 794 795 -40.72 -44.30 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 12 44 72 116 105 117 159 158 145
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 122
Number of all, selected real atoms : 997 997
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10830 10830
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2094
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 : 906.0555
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 : 1002 0 0 0.007 0.007 13.247 1.000
2 Bond angle potential : 1348 0 6 2.278 2.278 137.10 1.000
3 Stereochemical cosine torsion poten: 641 0 19 46.702 46.702 213.26 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.328 1.328 16.061 1.000
5 Soft-sphere overlap restraints : 2094 0 0 0.003 0.003 1.9584 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) : 2163 0 3 0.369 0.369 99.889 1.000
10 Distance restraints 2 (N-O) : 2304 0 6 0.428 0.428 137.14 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 120 0 3 5.094 5.094 36.716 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 73.648 73.648 29.393 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 1 65.725 65.725 27.820 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 66.134 66.134 20.199 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 87.987 87.987 14.723 1.000
18 Disulfide distance restraints : 3 0 0 0.007 0.007 0.26100E-01 1.000
19 Disulfide angle restraints : 6 0 0 2.020 2.020 0.54080 1.000
20 Disulfide dihedral angle restraints: 3 0 0 35.364 35.364 3.2175 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) : 1405 0 0 0.428 0.428 34.263 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: 119 6 15 27.623 41.428 70.416 1.000
26 Distance restraints 4 (SDCH-SDCH) : 629 0 0 0.764 0.764 40.985 1.000
27 Distance restraints 5 (X-Y) : 435 0 0 0.053 0.053 9.1069 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: with_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: 12313.5244
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 3429 19E 20A C N 159 161 -68.75 -62.50 11.22 1.69 -134.00 -169.88 8.85
1 20A 20A N CA 161 162 -31.58 -40.90 147.00
2 3442 32E 33S C N 268 270 -133.53 -64.10 76.56 8.09 -64.10 76.56 8.09
2 33S 33S N CA 270 271 -2.73 -35.00 -35.00
3 3473 63S 64N C N 519 521 -145.14 -63.20 97.29 15.99 -63.20 97.29 15.99
3 64N 64N N CA 521 522 -93.55 -41.10 -41.10
4 3478 68A 69G C N 554 556 171.52 82.20 98.81 4.65 -62.40 126.30 22.25
4 69G 69G N CA 556 557 -33.76 8.50 -41.20
5 3508 98H 99N C N 784 786 -89.90 -119.90 71.34 2.48 -63.20 116.48 13.27
5 99N 99N N CA 786 787 72.28 137.00 -41.10
6 3509 99N 100F C N 792 794 -60.45 -63.20 3.30 0.60 -124.20 -174.47 9.97
6 100F 100F N CA 794 795 -42.47 -44.30 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 15 11 51 69 94 96 115 140 152 171
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
with_lig.B99990001.pdb 946.52789
with_lig.B99990002.pdb 906.05548
In [29]:
Image(filename='lig.png')
Out[29]:
Скор стал лучше. (875->946)
Заменим все АК на АЛАНИН
In [31]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
mdl
Out[31]:
Model containing 1 chain, 132 residues, and 1042 atoms
In [32]:
ala_prot = 'A' * 132 + '...'
alignm.append_sequence(ala_prot)
alignm[0].code = '1lmp.pdb'
alignm[1].code = 'ala'
In [33]:
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [34]:
## Выбираем объект для моделирования
s2 = alignm[1]
pdb = alignm[0]
print(s2.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns=pdb.code, sequence=s2.code)
a.name = 'mod' + s2.code
a.starting_model = 1
a.ending_model = 2
a.make()
ala 1lmp.pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 132
atom names : C +N
atom indices : 659 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 132
atom names : C CA +N O
atom indices : 659 657 0 660
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10184 9531
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 135
Number of all, selected real atoms : 704 704
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9531 9531
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1226
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 : 604.0154
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 : 660 0 0 0.006 0.006 6.7691 1.000
2 Bond angle potential : 923 0 5 2.285 2.285 99.083 1.000
3 Stereochemical cosine torsion poten: 268 0 34 76.393 76.393 253.06 1.000
4 Stereochemical improper torsion pot: 264 0 0 0.933 0.933 6.2628 1.000
5 Soft-sphere overlap restraints : 1226 1 2 0.011 0.011 16.133 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) : 2404 0 0 0.218 0.218 45.855 1.000
10 Distance restraints 2 (N-O) : 2562 0 3 0.327 0.327 102.10 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: 131 0 5 4.926 4.926 37.483 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 726 0 0 0.238 0.238 5.4839 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: 130 21 13 28.075 66.078 16.832 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.383 0.383 1.0888 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.032 0.032 13.866 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: ala.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: 11179.0068
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 2130 15A 16A C N 74 76 78.12 55.40 26.28 1.94 -62.50 155.28 31.55
1 16A 16A N CA 76 77 24.98 38.20 -40.90
2 2133 18A 19A C N 89 91 65.13 55.40 22.92 0.83 -62.50 140.34 28.50
2 19A 19A N CA 91 92 17.45 38.20 -40.90
3 2135 20A 21A C N 99 101 53.88 55.40 3.33 0.32 -62.50 139.07 28.25
3 21A 21A N CA 101 102 35.23 38.20 -40.90
4 2136 21A 22A C N 104 106 62.53 55.40 9.18 0.56 -62.50 144.95 29.47
4 22A 22A N CA 106 107 32.43 38.20 -40.90
5 2151 36A 37A C N 179 181 67.51 55.40 16.33 0.93 -62.50 146.79 29.85
5 37A 37A N CA 181 182 27.25 38.20 -40.90
6 2152 37A 38A C N 184 186 63.07 55.40 12.17 0.55 -62.50 143.59 29.20
6 38A 38A N CA 186 187 28.75 38.20 -40.90
7 2163 48A 49A C N 239 241 84.12 55.40 39.13 2.18 -62.50 155.74 31.49
7 49A 49A N CA 241 242 11.62 38.20 -40.90
8 2168 53A 54A C N 264 266 89.67 -134.00 142.02 3.45 -62.50 -158.35 31.68
8 54A 54A N CA 266 267 -173.21 147.00 -40.90
9 2171 56A 57A C N 279 281 59.95 55.40 11.42 1.06 -62.50 151.71 30.74
9 57A 57A N CA 281 282 48.67 38.20 -40.90
10 2181 66A 67A C N 329 331 83.89 55.40 60.26 2.21 -62.50 148.68 29.51
10 67A 67A N CA 331 332 -14.90 38.20 -40.90
11 2183 68A 69A C N 339 341 -59.35 -62.50 19.02 3.28 -134.00 -175.13 8.17
11 69A 69A N CA 341 342 -22.14 -40.90 147.00
12 2184 69A 70A C N 344 346 71.70 -68.20 146.41 13.69 -68.20 146.41 13.69
12 70A 70A N CA 346 347 -171.50 145.30 145.30
13 2185 70A 71A C N 349 351 -53.85 -68.20 43.48 3.01 -62.50 145.41 24.26
13 71A 71A N CA 351 352 104.26 145.30 -40.90
14 2188 73A 74A C N 364 366 55.50 55.40 19.29 1.17 -62.50 153.63 30.99
14 74A 74A N CA 366 367 57.49 38.20 -40.90
15 2191 76A 77A C N 379 381 64.67 55.40 11.40 1.33 -62.50 153.37 31.14
15 77A 77A N CA 381 382 44.83 38.20 -40.90
16 2218 103A 104A C N 514 516 81.21 -134.00 159.70 3.63 -62.50 177.82 28.58
16 104A 104A N CA 516 517 -145.63 147.00 -40.90
17 2231 116A 117A C N 579 581 50.87 55.40 9.37 0.35 -62.50 143.09 28.95
17 117A 117A N CA 581 582 46.40 38.20 -40.90
18 2239 124A 125A C N 619 621 -53.59 -62.50 11.21 1.79 -68.20 167.64 14.03
18 125A 125A N CA 621 622 -47.70 -40.90 145.30
19 2242 127A 128A C N 634 636 53.33 55.40 14.00 0.68 -62.50 148.51 30.00
19 128A 128A N CA 636 637 52.05 38.20 -40.90
20 2244 129A 130A C N 644 646 -83.73 -68.20 21.04 1.33 -62.50 161.01 27.48
20 130A 130A N CA 646 647 159.50 145.30 -40.90
21 2245 130A 131A C N 649 651 -65.25 -68.20 2.96 0.24 -62.50 174.16 28.68
21 131A 131A N CA 651 652 144.97 145.30 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 2 3 38 46 69 60 81 95 111 94
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 135
Number of all, selected real atoms : 704 704
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9531 9531
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1223
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 : 645.4954
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 : 660 0 0 0.006 0.006 7.2575 1.000
2 Bond angle potential : 923 1 7 2.348 2.348 105.31 1.000
3 Stereochemical cosine torsion poten: 268 0 31 76.220 76.220 252.79 1.000
4 Stereochemical improper torsion pot: 264 0 0 0.886 0.886 5.9543 1.000
5 Soft-sphere overlap restraints : 1223 2 2 0.011 0.011 17.130 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) : 2404 0 0 0.244 0.244 55.099 1.000
10 Distance restraints 2 (N-O) : 2562 1 6 0.340 0.340 121.79 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: 131 0 3 4.744 4.744 34.769 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 726 0 0 0.285 0.285 5.2947 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: 130 20 13 27.363 64.548 23.194 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.610 0.610 2.0464 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.034 0.034 14.864 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: ala.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: 11519.8184
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 1026 53A 53A N CA 261 262 127.65 107.00 20.65 5.94 107.00 20.65 5.94
-------------------------------------------------------------------------------------------------
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 6012 58A 53A N O 286 265 5.38 2.96 2.42 5.75 2.96 2.42 5.75
-------------------------------------------------------------------------------------------------
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 2130 15A 16A C N 74 76 78.36 55.40 26.46 1.97 -62.50 155.53 31.60
1 16A 16A N CA 76 77 25.04 38.20 -40.90
2 2133 18A 19A C N 89 91 66.04 55.40 24.43 0.88 -62.50 140.66 28.56
2 19A 19A N CA 91 92 16.21 38.20 -40.90
3 2135 20A 21A C N 99 101 53.35 55.40 2.85 0.32 -62.50 139.17 28.26
3 21A 21A N CA 101 102 36.22 38.20 -40.90
4 2136 21A 22A C N 104 106 61.80 55.40 8.90 0.48 -62.50 144.11 29.30
4 22A 22A N CA 106 107 32.02 38.20 -40.90
5 2151 36A 37A C N 179 181 67.51 55.40 15.06 0.98 -62.50 147.72 30.04
5 37A 37A N CA 181 182 29.24 38.20 -40.90
6 2152 37A 38A C N 184 186 61.43 55.40 10.20 0.43 -62.50 142.76 29.03
6 38A 38A N CA 186 187 29.97 38.20 -40.90
7 2163 48A 49A C N 239 241 85.49 55.40 39.38 2.34 -62.50 157.42 31.84
7 49A 49A N CA 241 242 12.79 38.20 -40.90
8 2167 52A 53A C N 259 261 -73.94 -62.50 15.98 2.48 -134.00 -173.33 8.84
8 53A 53A N CA 261 262 -29.74 -40.90 147.00
9 2168 53A 54A C N 264 266 179.14 -134.00 81.22 2.97 -62.50 158.72 31.91
9 54A 54A N CA 266 267 -146.66 147.00 -40.90
10 2171 56A 57A C N 279 281 61.54 55.40 13.15 1.28 -62.50 153.68 31.14
10 57A 57A N CA 281 282 49.83 38.20 -40.90
11 2181 66A 67A C N 329 331 80.30 55.40 56.24 2.03 -62.50 145.64 29.00
11 67A 67A N CA 331 332 -12.23 38.20 -40.90
12 2185 70A 71A C N 349 351 55.85 55.40 7.57 0.49 -62.50 146.68 29.72
12 71A 71A N CA 351 352 45.76 38.20 -40.90
13 2188 73A 74A C N 364 366 53.18 55.40 22.06 1.15 -62.50 153.59 30.91
13 74A 74A N CA 366 367 60.15 38.20 -40.90
14 2191 76A 77A C N 379 381 62.19 55.40 10.92 1.18 -62.50 152.41 30.91
14 77A 77A N CA 381 382 46.74 38.20 -40.90
15 2218 103A 104A C N 514 516 79.07 -134.00 161.78 3.67 -62.50 175.91 28.22
15 104A 104A N CA 516 517 -145.31 147.00 -40.90
16 2231 116A 117A C N 579 581 50.49 55.40 9.96 0.37 -62.50 143.08 28.94
16 117A 117A N CA 581 582 46.87 38.20 -40.90
17 2240 125A 126A C N 624 626 138.21 -134.00 151.42 5.51 -62.50 166.57 33.55
17 126A 126A N CA 626 627 -89.62 147.00 -40.90
18 2242 127A 128A C N 634 636 159.52 -134.00 84.01 2.19 -62.50 -176.65 36.90
18 128A 128A N CA 636 637 -161.64 147.00 -40.90
19 2244 129A 130A C N 644 646 -73.42 -68.20 7.65 0.48 -62.50 168.57 28.17
19 130A 130A N CA 646 647 150.89 145.30 -40.90
20 2245 130A 131A C N 649 651 -70.39 -68.20 4.55 0.30 -62.50 170.00 28.25
20 131A 131A N CA 651 652 149.28 145.30 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 1 2 34 42 70 60 75 103 104 87
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ala.B99990001.pdb 604.01544
ala.B99990002.pdb 645.49542
In [36]:
Image(filename='ala.png')
Out[36]:
Скор упал с 946 до 604
In [ ]: