import sys
import modeller
import _modeller
import modeller.automodel
import nglview
import ipywidgets
# зададим параметры
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, Linux kodomo 3.16.0-6-amd64 x86_64
Date and time of compilation : 2020/04/06 19:06:24
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/05/26 17:40:40
Выбрала белок LYS_BOMMO из Bombyx mori, тутового шелкопряда, файл P48816.fasta, 2 pdb: 1GD6, 2RSC.
# скачаем белок заготовку
! wget http://www.pdb.org/pdb/files/1lmp.pdb
# скачаем последовательность
! wget https://www.uniprot.org/uniprot/P48816.fasta
--2021-05-26 17:40:47-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.159.96
Connecting to www.pdb.org (www.pdb.org)|128.6.159.96|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2021-05-26 17:40:47-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 128.6.159.248
Connecting to www.rcsb.org (www.rcsb.org)|128.6.159.248|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://files.rcsb.org/download/1lmp.pdb [following]
--2021-05-26 17:40:48-- https://files.rcsb.org/download/1lmp.pdb
Resolving files.rcsb.org (files.rcsb.org)... 128.6.158.49
Connecting to files.rcsb.org (files.rcsb.org)|128.6.158.49|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/octet-stream]
Saving to: `1lmp.pdb.2'
[ <=> ] 128,871 357K/s in 0.4s
2021-05-26 17:40:50 (357 KB/s) - `1lmp.pdb.2' saved [128871]
--2021-05-26 17:40:50-- https://www.uniprot.org/uniprot/P48816.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.240.206, 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.240.206|:443... connected.
HTTP request sent, awaiting response... 200
Length: 203 [text/plain]
Saving to: `P48816.fasta.2'
100%[======================================>] 203 --.-K/s in 0s
2021-05-26 17:40:52 (111 MB/s) - `P48816.fasta.2' saved [203/203]
# создадим объект выравнивание
alignm=modeller.alignment(env)
alignm.append(file='P48816.fasta', align_codes='all',alignment_format='FASTA')
# создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
# и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
# есть смысл поправить идентификаторы
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
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.
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.
В 1lmp.pdb лиганд находится на B-цепи, поэтому пришлось и ее тоже считывать.
# делаем выравнивание.
alignm.salign()
# сохраняем в файл.
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
!cat all_in_one.ali
>P1;seq sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC--------* >P1;pdb structureX:1lmp.pdb: 1 :A:+132 :B: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 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...*
Выравнивание в порядке, в 1lmp.pdb лиганд есть, в последовательности - нет.
alignm
Alignment of Sequence 'seq', Structure 'pdb'
# 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()
seq pdb
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
----------------------------------------------
88 1 73 76 D C 8.895
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: 11705 10745
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 : 137
Number of all, selected real atoms : 1096 1096
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10745 10745
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2272
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 : 877.8369
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 : 1119 0 2 0.009 0.009 23.329 1.000
2 Bond angle potential : 1504 1 9 2.091 2.091 134.42 1.000
3 Stereochemical cosine torsion poten: 713 0 24 47.138 47.138 248.76 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.109 1.109 13.062 1.000
5 Soft-sphere overlap restraints : 2272 0 0 0.002 0.002 1.3059 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) : 2215 0 2 0.314 0.314 99.384 1.000
10 Distance restraints 2 (N-O) : 2371 0 5 0.346 0.346 129.75 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: 136 0 2 4.382 4.382 30.797 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 73.234 73.234 26.316 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 81.767 81.767 37.193 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 67.405 67.405 20.713 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 73.266 73.266 14.829 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.28859 1.000
19 Disulfide angle restraints : 6 0 0 2.855 2.855 1.0798 1.000
20 Disulfide dihedral angle restraints: 3 0 0 23.901 23.901 1.7229 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) : 1316 0 0 0.335 0.335 23.138 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: 135 15 16 24.280 55.818 54.370 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.470 0.470 17.377 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: seq.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: 14389.2441
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 2080 88D 88D N CA 697 698 127.43 107.00 20.43 5.87 107.00 20.43 5.87
-------------------------------------------------------------------------------------------------
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 3811 2Q 3K C N 16 18 -120.51 -118.00 27.63 1.31 -62.90 163.09 24.62
1 3K 3K N CA 18 19 166.62 139.10 -40.80
2 3812 3K 4L C N 25 27 -68.76 -70.70 4.20 0.39 -63.50 173.56 24.40
2 4L 4L N CA 27 28 145.32 141.60 -41.20
3 3816 7F 8A C N 60 62 -56.28 -68.20 12.24 1.12 -62.50 171.15 27.75
3 8A 8A N CA 62 63 148.06 145.30 -40.90
4 3817 8A 9L C N 65 67 -69.43 -70.70 6.17 0.52 -63.50 171.26 24.12
4 9L 9L N CA 67 68 147.64 141.60 -41.20
5 3820 11V 12L C N 87 89 -73.53 -70.70 14.63 1.01 -63.50 163.15 23.24
5 12L 12L N CA 89 90 155.96 141.60 -41.20
6 3823 14V 15G C N 108 110 -108.25 -80.20 45.32 3.07 82.20 -146.35 16.65
6 15G 15G N CA 110 111 138.50 174.10 8.50
7 3824 15G 16S C N 112 114 -138.90 -136.60 3.79 0.13 -64.10 -173.56 18.83
7 16S 16S N CA 114 115 154.21 151.20 -35.00
8 3844 35F 36E C N 274 276 54.12 54.60 6.97 0.57 -63.60 139.99 24.09
8 36E 36E N CA 276 277 35.45 42.40 -40.30
9 3860 51S 52S C N 411 413 64.53 56.90 9.75 0.68 -64.10 144.28 19.15
9 52S 52S N CA 413 414 30.34 36.40 -35.00
10 3896 87K 88D C N 695 697 -143.87 -63.30 83.23 13.97 -63.30 83.23 13.97
10 88D 88D N CA 697 698 -60.88 -40.00 -40.00
11 3920 111I 112Y C N 872 874 -53.05 -98.40 46.21 2.09 -63.50 163.26 26.44
11 112Y 112Y N CA 874 875 119.53 128.40 -43.40
12 3923 114R 115H C N 904 906 -100.81 -125.60 62.11 1.85 -63.20 129.73 14.29
12 115H 115H N CA 906 907 81.85 138.80 -42.30
13 3924 115H 116R C N 914 916 -59.85 -63.00 31.63 4.07 -125.20 160.72 8.79
13 116R 116R N CA 916 917 -72.57 -41.10 140.60
14 3934 125N 126H C N 1010 1012 -123.58 -63.20 80.99 9.32 -63.20 80.99 9.32
14 126H 126H N CA 1012 1013 11.66 -42.30 -42.30
15 3935 126H 127C C N 1020 1022 -123.13 -63.00 60.37 9.77 -63.00 60.37 9.77
15 127C 127C N CA 1022 1023 -35.71 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 5 13 57 75 107 117 118 157 160 172
<< 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.
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 : 137
Number of all, selected real atoms : 1096 1096
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10745 10745
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2149
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 : 996.5659
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 : 1119 0 1 0.009 0.009 25.210 1.000
2 Bond angle potential : 1504 2 10 2.295 2.295 159.11 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.634 47.634 252.00 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.419 1.419 19.672 1.000
5 Soft-sphere overlap restraints : 2149 0 0 0.002 0.002 1.3963 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) : 2215 0 3 0.322 0.322 116.05 1.000
10 Distance restraints 2 (N-O) : 2371 0 9 0.367 0.367 160.13 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: 136 0 4 4.799 4.799 36.930 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 71.006 71.006 39.859 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 69.484 69.484 31.915 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 1 76.364 76.364 29.394 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 97.594 97.594 16.320 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.39878 1.000
19 Disulfide angle restraints : 6 0 0 2.707 2.707 0.97100 1.000
20 Disulfide dihedral angle restraints: 3 0 0 30.586 30.586 2.5413 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) : 1316 0 0 0.311 0.311 20.130 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: 135 18 21 24.627 65.128 55.627 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.597 0.597 28.904 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: seq.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: 15401.2510
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 1981 78W 78W N CA 627 628 122.90 107.00 15.90 4.57 107.00 15.90 4.57
2 2080 88D 88D N CA 697 698 124.32 107.00 17.32 4.98 107.00 17.32 4.98
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -78.62 -73.00 9.62 0.55 -63.80 171.83 26.05
1 2Q 2Q N CA 9 10 148.51 140.70 -40.30
2 3811 2Q 3K C N 16 18 -108.84 -118.00 10.82 0.36 -62.90 -179.91 21.32
2 3K 3K N CA 18 19 133.33 139.10 -40.80
3 3815 6I 7F C N 49 51 -121.35 -124.20 2.88 0.10 -63.20 -177.65 29.18
3 7F 7F N CA 51 52 142.87 143.30 -44.30
4 3816 7F 8A C N 60 62 -130.03 -134.00 4.89 0.12 -62.50 -172.46 34.35
4 8A 8A N CA 62 63 144.15 147.00 -40.90
5 3817 8A 9L C N 65 67 -77.14 -70.70 9.58 0.60 -63.50 170.65 24.50
5 9L 9L N CA 67 68 148.69 141.60 -41.20
6 3818 9L 10V C N 73 75 -58.51 -62.40 6.94 0.76 -125.40 -178.66 10.23
6 10V 10V N CA 75 76 -48.14 -42.40 143.30
7 3820 11V 12L C N 87 89 -140.12 -108.50 78.32 3.84 -63.50 137.89 23.82
7 12L 12L N CA 89 90 -155.85 132.50 -41.20
8 3823 14V 15G C N 108 110 -110.37 -80.20 45.09 1.33 82.20 -127.79 7.43
8 15G 15G N CA 110 111 -152.40 174.10 8.50
9 3824 15G 16S C N 112 114 -79.89 -72.40 29.78 2.01 -64.10 159.37 10.71
9 16S 16S N CA 114 115 123.58 152.40 -35.00
10 3844 35F 36E C N 274 276 51.91 54.60 4.70 0.56 -63.60 139.86 24.05
10 36E 36E N CA 276 277 38.55 42.40 -40.30
11 3859 50E 51S C N 405 407 -142.54 -64.10 89.50 9.05 -64.10 89.50 9.05
11 51S 51S N CA 407 408 8.12 -35.00 -35.00
12 3860 51S 52S C N 411 413 52.75 56.90 6.16 0.34 -64.10 139.37 18.19
12 52S 52S N CA 413 414 40.95 36.40 -35.00
13 3896 87K 88D C N 695 697 -148.15 -63.30 89.55 15.16 -63.30 89.55 15.16
13 88D 88D N CA 697 698 -68.61 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -38.49 -98.40 60.23 2.48 -63.50 167.52 27.87
14 112Y 112Y N CA 874 875 122.24 128.40 -43.40
15 3923 114R 115H C N 904 906 -98.08 -125.60 61.03 1.75 -63.20 131.35 14.59
15 115H 115H N CA 906 907 84.33 138.80 -42.30
16 3924 115H 116R C N 914 916 -60.95 -63.00 25.07 3.25 -125.20 166.23 9.06
16 116R 116R N CA 916 917 -66.09 -41.10 140.60
17 3936 127C 128Q C N 1026 1028 -55.78 -63.80 18.92 2.45 -121.10 175.47 9.10
17 128Q 128Q N CA 1028 1029 -57.44 -40.30 139.70
18 3937 128Q 129G C N 1035 1037 -73.54 -62.40 13.17 1.98 82.20 161.48 12.09
18 129G 129G N CA 1037 1038 -34.17 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 3 8 45 63 106 91 132 152 179 195
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 877.83691
seq.B99990002.pdb 996.56592
# поглядим
w1 = nglview.show_structure_file('seq.B99990001.pdb')
w1.clear_representations()
w1.add_cartoon('protein', color_scheme='residueindex')
w1.add_ball_and_stick('ligand', opacity=0.5)
w1
w_1lmp = nglview.show_structure_file('1lmp.pdb')
w_1lmp.clear_representations()
w_1lmp.add_cartoon('protein', color_scheme='residueindex')
w_1lmp.add_ball_and_stick('ligand', opacity=0.5)
w_1lmp
Общие черты, конечно, прослеживаются, но, вообще, белки довольно сильно отличаются, у белка без лиганда нарущены некоторые альфа-спирали.
seq_liganded = ''
for res in alignm[0].residues:
seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'seq_liganded'
del alignm[0]
# делаем выравнивание.
alignm.salign()
# сохраняем в файл.
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
!cat all_in_one2.ali
>P1;pdb structureX:1lmp.pdb: 1 :A:+132 :B: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 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...* >P1;seq_liganded sequence::1 : :+140 : :undefined:undefined:-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQG----SLPDISSC-...*
Лиганд добавился.
len(list(alignm[1].residues)) # длина последовательности целевого лизоцима
140
# Выбираем объект для моделирования.
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_liganded 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
----------------------------------------------
88 1 73 76 D C 8.895
132 1 117 122 G S 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13050 12090
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12090 12090
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2544
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 : 1411.8652
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 : 1119 0 3 0.011 0.011 39.126 1.000
2 Bond angle potential : 1504 3 15 2.567 2.567 200.54 1.000
3 Stereochemical cosine torsion poten: 713 0 40 50.143 50.143 281.17 1.000
4 Stereochemical improper torsion pot: 461 0 1 1.561 1.561 23.199 1.000
5 Soft-sphere overlap restraints : 2544 1 2 0.008 0.008 19.388 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) : 2200 3 19 0.426 0.426 193.84 1.000
10 Distance restraints 2 (N-O) : 2356 1 24 0.453 0.453 241.07 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: 136 0 8 5.362 5.362 46.107 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 79.217 79.217 45.869 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 76.667 76.667 44.581 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 83.469 83.469 26.255 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 73.816 73.816 12.502 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.41798 1.000
19 Disulfide angle restraints : 6 0 0 3.942 3.942 2.0590 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.230 22.230 1.5512 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) : 1299 0 0 0.407 0.407 31.558 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: 135 25 27 36.580 70.400 133.91 1.000
26 Distance restraints 4 (SDCH-SDCH) : 501 0 0 0.772 0.772 39.445 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.051 0.051 29.274 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: seq_liganded.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: 18209.3398
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 2080 88D 88D N CA 697 698 130.12 107.00 23.12 6.65 107.00 23.12 6.65
2 2555 129G 130S C N 1039 1041 140.52 120.00 20.52 4.66 120.00 20.52 4.66
3 2558 130S 130S N CA 1041 1042 124.57 107.00 17.57 5.05 107.00 17.57 5.05
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6473 118D 128Q CA CA 939 1029 11.76 8.51 3.25 4.54 8.51 3.25 4.54
-------------------------------------------------------------------------------------------------
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 7525 65S 85P N O 513 683 8.86 6.49 2.36 4.52 6.49 2.36 4.52
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -79.80 -73.00 26.57 1.61 -63.80 154.15 23.52
1 2Q 2Q N CA 9 10 166.38 140.70 -40.30
2 3811 2Q 3K C N 16 18 -61.02 -70.20 10.18 0.83 -62.90 174.42 22.55
2 3K 3K N CA 18 19 144.79 140.40 -40.80
3 3812 3K 4L C N 25 27 -100.35 -108.50 13.18 0.75 -63.50 179.75 27.20
3 4L 4L N CA 27 28 142.86 132.50 -41.20
4 3815 6I 7F C N 49 51 -146.41 -124.20 22.32 0.81 -63.20 -170.56 31.67
4 7F 7F N CA 51 52 145.51 143.30 -44.30
5 3816 7F 8A C N 60 62 -134.56 -134.00 2.31 0.12 -62.50 -175.48 34.10
5 8A 8A N CA 62 63 149.24 147.00 -40.90
6 3817 8A 9L C N 65 67 -109.79 -108.50 16.78 0.92 -63.50 163.66 20.58
6 9L 9L N CA 67 68 115.77 132.50 -41.20
7 3820 11V 12L C N 87 89 -141.69 -108.50 41.79 1.85 -63.50 178.89 29.67
7 12L 12L N CA 89 90 157.90 132.50 -41.20
8 3823 14V 15G C N 108 110 83.13 78.70 21.12 0.43 82.20 164.75 8.04
8 15G 15G N CA 110 111 173.25 -166.10 8.50
9 3824 15G 16S C N 112 114 -118.42 -136.60 19.13 0.62 -64.10 -172.22 17.38
9 16S 16S N CA 114 115 145.24 151.20 -35.00
10 3844 35F 36E C N 274 276 54.12 54.60 7.26 0.60 -63.60 139.82 24.06
10 36E 36E N CA 276 277 35.15 42.40 -40.30
11 3860 51S 52S C N 411 413 62.51 56.90 6.24 0.55 -64.10 144.04 19.05
11 52S 52S N CA 413 414 33.68 36.40 -35.00
12 3893 84S 85P C N 675 677 -45.78 -58.70 61.73 4.15 -64.50 123.37 10.22
12 85P 85P N CA 677 678 -90.86 -30.50 147.20
13 3894 85P 86G C N 682 684 -65.17 -62.40 20.64 3.22 82.20 163.22 12.65
13 86G 86G N CA 684 685 -61.66 -41.20 8.50
14 3895 86G 87K C N 686 688 77.09 -70.20 147.32 10.82 -70.20 147.32 10.82
14 87K 87K N CA 688 689 143.21 140.40 140.40
15 3896 87K 88D C N 695 697 -165.64 -63.30 102.70 16.67 -63.30 102.70 16.67
15 88D 88D N CA 697 698 -48.61 -40.00 -40.00
16 3898 89C 90N C N 709 711 173.10 -63.20 124.26 19.32 55.90 149.16 10.13
16 90N 90N N CA 711 712 -52.77 -41.10 39.50
17 3920 111I 112Y C N 872 874 -33.06 -98.40 68.17 3.45 -63.50 155.36 26.21
17 112Y 112Y N CA 874 875 108.95 128.40 -43.40
18 3922 113K 114R C N 893 895 -80.04 -125.20 87.66 3.06 -63.00 107.92 13.51
18 114R 114R N CA 895 896 65.47 140.60 -41.10
19 3923 114R 115H C N 904 906 -154.43 -63.20 91.26 14.38 -63.20 91.26 14.38
19 115H 115H N CA 906 907 -40.24 -42.30 -42.30
20 3935 126H 127C C N 1020 1022 -84.62 -117.90 76.46 2.43 -63.00 115.41 12.77
20 127C 127C N CA 1022 1023 72.27 141.10 -41.10
21 3937 128Q 129G C N 1035 1037 112.60 78.70 68.71 1.03 82.20 129.26 7.75
21 129G 129G N CA 1037 1038 134.14 -166.10 8.50
22 3938 129G 130S C N 1039 1041 45.72 56.90 15.31 0.96 -64.10 136.97 17.63
22 130S 130S N CA 1041 1042 46.85 36.40 -35.00
23 3941 132P 133D C N 1060 1062 -34.06 -70.90 47.87 2.13 -63.30 162.38 21.90
23 133D 133D N CA 1062 1063 119.73 150.30 -40.00
24 3942 133D 134I C N 1068 1070 1.73 -97.30 108.27 6.51 -120.60 131.00 7.34
24 134I 134I N CA 1070 1071 83.44 127.20 130.30
25 3944 135S 136S C N 1082 1084 56.23 56.90 8.29 0.47 -64.10 144.31 18.81
25 136S 136S N CA 1084 1085 44.66 36.40 -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 1 17 17 74 86 120 141 156 158 190 193
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12090 12090
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2425
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 : 1251.5178
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 : 1119 0 3 0.011 0.011 36.708 1.000
2 Bond angle potential : 1504 1 10 2.349 2.349 168.35 1.000
3 Stereochemical cosine torsion poten: 713 0 29 48.566 48.566 263.54 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.460 1.460 21.040 1.000
5 Soft-sphere overlap restraints : 2425 2 2 0.008 0.008 19.590 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) : 2200 2 16 0.431 0.431 197.37 1.000
10 Distance restraints 2 (N-O) : 2356 0 15 0.437 0.437 214.96 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: 136 0 3 4.738 4.738 36.001 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 81.087 81.087 40.371 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 66.654 66.654 34.884 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.105 80.105 22.533 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 75.986 75.986 13.146 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.41918 1.000
19 Disulfide angle restraints : 6 0 0 2.740 2.740 0.99448 1.000
20 Disulfide dihedral angle restraints: 3 0 0 32.473 32.473 2.6740 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) : 1299 0 0 0.390 0.390 30.209 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: 135 19 19 31.220 67.994 94.794 1.000
26 Distance restraints 4 (SDCH-SDCH) : 501 0 1 0.608 0.608 27.251 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 26.678 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: seq_liganded.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: 16878.5898
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 2080 88D 88D N CA 697 698 130.29 107.00 23.29 6.70 107.00 23.29 6.70
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -73.06 -73.00 17.99 1.18 -63.80 161.27 24.20
1 2Q 2Q N CA 9 10 158.70 140.70 -40.30
2 3811 2Q 3K C N 16 18 -68.16 -70.20 3.39 0.28 -62.90 176.17 23.17
2 3K 3K N CA 18 19 143.11 140.40 -40.80
3 3812 3K 4L C N 25 27 -103.54 -108.50 5.27 0.27 -63.50 179.99 23.02
3 4L 4L N CA 27 28 134.28 132.50 -41.20
4 3815 6I 7F C N 49 51 -137.70 -124.20 20.73 0.58 -63.20 173.47 28.90
4 7F 7F N CA 51 52 159.04 143.30 -44.30
5 3816 7F 8A C N 60 62 -101.69 -134.00 37.70 0.89 -62.50 172.97 26.71
5 8A 8A N CA 62 63 127.57 147.00 -40.90
6 3817 8A 9L C N 65 67 -122.78 -108.50 18.44 0.82 -63.50 -175.59 29.27
6 9L 9L N CA 67 68 144.17 132.50 -41.20
7 3820 11V 12L C N 87 89 -63.13 -70.70 20.02 1.28 -63.50 164.27 22.83
7 12L 12L N CA 89 90 123.07 141.60 -41.20
8 3823 14V 15G C N 108 110 -73.22 -80.20 13.83 0.33 82.20 -141.44 6.88
8 15G 15G N CA 110 111 162.16 174.10 8.50
9 3824 15G 16S C N 112 114 -73.49 -72.40 6.72 0.43 -64.10 179.47 13.58
9 16S 16S N CA 114 115 145.77 152.40 -35.00
10 3844 35F 36E C N 274 276 54.21 54.60 6.50 0.53 -63.60 140.31 24.14
10 36E 36E N CA 276 277 35.91 42.40 -40.30
11 3860 51S 52S C N 411 413 63.43 56.90 7.19 0.64 -64.10 144.72 19.15
11 52S 52S N CA 413 414 33.39 36.40 -35.00
12 3896 87K 88D C N 695 697 -157.14 -63.30 93.85 14.83 -63.30 93.85 14.83
12 88D 88D N CA 697 698 -38.70 -40.00 -40.00
13 3920 111I 112Y C N 872 874 -49.72 -98.40 53.29 3.14 -63.50 150.76 24.63
13 112Y 112Y N CA 874 875 106.73 128.40 -43.40
14 3935 126H 127C C N 1020 1022 -74.67 -63.00 93.39 12.23 -63.00 93.39 12.23
14 127C 127C N CA 1022 1023 -133.76 -41.10 -41.10
15 3937 128Q 129G C N 1035 1037 155.91 78.70 79.57 3.47 82.20 -178.22 12.23
15 129G 129G N CA 1037 1038 174.67 -166.10 8.50
16 3938 129G 130S C N 1039 1041 -98.55 -72.40 59.35 4.36 -64.10 138.48 8.62
16 130S 130S N CA 1041 1042 99.13 152.40 -35.00
17 3941 132P 133D C N 1060 1062 -39.75 -70.90 39.86 1.81 -63.30 167.09 22.11
17 133D 133D N CA 1062 1063 125.42 150.30 -40.00
18 3942 133D 134I C N 1068 1070 21.03 -97.30 123.51 6.51 -120.60 146.77 8.80
18 134I 134I N CA 1070 1071 91.79 127.20 130.30
19 3943 134I 135S C N 1076 1078 -154.33 -136.60 52.32 2.92 -64.10 164.02 11.24
19 135S 135S N CA 1078 1079 101.97 151.20 -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 1 20 11 91 73 111 126 129 164 188 159
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_liganded.B99990001.pdb 1411.86523
seq_liganded.B99990002.pdb 1251.51782
w_liganded = nglview.show_structure_file('seq_liganded.B99990001.pdb')
w_liganded.clear_representations()
w_liganded.add_cartoon('protein', color_scheme='residueindex')
w_liganded.add_ball_and_stick('ligand', opacity=0.5)
w_liganded
w_1lmp
w1
Добавление лиганда изменило структуру белка шелкопряда, но, кажется, не особо сделало его более похожим на 1lmp.
! rm seq_liganded.rsr
# как выглядит лиганд в последовательности
['/',alignm[1].residues[-3],alignm[1].residues[-2],alignm[1].residues[-1]]
['/', Residue BLK, Residue BLK, Residue BLK]
alignm
Alignment of Structure 'pdb', Sequence 'seq_liganded'
len(list(alignm[0].residues)) # длина белка 1lmp
132
Я выбрала карман 24cys-45cys и решила переместить лиганд в него. Он достаточно удален от реального положения лиганда.
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:24','O6:138'), ('N:45', 'O6:140')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
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()
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
132 1 117 122 G S 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13052 12092
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12092 12092
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2678
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 : 8588.7295
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 : 1119 5 12 0.022 0.022 169.00 1.000
2 Bond angle potential : 1504 12 41 3.906 3.906 444.89 1.000
3 Stereochemical cosine torsion poten: 713 0 40 51.192 51.192 287.66 1.000
4 Stereochemical improper torsion pot: 461 2 3 2.235 2.235 56.437 1.000
5 Soft-sphere overlap restraints : 2678 3 7 0.014 0.014 64.892 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) : 2200 65 207 0.932 0.932 1806.6 1.000
10 Distance restraints 2 (N-O) : 2356 52 144 0.798 0.798 1333.7 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: 136 2 9 9.778 9.778 153.34 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 81.543 81.543 51.670 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 74.267 74.267 49.518 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 65.673 65.673 22.245 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 81.635 81.635 13.543 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.30756 1.000
19 Disulfide angle restraints : 6 0 1 5.510 5.510 4.0222 1.000
20 Disulfide dihedral angle restraints: 3 0 0 31.625 31.625 2.0131 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) : 1299 0 0 0.427 0.427 43.186 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: 135 24 28 31.760 66.341 171.82 1.000
26 Distance restraints 4 (SDCH-SDCH) : 501 0 9 1.036 1.036 91.257 1.000
27 Distance restraints 5 (X-Y) : 1391 23 79 0.365 0.365 3822.6 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: seq_liganded.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: 26684.2910
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 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 180 23R 24C C N 177 179 1.53 1.35 0.18 6.41 1.35 0.18 6.41
2 183 24C 24C N CA 179 180 1.77 1.43 0.34 11.14 1.43 0.34 11.14
3 185 24C 24C C CA 183 180 1.74 1.49 0.25 7.33 1.49 0.25 7.33
4 364 44V 45C C N 356 358 1.53 1.35 0.19 6.71 1.35 0.19 6.71
5 367 45C 45C N CA 358 359 1.68 1.43 0.25 8.19 1.43 0.25 8.19
-------------------------------------------------------------------------------------------------
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 1352 23R 23R N CA 168 169 123.79 107.00 16.79 4.83 107.00 16.79 4.83
2 1355 23R 23R CA C 169 177 134.58 116.50 18.08 5.20 116.50 18.08 5.20
3 1366 24C 24C N CA 179 180 138.33 107.00 31.33 9.01 107.00 31.33 9.01
4 1607 44V 44V CA C 352 356 135.26 116.50 18.76 5.40 116.50 18.76 5.40
5 1613 45C 45C N CA 358 359 136.06 107.00 29.07 8.36 107.00 29.07 8.36
6 1670 50E 50E N CA 398 399 125.00 107.00 18.00 5.17 107.00 18.00 5.17
7 2080 88D 88D N CA 697 698 124.67 107.00 17.67 5.08 107.00 17.67 5.08
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3417 23R 23R C CA 177 169 12.86 0.00 12.86 4.53 0.00 12.86 4.53
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4416 18A 44V CA CA 130 352 12.90 10.72 2.18 4.65 10.72 2.18 4.65
2 4482 20T 44V CA CA 144 352 10.34 7.32 3.03 6.63 7.32 3.03 6.63
3 4483 20T 45C CA CA 144 359 11.73 9.43 2.30 4.55 9.43 2.30 4.55
4 4505 21F 24C CA CA 151 180 6.48 4.70 1.78 5.88 4.70 1.78 5.88
5 4637 24C 135S CA CA 180 1079 8.96 7.12 1.84 5.50 7.12 1.84 5.50
6 4639 24C 137C CA CA 180 1091 9.81 7.50 2.30 5.46 7.50 2.30 5.46
7 5036 41R 44V CA CA 319 352 7.06 5.11 1.94 4.96 5.11 1.94 4.96
8 5092 43W 46L CA CA 338 365 7.34 5.37 1.97 5.40 5.37 1.97 5.40
9 5093 43W 47V CA CA 338 373 8.10 6.19 1.92 5.06 6.19 1.92 5.06
10 5161 44V 131L CA CA 352 1048 8.49 6.16 2.33 5.98 6.16 2.33 5.98
11 5162 44V 132P CA CA 352 1056 10.17 7.54 2.63 6.22 7.54 2.63 6.22
12 5168 45C 48E CA CA 359 380 8.04 5.24 2.80 6.67 5.24 2.80 6.67
13 5169 45C 49H CA CA 359 389 8.71 6.42 2.28 5.21 6.42 2.28 5.21
14 5173 45C 53R CA CA 359 420 11.85 9.74 2.11 4.55 9.74 2.11 4.55
15 5191 45C 131L CA CA 359 1048 8.06 6.16 1.90 4.77 6.16 1.90 4.77
-------------------------------------------------------------------------------------------------
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 6583 18A 44V N O 129 357 13.29 10.79 2.50 4.94 10.79 2.50 4.94
2 6617 20T 44V N O 143 357 11.76 8.36 3.41 6.38 8.36 3.41 6.38
3 6636 21F 44V N O 150 357 11.57 9.02 2.55 4.99 9.02 2.55 4.99
4 6686 24C 20T N O 179 149 5.10 2.96 2.14 6.12 2.96 2.14 6.12
5 6687 24C 21F N O 179 160 5.61 3.17 2.44 7.82 3.17 2.44 7.82
6 6688 24C 22T N O 179 167 5.28 3.64 1.64 4.58 3.64 1.64 4.58
7 6706 24C 135S N O 179 1083 10.74 7.89 2.85 7.07 7.89 2.85 7.07
8 7086 45C 20T N O 358 149 11.19 8.20 3.00 5.64 8.20 3.00 5.64
9 7092 45C 40M N O 358 317 7.32 5.11 2.22 5.64 5.11 2.22 5.64
10 7093 45C 41R N O 358 328 6.41 2.99 3.42 8.45 2.99 3.42 8.45
11 7097 45C 48E N O 358 387 10.46 7.84 2.62 5.07 7.84 2.62 5.07
12 7099 45C 52S N O 358 418 14.05 10.92 3.13 4.82 10.92 3.13 4.82
13 7104 45C 126H N O 358 1021 10.81 8.06 2.75 5.06 8.06 2.75 5.06
14 7106 45C 130S N O 358 1046 11.50 8.42 3.08 5.11 8.42 3.08 5.11
15 7107 45C 131L N O 358 1054 10.10 6.31 3.80 8.20 6.31 3.80 8.20
16 7108 45C 132P N O 358 1061 13.03 10.56 2.47 4.71 10.56 2.47 4.71
17 7143 47V 43W N O 372 350 5.69 3.22 2.48 6.84 3.22 2.48 6.84
18 7172 48E 43W N O 379 350 7.74 5.22 2.52 5.29 5.22 2.52 5.29
19 7173 48E 44V N O 379 357 5.31 3.06 2.25 5.08 3.06 2.25 5.08
20 7192 49H 43W N O 388 350 9.78 7.34 2.44 4.94 7.34 2.44 4.94
21 7194 49H 45C N O 388 363 5.98 3.16 2.83 6.53 3.16 2.83 6.53
22 7214 50E 43W N O 398 350 10.03 7.97 2.06 4.66 7.97 2.06 4.66
23 7216 50E 45C N O 398 363 6.86 4.95 1.91 4.71 4.95 1.91 4.71
24 7241 51S 43W N O 407 350 10.78 8.80 1.98 4.57 8.80 1.98 4.57
25 7294 53R 43W N O 419 350 11.73 8.71 3.02 6.49 8.71 3.02 6.49
26 7295 53R 44V N O 419 357 9.46 7.07 2.39 5.38 7.07 2.39 5.38
27 7315 54D 43W N O 430 350 13.05 10.41 2.63 4.77 10.41 2.63 4.77
28 8826 131L 44V N O 1047 357 10.39 7.69 2.69 5.61 7.69 2.69 5.61
29 8842 132P 44V N O 1055 357 10.72 8.04 2.68 5.54 8.04 2.68 5.54
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3988 44V 44V CA C 352 356 -102.65 -180.00 77.35 15.46 -180.00 77.35 15.46
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -75.34 -73.00 5.48 0.32 -63.80 174.42 26.26
1 2Q 2Q N CA 9 10 145.66 140.70 -40.30
2 3811 2Q 3K C N 16 18 -62.85 -70.20 11.61 0.70 -62.90 172.21 22.37
2 3K 3K N CA 18 19 131.41 140.40 -40.80
3 3812 3K 4L C N 25 27 -118.47 -108.50 13.59 0.61 -63.50 -174.60 29.13
3 4L 4L N CA 27 28 141.73 132.50 -41.20
4 3815 6I 7F C N 49 51 -116.73 -124.20 7.87 0.24 -63.20 -177.13 28.96
4 7F 7F N CA 51 52 140.83 143.30 -44.30
5 3816 7F 8A C N 60 62 -111.93 -134.00 22.32 0.62 -62.50 -177.72 32.49
5 8A 8A N CA 62 63 143.65 147.00 -40.90
6 3817 8A 9L C N 65 67 -76.32 -70.70 48.83 3.92 -63.50 134.90 18.04
6 9L 9L N CA 67 68 93.09 141.60 -41.20
7 3820 11V 12L C N 87 89 -90.53 -108.50 37.03 1.77 -63.50 143.89 18.61
7 12L 12L N CA 89 90 100.12 132.50 -41.20
8 3823 14V 15G C N 108 110 -119.52 -80.20 52.58 3.77 82.20 -154.74 15.95
8 15G 15G N CA 110 111 139.18 174.10 8.50
9 3824 15G 16S C N 112 114 -122.52 -136.60 18.56 0.58 -64.10 -176.36 11.31
9 16S 16S N CA 114 115 139.10 151.20 -35.00
10 3831 22T 23R C N 166 168 -114.53 -63.00 73.75 13.18 -63.00 73.75 13.18
10 23R 23R N CA 168 169 -93.86 -41.10 -41.10
11 3832 23R 24C C N 177 179 4.21 -63.00 69.49 10.50 -63.00 69.49 10.50
11 24C 24C N CA 179 180 -58.72 -41.10 -41.10
12 3844 35F 36E C N 274 276 56.81 54.60 10.36 0.63 -63.60 140.59 24.19
12 36E 36E N CA 276 277 32.28 42.40 -40.30
13 3852 43W 44V C N 349 351 -105.07 -125.40 65.27 2.66 -62.40 130.83 14.62
13 44V 44V N CA 351 352 81.28 143.30 -42.40
14 3854 45C 46L C N 362 364 -81.95 -63.50 57.46 7.16 -63.50 57.46 7.16
14 46L 46L N CA 364 365 13.22 -41.20 -41.20
15 3860 51S 52S C N 411 413 61.39 56.90 6.87 0.37 -64.10 141.89 18.80
15 52S 52S N CA 413 414 31.21 36.40 -35.00
16 3896 87K 88D C N 695 697 -134.89 -63.30 80.78 13.79 -63.30 80.78 13.79
16 88D 88D N CA 697 698 -77.42 -40.00 -40.00
17 3920 111I 112Y C N 872 874 -19.63 -98.40 80.06 3.56 -63.50 163.44 28.17
17 112Y 112Y N CA 874 875 114.04 128.40 -43.40
18 3923 114R 115H C N 904 906 -83.68 -125.60 72.40 1.90 -63.20 123.77 14.31
18 115H 115H N CA 906 907 79.76 138.80 -42.30
19 3924 115H 116R C N 914 916 -50.83 -63.00 32.87 3.80 -125.20 165.43 9.10
19 116R 116R N CA 916 917 -71.63 -41.10 140.60
20 3934 125N 126H C N 1010 1012 -133.32 -63.20 77.78 10.24 -63.20 77.78 10.24
20 126H 126H N CA 1012 1013 -8.66 -42.30 -42.30
21 3938 129G 130S C N 1039 1041 -150.12 -136.60 62.47 3.40 -64.10 151.91 10.56
21 130S 130S N CA 1041 1042 90.21 151.20 -35.00
22 3941 132P 133D C N 1060 1062 47.76 54.50 15.03 0.73 -63.30 145.71 24.54
22 133D 133D N CA 1062 1063 54.33 40.90 -40.00
23 3942 133D 134I C N 1068 1070 38.18 -97.30 144.08 8.07 -120.60 167.12 9.68
23 134I 134I N CA 1070 1071 78.17 127.20 130.30
24 3944 135S 136S C N 1082 1084 51.83 56.90 5.50 0.51 -64.10 137.29 17.96
24 136S 136S N CA 1084 1085 38.54 36.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12050 140. 140. O4 O6 1136 1138 3.68 3.43 0.24 4.82 3.43 0.24 4.82
2 12075 140. 140. O6 O4 1138 1136 3.68 3.43 0.24 4.82 3.43 0.24 4.82
3 12091 24C 138. N O6 179 1108 10.97 3.00 7.97 79.73 3.00 7.97 79.73
4 12092 45C 140. N O6 358 1138 9.65 3.00 6.65 66.46 3.00 6.65 66.46
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 2 14 31 93 105 119 135 165 185 196 203
<< 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.
iupac_m_484W> Dihedral still outside +-90: -91.8296
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12092 12092
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2695
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 : 8644.8525
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 : 1119 7 12 0.023 0.023 184.74 1.000
2 Bond angle potential : 1504 11 39 4.035 4.035 480.35 1.000
3 Stereochemical cosine torsion poten: 713 0 37 51.096 51.096 282.20 1.000
4 Stereochemical improper torsion pot: 461 1 2 1.916 1.916 41.716 1.000
5 Soft-sphere overlap restraints : 2695 3 7 0.016 0.016 77.804 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) : 2200 60 201 0.922 0.922 1770.4 1.000
10 Distance restraints 2 (N-O) : 2356 51 145 0.798 0.798 1348.6 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: 136 1 5 7.653 7.653 93.927 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 81.484 81.484 59.602 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 74.388 74.388 41.733 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 58.782 58.782 18.436 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 88.341 88.341 12.935 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.25621 1.000
19 Disulfide angle restraints : 6 0 0 2.839 2.839 1.0679 1.000
20 Disulfide dihedral angle restraints: 3 0 0 36.267 36.267 2.9239 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) : 1299 0 0 0.436 0.436 44.835 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: 135 26 31 33.372 68.070 182.73 1.000
26 Distance restraints 4 (SDCH-SDCH) : 501 1 8 1.094 1.094 100.94 1.000
27 Distance restraints 5 (X-Y) : 1391 25 75 0.370 0.370 3899.6 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: seq_liganded.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: 26451.4316
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 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 180 23R 24C C N 177 179 1.54 1.35 0.19 6.81 1.35 0.19 6.81
2 183 24C 24C N CA 179 180 1.79 1.43 0.36 11.89 1.43 0.36 11.89
3 185 24C 24C C CA 183 180 1.74 1.49 0.25 7.17 1.49 0.25 7.17
4 363 44V 44V C CA 356 352 1.65 1.49 0.16 4.65 1.49 0.16 4.65
5 364 44V 45C C N 356 358 1.61 1.35 0.27 9.55 1.35 0.27 9.55
6 367 45C 45C N CA 358 359 1.62 1.43 0.19 6.23 1.43 0.19 6.23
-------------------------------------------------------------------------------------------------
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 1366 24C 24C N CA 179 180 137.71 107.00 30.71 8.83 107.00 30.71 8.83
2 1607 44V 44V CA C 352 356 149.19 116.50 32.69 9.40 116.50 32.69 9.40
3 1613 45C 45C N CA 358 359 124.27 107.00 17.27 4.97 107.00 17.27 4.97
4 1670 50E 50E N CA 398 399 124.50 107.00 17.50 5.03 107.00 17.50 5.03
5 2080 88D 88D N CA 697 698 126.78 107.00 19.78 5.69 107.00 19.78 5.69
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3417 23R 23R C CA 177 169 12.82 0.00 12.82 4.51 0.00 12.82 4.51
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4482 20T 44V CA CA 144 352 9.60 7.32 2.28 5.00 7.32 2.28 5.00
2 4505 21F 24C CA CA 151 180 6.55 4.70 1.85 6.10 4.70 1.85 6.10
3 4637 24C 135S CA CA 180 1079 9.11 7.12 2.00 5.95 7.12 2.00 5.95
4 4639 24C 137C CA CA 180 1091 10.02 7.50 2.51 5.95 7.50 2.51 5.95
5 4968 38N 46L CA CA 295 365 13.77 11.41 2.35 4.75 11.41 2.35 4.75
6 5092 43W 46L CA CA 338 365 7.53 5.37 2.16 5.90 5.37 2.16 5.90
7 5093 43W 47V CA CA 338 373 7.95 6.19 1.76 4.66 6.19 1.76 4.66
8 5161 44V 131L CA CA 352 1048 8.05 6.16 1.89 4.85 6.16 1.89 4.85
9 5168 45C 48E CA CA 359 380 7.76 5.24 2.53 6.01 5.24 2.53 6.01
10 5169 45C 49H CA CA 359 389 8.45 6.42 2.03 4.64 6.42 2.03 4.64
11 5173 45C 53R CA CA 359 420 11.87 9.74 2.13 4.60 9.74 2.13 4.60
12 5191 45C 131L CA CA 359 1048 7.97 6.16 1.81 4.55 6.16 1.81 4.55
-------------------------------------------------------------------------------------------------
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 6583 18A 44V N O 129 357 14.40 10.79 3.61 7.13 10.79 3.61 7.13
2 6602 19K 44V N O 134 357 13.66 10.28 3.38 5.07 10.28 3.38 5.07
3 6617 20T 44V N O 143 357 11.77 8.36 3.41 6.40 8.36 3.41 6.40
4 6686 24C 20T N O 179 149 5.27 2.96 2.31 6.62 2.96 2.31 6.62
5 6687 24C 21F N O 179 160 5.82 3.17 2.65 8.49 3.17 2.65 8.49
6 6688 24C 22T N O 179 167 5.49 3.64 1.85 5.19 3.64 1.85 5.19
7 6706 24C 135S N O 179 1083 10.48 7.89 2.59 6.42 7.89 2.59 6.42
8 7086 45C 20T N O 358 149 10.91 8.20 2.71 5.10 8.20 2.71 5.10
9 7092 45C 40M N O 358 317 6.91 5.11 1.80 4.58 5.11 1.80 4.58
10 7093 45C 41R N O 358 328 5.86 2.99 2.87 7.08 2.99 2.87 7.08
11 7097 45C 48E N O 358 387 10.18 7.84 2.34 4.52 7.84 2.34 4.52
12 7099 45C 52S N O 358 418 13.99 10.92 3.07 4.73 10.92 3.07 4.73
13 7106 45C 130S N O 358 1046 11.90 8.42 3.48 5.77 8.42 3.48 5.77
14 7107 45C 131L N O 358 1054 9.95 6.31 3.64 7.87 6.31 3.64 7.87
15 7114 46L 42N N O 364 336 5.12 3.02 2.11 5.18 3.02 2.11 5.18
16 7115 46L 43W N O 364 350 5.51 3.67 1.84 5.01 3.67 1.84 5.01
17 7143 47V 43W N O 372 350 5.46 3.22 2.24 6.19 3.22 2.24 6.19
18 7172 48E 43W N O 379 350 7.40 5.22 2.17 4.56 5.22 2.17 4.56
19 7173 48E 44V N O 379 357 6.17 3.06 3.12 7.04 3.06 3.12 7.04
20 7192 49H 43W N O 388 350 9.58 7.34 2.24 4.54 7.34 2.24 4.54
21 7193 49H 44V N O 388 357 7.63 5.19 2.44 5.28 5.19 2.44 5.28
22 7194 49H 45C N O 388 363 5.27 3.16 2.12 4.90 3.16 2.12 4.90
23 7270 52S 44V N O 413 357 11.07 7.80 3.28 5.54 7.80 3.28 5.54
24 7294 53R 43W N O 419 350 11.40 8.71 2.69 5.78 8.71 2.69 5.78
25 7295 53R 44V N O 419 357 11.10 7.07 4.03 9.05 7.07 4.03 9.05
26 7316 54D 44V N O 430 357 12.85 9.46 3.38 6.29 9.46 3.38 6.29
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -76.21 -73.00 17.47 1.08 -63.80 162.30 24.52
1 2Q 2Q N CA 9 10 157.88 140.70 -40.30
2 3811 2Q 3K C N 16 18 -69.53 -70.20 1.62 0.10 -62.90 179.85 23.00
2 3K 3K N CA 18 19 138.92 140.40 -40.80
3 3812 3K 4L C N 25 27 -96.55 -108.50 28.01 1.59 -63.50 164.32 24.83
3 4L 4L N CA 27 28 157.83 132.50 -41.20
4 3815 6I 7F C N 49 51 -155.76 -124.20 32.97 1.01 -63.20 -172.67 31.87
4 7F 7F N CA 51 52 152.84 143.30 -44.30
5 3816 7F 8A C N 60 62 -113.82 -134.00 26.14 0.70 -62.50 178.80 27.28
5 8A 8A N CA 62 63 130.38 147.00 -40.90
6 3817 8A 9L C N 65 67 -108.63 -108.50 22.78 1.23 -63.50 157.52 19.79
6 9L 9L N CA 67 68 109.72 132.50 -41.20
7 3820 11V 12L C N 87 89 -120.27 -108.50 14.46 0.79 -63.50 174.78 21.76
7 12L 12L N CA 89 90 124.10 132.50 -41.20
8 3823 14V 15G C N 108 110 -161.76 -167.20 35.92 1.33 82.20 174.70 13.23
8 15G 15G N CA 110 111 139.10 174.60 8.50
9 3824 15G 16S C N 112 114 -147.01 -136.60 14.20 0.45 -64.10 -176.10 19.27
9 16S 16S N CA 114 115 160.85 151.20 -35.00
10 3830 21F 22T C N 159 161 -83.48 -63.20 80.23 9.10 -63.20 80.23 9.10
10 22T 22T N CA 161 162 35.52 -42.10 -42.10
11 3831 22T 23R C N 166 168 -126.65 -63.00 95.02 16.87 -63.00 95.02 16.87
11 23R 23R N CA 168 169 -111.65 -41.10 -41.10
12 3832 23R 24C C N 177 179 20.17 -63.00 97.34 12.64 -63.00 97.34 12.64
12 24C 24C N CA 179 180 -91.66 -41.10 -41.10
13 3844 35F 36E C N 274 276 52.81 54.60 8.89 0.83 -63.60 137.93 23.73
13 36E 36E N CA 276 277 33.69 42.40 -40.30
14 3852 43W 44V C N 349 351 -75.54 -125.40 57.20 1.53 -62.40 158.21 19.29
14 44V 44V N CA 351 352 115.26 143.30 -42.40
15 3854 45C 46L C N 362 364 -99.05 -63.50 71.92 8.81 -63.50 71.92 8.81
15 46L 46L N CA 364 365 21.32 -41.20 -41.20
16 3860 51S 52S C N 411 413 59.01 56.90 4.06 0.44 -64.10 144.09 18.92
16 52S 52S N CA 413 414 39.87 36.40 -35.00
17 3896 87K 88D C N 695 697 -137.69 -63.30 81.33 13.86 -63.30 81.33 13.86
17 88D 88D N CA 697 698 -72.86 -40.00 -40.00
18 3920 111I 112Y C N 872 874 -17.18 -98.40 82.10 3.52 -63.50 166.40 28.76
18 112Y 112Y N CA 874 875 116.42 128.40 -43.40
19 3923 114R 115H C N 904 906 -84.13 -125.60 72.99 1.93 -63.20 122.83 14.17
19 115H 115H N CA 906 907 78.73 138.80 -42.30
20 3924 115H 116R C N 914 916 -50.67 -63.00 35.67 4.15 -125.20 162.89 8.97
20 116R 116R N CA 916 917 -74.57 -41.10 140.60
21 3934 125N 126H C N 1010 1012 -128.29 -63.20 75.20 9.53 -63.20 75.20 9.53
21 126H 126H N CA 1012 1013 -4.65 -42.30 -42.30
22 3937 128Q 129G C N 1035 1037 103.50 78.70 30.39 1.69 82.20 158.47 6.62
22 129G 129G N CA 1037 1038 -148.53 -166.10 8.50
23 3938 129G 130S C N 1039 1041 -106.70 -136.60 53.03 1.91 -64.10 148.64 9.18
23 130S 130S N CA 1041 1042 107.40 151.20 -35.00
24 3941 132P 133D C N 1060 1062 47.74 -70.90 133.89 11.24 -63.30 154.65 17.58
24 133D 133D N CA 1062 1063 -147.64 150.30 -40.00
25 3943 134I 135S C N 1076 1078 -117.59 -136.60 76.64 3.44 -64.10 124.07 7.84
25 135S 135S N CA 1078 1079 76.95 151.20 -35.00
26 3944 135S 136S C N 1082 1084 -72.17 -72.40 56.64 3.32 -64.10 131.01 9.04
26 136S 136S N CA 1084 1085 95.76 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10318 43W 46L CE3 CG 345 367 10.53 4.66 5.87 4.67 4.66 5.87 4.67
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12050 140. 140. O4 O6 1136 1138 3.69 3.43 0.25 5.01 3.43 0.25 5.01
2 12075 140. 140. O6 O4 1138 1136 3.69 3.43 0.25 5.01 3.43 0.25 5.01
3 12091 24C 138. N O6 179 1108 10.88 3.00 7.88 78.79 3.00 7.88 78.79
4 12092 45C 140. N O6 358 1138 9.88 3.00 6.88 68.81 3.00 6.88 68.81
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 357 362 2.275
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 1 0 3 16 33 100 88 126 148 147 199 183 212
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_liganded.B99990001.pdb 8588.72949
seq_liganded.B99990002.pdb 8644.85254
w_move_lig = nglview.show_structure_file('seq_liganded.B99990001.pdb')
w_move_lig.clear_representations()
w_move_lig.add_cartoon('protein', color_scheme='residueindex')
w_move_lig.add_ball_and_stick('ligand', opacity=0.5)
w_move_lig
Похоже, modeller оскорбился на предложение засунуть лиганд в случайно выбранный карман, и не стал этого делать, но зато он, похоже, просто немного поменял конформацию лиганда, который теперь не совпадает с таковой из 1lmp. В результате и конформация белка чуть-чуть поменялась: нарушилась структура, по крайней мере, у одной альфа-спирали (находящейся рядом с лигандом, кстати), торчащий "хвост" перегнулся в другую сторону.
# 132 остатка в 1lmp
# 140 остатка в целевом лизоциме
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
seq_ala = 'A' * 140 + '...'
alignm.append_sequence(seq_ala)
alignm[0].code = 'pdb'
alignm[1].code = 'seq_ala'
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
! cat all_in_one3.ali
>P1;pdb structureX:1lmp.pdb: 1 :A:+132 :B: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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAW-----------RLHCQNQDLRSYVAGCGV/...* >P1;seq_ala sequence::1 : :+143 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-...*
Аланиновый лизоцим получился, лиганд в него добавился.
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_ala 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: 1 140
atom names : C +N
atom indices : 699 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 140
atom names : C CA +N O
atom indices : 699 697 0 700
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: 10362 9669
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 143
Number of all, selected real atoms : 744 744
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9669 9669
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1308
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 : 731.1749
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 : 700 0 0 0.006 0.006 7.3060 1.000
2 Bond angle potential : 979 0 6 2.330 2.330 108.27 1.000
3 Stereochemical cosine torsion poten: 284 0 34 76.181 76.181 272.20 1.000
4 Stereochemical improper torsion pot: 280 0 0 1.005 1.005 7.5644 1.000
5 Soft-sphere overlap restraints : 1308 2 2 0.011 0.011 17.743 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) : 2405 0 0 0.224 0.224 47.913 1.000
10 Distance restraints 2 (N-O) : 2564 0 9 0.387 0.387 128.03 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: 139 1 5 5.530 5.530 50.132 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) : 717 0 0 0.242 0.242 5.3761 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: 138 27 19 31.813 76.314 67.596 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.356 0.356 0.87062 1.000
27 Distance restraints 5 (X-Y) : 1401 0 1 0.038 0.038 18.174 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: seq_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: 13655.6240
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 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2504 123A 123A CA C 612 614 -151.64 -180.00 28.36 5.67 -180.00 28.36 5.67
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2258 15A 16A C N 74 76 78.17 55.40 27.50 1.88 -62.50 154.41 31.36
1 16A 16A N CA 76 77 22.78 38.20 -40.90
2 2261 18A 19A C N 89 91 63.88 55.40 21.86 0.80 -62.50 139.45 28.33
2 19A 19A N CA 91 92 18.05 38.20 -40.90
3 2263 20A 21A C N 99 101 62.34 -68.20 145.36 14.03 -62.50 166.30 26.08
3 21A 21A N CA 101 102 -150.76 145.30 -40.90
4 2264 21A 22A C N 104 106 -111.79 -134.00 70.76 3.37 -62.50 130.39 19.64
4 22A 22A N CA 106 107 79.82 147.00 -40.90
5 2279 36A 37A C N 179 181 66.67 55.40 14.63 0.88 -62.50 146.80 29.86
5 37A 37A N CA 181 182 28.87 38.20 -40.90
6 2280 37A 38A C N 184 186 61.67 55.40 9.18 0.46 -62.50 143.73 29.23
6 38A 38A N CA 186 187 31.50 38.20 -40.90
7 2291 48A 49A C N 239 241 86.63 55.40 42.32 2.38 -62.50 157.46 31.80
7 49A 49A N CA 241 242 9.65 38.20 -40.90
8 2296 53A 54A C N 264 266 91.59 -134.00 139.58 3.42 -62.50 -155.48 32.11
8 54A 54A N CA 266 267 -175.37 147.00 -40.90
9 2299 56A 57A C N 279 281 59.95 55.40 13.94 1.21 -62.50 153.32 31.04
9 57A 57A N CA 281 282 51.37 38.20 -40.90
10 2309 66A 67A C N 329 331 82.72 55.40 56.16 2.07 -62.50 148.29 29.55
10 67A 67A N CA 331 332 -10.87 38.20 -40.90
11 2312 69A 70A C N 344 346 -63.62 -62.50 20.03 3.34 -68.20 153.87 12.57
11 70A 70A N CA 346 347 -60.90 -40.90 145.30
12 2313 70A 71A C N 349 351 -113.75 -134.00 52.91 2.38 -62.50 148.16 22.40
12 71A 71A N CA 351 352 98.11 147.00 -40.90
13 2316 73A 74A C N 364 366 54.57 55.40 23.93 1.37 -62.50 155.94 31.38
13 74A 74A N CA 366 367 62.12 38.20 -40.90
14 2319 76A 77A C N 379 381 62.30 55.40 10.24 1.13 -62.50 151.93 30.83
14 77A 77A N CA 381 382 45.76 38.20 -40.90
15 2346 103A 104A C N 514 516 82.74 -134.00 157.43 3.58 -62.50 -179.70 28.94
15 104A 104A N CA 516 517 -147.73 147.00 -40.90
16 2354 111A 112A C N 554 556 7.63 -68.20 78.70 5.92 -62.50 179.43 33.16
16 112A 112A N CA 556 557 124.26 145.30 -40.90
17 2355 112A 113A C N 559 561 -71.87 -68.20 4.85 0.31 -62.50 170.90 28.48
17 113A 113A N CA 561 562 148.46 145.30 -40.90
18 2356 113A 114A C N 564 566 -68.53 -68.20 7.23 0.57 -62.50 166.69 27.62
18 114A 114A N CA 566 567 152.52 145.30 -40.90
19 2357 114A 115A C N 569 571 -148.88 -134.00 21.44 0.66 -62.50 178.90 33.93
19 115A 115A N CA 571 572 162.44 147.00 -40.90
20 2359 116A 117A C N 579 581 -158.48 -134.00 24.48 0.80 -62.50 -163.14 37.39
20 117A 117A N CA 581 582 147.23 147.00 -40.90
21 2360 117A 118A C N 584 586 -141.17 -134.00 7.28 0.29 -62.50 -169.64 35.41
21 118A 118A N CA 586 587 145.76 147.00 -40.90
22 2362 119A 120A C N 594 596 -167.92 -134.00 35.69 1.61 -62.50 -154.16 30.85
22 120A 120A N CA 596 597 135.90 147.00 -40.90
23 2363 120A 121A C N 599 601 170.85 -134.00 55.29 1.69 -62.50 -149.41 41.16
23 121A 121A N CA 601 602 150.85 147.00 -40.90
24 2364 121A 122A C N 604 606 -111.01 -134.00 35.82 1.20 -62.50 167.60 25.57
24 122A 122A N CA 606 607 119.53 147.00 -40.90
25 2370 127A 128A C N 634 636 53.12 55.40 4.00 0.16 -62.50 141.97 28.79
25 128A 128A N CA 636 637 41.48 38.20 -40.90
26 2379 136A 137A C N 679 681 68.81 55.40 39.96 1.51 -62.50 137.70 27.75
26 137A 137A N CA 681 682 0.55 38.20 -40.90
27 2381 138A 139A C N 689 691 126.06 -134.00 137.63 4.02 -62.50 -171.87 38.21
27 139A 139A N CA 691 692 -118.38 147.00 -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 6 5 40 53 71 73 73 98 113 86
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 143
Number of all, selected real atoms : 744 744
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9669 9669
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1355
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 : 814.4443
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 : 700 0 0 0.007 0.007 9.7189 1.000
2 Bond angle potential : 979 0 10 2.531 2.531 130.43 1.000
3 Stereochemical cosine torsion poten: 284 0 32 75.648 75.648 266.52 1.000
4 Stereochemical improper torsion pot: 280 0 0 1.024 1.024 7.7049 1.000
5 Soft-sphere overlap restraints : 1355 2 2 0.011 0.011 18.491 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) : 2405 0 0 0.278 0.278 64.992 1.000
10 Distance restraints 2 (N-O) : 2564 0 6 0.364 0.364 112.60 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: 139 1 5 5.936 5.936 57.763 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) : 717 0 0 0.252 0.252 5.5378 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: 138 29 18 28.816 72.768 113.18 1.000
26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.379 0.379 1.0242 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.047 0.047 26.496 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: seq_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: 13715.1045
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 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2484 103A 103A CA C 512 514 -143.66 -180.00 36.34 7.26 -180.00 36.34 7.26
-------------------------------------------------------------------------------------------------
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 2258 15A 16A C N 74 76 77.88 55.40 26.17 1.91 -62.50 154.99 31.49
1 16A 16A N CA 76 77 24.80 38.20 -40.90
2 2261 18A 19A C N 89 91 63.79 55.40 21.27 0.77 -62.50 139.63 28.37
2 19A 19A N CA 91 92 18.66 38.20 -40.90
3 2263 20A 21A C N 99 101 62.20 -68.20 145.25 14.02 -62.50 166.18 26.06
3 21A 21A N CA 101 102 -150.73 145.30 -40.90
4 2264 21A 22A C N 104 106 -111.85 -134.00 74.00 3.56 -62.50 127.25 19.15
4 22A 22A N CA 106 107 76.39 147.00 -40.90
5 2279 36A 37A C N 179 181 66.44 55.40 13.51 0.90 -62.50 147.34 29.97
5 37A 37A N CA 181 182 30.40 38.20 -40.90
6 2280 37A 38A C N 184 186 62.36 55.40 10.84 0.50 -62.50 143.53 29.19
6 38A 38A N CA 186 187 29.89 38.20 -40.90
7 2291 48A 49A C N 239 241 86.16 55.40 42.42 2.32 -62.50 156.80 31.65
7 49A 49A N CA 241 242 8.98 38.20 -40.90
8 2296 53A 54A C N 264 266 92.84 -134.00 138.87 3.36 -62.50 -155.70 32.16
8 54A 54A N CA 266 267 -173.60 147.00 -40.90
9 2299 56A 57A C N 279 281 58.21 55.40 11.97 0.95 -62.50 151.01 30.58
9 57A 57A N CA 281 282 49.84 38.20 -40.90
10 2309 66A 67A C N 329 331 81.23 55.40 58.99 2.13 -62.50 146.07 29.01
10 67A 67A N CA 331 332 -14.84 38.20 -40.90
11 2313 70A 71A C N 349 351 52.37 55.40 12.57 0.53 -62.50 146.73 29.65
11 71A 71A N CA 351 352 50.40 38.20 -40.90
12 2316 73A 74A C N 364 366 53.34 55.40 19.30 1.00 -62.50 151.92 30.62
12 74A 74A N CA 366 367 57.39 38.20 -40.90
13 2319 76A 77A C N 379 381 64.21 55.40 10.54 1.24 -62.50 152.51 30.97
13 77A 77A N CA 381 382 43.98 38.20 -40.90
14 2345 102A 103A C N 509 511 -71.05 -62.50 48.82 7.63 -62.50 48.82 7.63
14 103A 103A N CA 511 512 7.17 -40.90 -40.90
15 2346 103A 104A C N 514 516 -26.17 -62.50 52.64 8.10 -62.50 52.64 8.10
15 104A 104A N CA 516 517 -78.99 -40.90 -40.90
16 2354 111A 112A C N 554 556 -64.34 -68.20 5.00 0.49 -62.50 170.63 28.05
16 112A 112A N CA 556 557 148.48 145.30 -40.90
17 2355 112A 113A C N 559 561 -140.91 -134.00 29.77 1.50 -62.50 163.22 30.94
17 113A 113A N CA 561 562 175.96 147.00 -40.90
18 2356 113A 114A C N 564 566 -54.38 -68.20 15.30 1.06 -62.50 179.82 29.87
18 114A 114A N CA 566 567 138.74 145.30 -40.90
19 2357 114A 115A C N 569 571 164.20 -134.00 71.89 1.69 -62.50 -170.01 37.92
19 115A 115A N CA 571 572 -176.28 147.00 -40.90
20 2358 115A 116A C N 574 576 -109.57 -134.00 29.76 0.74 -62.50 177.26 27.16
20 116A 116A N CA 576 577 129.99 147.00 -40.90
21 2359 116A 117A C N 579 581 -139.12 -134.00 5.19 0.20 -62.50 -170.85 35.10
21 117A 117A N CA 581 582 146.16 147.00 -40.90
22 2362 119A 120A C N 594 596 -179.47 -134.00 48.54 1.12 -62.50 -165.74 37.97
22 120A 120A N CA 596 597 164.00 147.00 -40.90
23 2363 120A 121A C N 599 601 -67.11 -68.20 3.91 0.28 -62.50 177.61 29.34
23 121A 121A N CA 601 602 141.55 145.30 -40.90
24 2364 121A 122A C N 604 606 -78.12 -68.20 11.26 1.09 -62.50 179.80 30.26
24 122A 122A N CA 606 607 139.98 145.30 -40.90
25 2365 122A 123A C N 609 611 -76.60 -62.50 51.55 9.20 -62.50 51.55 9.20
25 123A 123A N CA 611 612 -90.49 -40.90 -40.90
26 2366 123A 124A C N 614 616 -85.58 -62.50 39.95 7.76 -62.50 39.95 7.76
26 124A 124A N CA 616 617 -73.50 -40.90 -40.90
27 2370 127A 128A C N 634 636 54.47 55.40 5.84 0.28 -62.50 144.51 29.29
27 128A 128A N CA 636 637 43.97 38.20 -40.90
28 2379 136A 137A C N 679 681 67.89 55.40 39.38 1.51 -62.50 136.92 27.61
28 137A 137A N CA 681 682 0.86 38.20 -40.90
29 2381 138A 139A C N 689 691 132.45 -134.00 127.17 3.65 -62.50 -173.90 37.84
29 139A 139A N CA 691 692 -126.86 147.00 -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 5 4 49 55 81 69 67 108 121 100
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 731.17487
seq_ala.B99990002.pdb 814.44434
w_ala = nglview.show_structure_file('seq_ala.B99990001.pdb')
w_ala.clear_representations()
w_ala.add_cartoon('protein', color_scheme='residueindex')
w_ala.add_ball_and_stick('ligand', opacity=0.5)
w_ala
w_1lmp
Ну, как-то аланиновый лизоцим подозрительно очень похож на 1lmp.
Сравним скоры:
import pandas as pd
import numpy as np
d = {'без лиганда': [877.83691, 996.56592, np.mean([877.83691, 996.56592])],
'с лигандом': [1411.86523, 1251.51782, np.mean([1411.86523, 1251.51782])],
'со смещенным лигандом': [8588.72949, 8644.85254, np.mean([8588.72949, 8644.85254])],
'аланины': [731.17487, 814.44434, np.mean([731.17487, 814.44434])]}
s = pd.Series(['B99990001', 'B99990002', 'средний скор'])
pd.DataFrame(d).set_index([s])
# чем меньше скор - тем лучше
| без лиганда | с лигандом | со смещенным лигандом | аланины | |
|---|---|---|---|---|
| B99990001 | 877.836910 | 1411.865230 | 8588.729490 | 731.174870 |
| B99990002 | 996.565920 | 1251.517820 | 8644.852540 | 814.444340 |
| средний скор | 937.201415 | 1331.691525 | 8616.791015 | 772.809605 |
Получается, самый лучший лизоцим - аланиновый, несколько хуже - лизоцим без лиганда, еще немного хуже - лизоцим с лигандом. Лизоцим со смещенным лигандом гораздо хуже, потому что в этой модели неудовлетворённое ограничение на расстояние между лигандом и далёкими аминокислотами. Я, наверное, ожидала, что будет ровно наоборот, то есть самой лучшей окажется модель с лигандом, чуть хуже без лиганда, еще чуть хуже аланиновая. Возможно, так произошло из-за того, что лизоцимы форели и тутового шелкопряда все-таки уже сильно различаются, и добавление в лизоцим шелкопряда лиганда из лизоцима форели не делает погоды. Поучительно то, что даже ерунда (аланиновый лизоцим) дает хорошую (лучшую, вобщем-то...) модель. Это значит, что смоделировать можно все что угодно, но хороший скор еще не говорит о том, что модель имеет биологический смысл. Возможно, нужно проводить несколько моделирований, чтобы получать более достоверные скоры.