In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.18, 2017/02/17, r11002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 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 srv 4.15.0-54-generic x86_64
Date and time of compilation : 2017/02/17 14:47:45
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2020/04/15 15:15:23
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-04-15 15:15:54-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-04-15 15:15:54-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: http://files.rcsb.org/view/1lmp.pdb [following] --2020-04-15 15:15:55-- http://files.rcsb.org/view/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 128.6.244.12 Connecting to files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb’ 1lmp.pdb [ <=> ] 127.35K 356KB/s in 0.4s 2020-04-15 15:15:56 (356 KB/s) - ‘1lmp.pdb’ saved [130410]
In [28]:
! wget http://www.uniprot.org/uniprot/P48816.fasta
# (LYS_BOMMO))
--2020-04-15 15:35:55-- http://www.uniprot.org/uniprot/P48816.fasta Resolving www.uniprot.org (www.uniprot.org)... 193.62.192.81, 128.175.245.202 Connecting to www.uniprot.org (www.uniprot.org)|193.62.192.81|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/P48816.fasta [following] --2020-04-15 15:35:56-- https://www.uniprot.org/uniprot/P48816.fasta Connecting to www.uniprot.org (www.uniprot.org)|193.62.192.81|:443... connected. HTTP request sent, awaiting response... 200 Length: 203 [text/plain] Saving to: ‘P48816.fasta’ P48816.fasta 100%[===================>] 203 --.-KB/s in 0s 2020-04-15 15:35:56 (32.7 MB/s) - ‘P48816.fasta’ saved [203/203]
In [35]:
alignm=modeller.alignment(env)
In [36]:
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:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'sequence'
alignm[1].code = '3D'
In [37]:
alignm.salign()
alignm.write(file='1lmp_bommo.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [39]:
#проверим выравнивание - нет лиганда
%cat 1lmp_bommo.ali
>P1;sequence sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC-------* >P1;3D structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
In [40]:
with open('1lmp_bommo.ali','r') as old:
lines = old.readlines()
with open('1lmp_bommo_lig.ali','w') as new:
for c, line in enumerate(lines):
if c == 4:
line = line[:-5]+'...*'
new.write(line)
%cat 1lmp_bommo_lig.ali
>P1;sequence sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC----...* >P1;3D structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Теперь можно создавать гомологичную модель
In [43]:
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='1lmp_bommo_lig.ali', knowns = alignm[1].code, sequence = alignm[0].code )
a.name='mod'+alignm[0].code
a.starting_model = 1
a.ending_model = 2
a.make()
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
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: 13094 12134
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 : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2475
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 : 1047.8652
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 2 0.009 0.009 27.769 1.000
2 Bond angle potential : 1504 1 7 2.204 2.204 146.14 1.000
3 Stereochemical cosine torsion poten: 713 0 31 49.225 49.225 269.18 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.297 1.297 16.740 1.000
5 Soft-sphere overlap restraints : 2475 1 2 0.008 0.008 18.436 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 4 0.293 0.293 93.297 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.336 0.336 134.43 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 4.548 4.548 33.178 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 82.839 82.839 47.058 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 77.377 77.377 36.838 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 68.146 68.146 21.177 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 82.742 82.742 14.932 1.000
18 Disulfide distance restraints : 3 0 0 0.031 0.031 0.49328 1.000
19 Disulfide angle restraints : 6 0 0 3.040 3.040 1.2241 1.000
20 Disulfide dihedral angle restraints: 3 0 0 24.670 24.670 1.8416 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 0.365 0.365 30.168 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 19 31.070 59.331 96.269 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.630 0.630 33.620 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.045 0.045 25.071 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: sequence.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: 16273.3477
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 697 698 126.53 107.00 19.53 5.62 107.00 19.53 5.62
-------------------------------------------------------------------------------------------------
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 -70.37 -73.00 22.36 1.52 -63.80 156.93 23.42
1 2Q 2Q N CA 9 10 162.90 140.70 -40.30
2 3811 2Q 3K C N 16 18 -61.23 -70.20 16.00 1.33 -62.90 165.56 21.41
2 3K 3K N CA 18 19 153.65 140.40 -40.80
3 3812 3K 4L C N 25 27 -58.98 -70.70 20.64 1.28 -63.50 165.88 23.29
3 4L 4L N CA 27 28 124.61 141.60 -41.20
4 3815 6I 7F C N 49 51 -64.27 -71.40 20.70 1.44 -63.20 165.58 22.92
4 7F 7F N CA 51 52 121.27 140.70 -44.30
5 3816 7F 8A C N 60 62 159.82 -134.00 68.09 1.72 -62.50 -151.83 41.22
5 8A 8A N CA 62 63 162.97 147.00 -40.90
6 3817 8A 9L C N 65 67 -94.14 -108.50 31.44 1.52 -63.50 148.92 19.14
6 9L 9L N CA 67 68 104.53 132.50 -41.20
7 3820 11V 12L C N 87 89 -92.38 -108.50 38.06 1.85 -63.50 142.19 18.29
7 12L 12L N CA 89 90 98.02 132.50 -41.20
8 3823 14V 15G C N 108 110 -114.63 -80.20 49.34 3.47 82.20 -151.22 16.25
8 15G 15G N CA 110 111 138.75 174.10 8.50
9 3824 15G 16S C N 112 114 -129.58 -136.60 7.43 0.24 -64.10 -171.98 18.24
9 16S 16S N CA 114 115 148.75 151.20 -35.00
10 3844 35F 36E C N 274 276 56.95 54.60 9.54 0.56 -63.60 141.17 24.29
10 36E 36E N CA 276 277 33.16 42.40 -40.30
11 3859 50E 51S C N 405 407 -140.56 -64.10 85.25 8.88 -64.10 85.25 8.88
11 51S 51S N CA 407 408 2.70 -35.00 -35.00
12 3860 51S 52S C N 411 413 57.67 56.90 4.41 0.35 -64.10 143.40 18.79
12 52S 52S N CA 413 414 40.74 36.40 -35.00
13 3896 87K 88D C N 695 697 -139.24 -63.30 84.13 14.36 -63.30 84.13 14.36
13 88D 88D N CA 697 698 -76.21 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -42.47 -98.40 62.23 3.82 -63.50 146.04 24.26
14 112Y 112Y N CA 874 875 101.12 128.40 -43.40
15 3922 113K 114R C N 893 895 -84.56 -125.20 78.47 2.74 -63.00 116.58 14.42
15 114R 114R N CA 895 896 73.47 140.60 -41.10
16 3923 114R 115H C N 904 906 -157.13 -63.20 94.53 14.44 -63.20 94.53 14.44
16 115H 115H N CA 906 907 -31.67 -42.30 -42.30
17 3934 125N 126H C N 1010 1012 -122.97 -63.20 77.81 9.09 -63.20 77.81 9.09
17 126H 126H N CA 1012 1013 7.51 -42.30 -42.30
18 3935 126H 127C C N 1020 1022 -125.93 -63.00 64.48 9.90 -63.00 64.48 9.90
18 127C 127C N CA 1022 1023 -27.01 -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 1 7 17 61 86 122 132 140 177 174 192
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2409
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 : 1057.4894
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 25.862 1.000
2 Bond angle potential : 1504 1 9 2.228 2.228 151.24 1.000
3 Stereochemical cosine torsion poten: 713 0 33 48.548 48.548 263.31 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.300 1.300 17.383 1.000
5 Soft-sphere overlap restraints : 2409 2 2 0.008 0.008 18.890 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 4 0.293 0.293 98.534 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.333 0.333 139.50 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.665 4.665 34.909 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 76.526 76.526 43.977 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 82.350 82.350 42.830 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 82.328 82.328 23.634 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 75.469 75.469 14.848 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.31739 1.000
19 Disulfide angle restraints : 6 0 0 2.732 2.732 0.98916 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.964 21.964 1.4059 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 0.398 0.398 37.855 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 19 25.153 60.298 85.103 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.627 0.627 32.538 1.000
27 Distance restraints 5 (X-Y) : 1389 0 1 0.046 0.046 24.368 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: sequence.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: 16027.3486
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 697 698 128.06 107.00 21.06 6.05 107.00 21.06 6.05
-------------------------------------------------------------------------------------------------
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 -107.21 -121.10 48.82 2.50 -63.80 140.09 22.91
1 2Q 2Q N CA 9 10 -173.49 139.70 -40.30
2 3811 2Q 3K C N 16 18 -60.49 -70.20 21.56 1.76 -62.90 159.57 20.59
2 3K 3K N CA 18 19 159.65 140.40 -40.80
3 3812 3K 4L C N 25 27 -64.41 -70.70 38.76 2.71 -63.50 144.55 20.02
3 4L 4L N CA 27 28 103.35 141.60 -41.20
4 3815 6I 7F C N 49 51 -161.55 -124.20 37.98 1.28 -63.20 -167.47 32.92
4 7F 7F N CA 51 52 150.18 143.30 -44.30
5 3816 7F 8A C N 60 62 -171.84 -134.00 45.23 1.10 -62.50 -176.54 35.81
5 8A 8A N CA 62 63 171.79 147.00 -40.90
6 3817 8A 9L C N 65 67 -68.19 -70.70 10.74 0.91 -63.50 166.82 23.43
6 9L 9L N CA 67 68 152.04 141.60 -41.20
7 3820 11V 12L C N 87 89 -141.14 -108.50 37.77 1.67 -63.50 -175.57 30.41
7 12L 12L N CA 89 90 151.51 132.50 -41.20
8 3823 14V 15G C N 108 110 -96.36 -80.20 33.19 0.78 82.20 -116.59 18.79
8 15G 15G N CA 110 111 -156.92 174.10 8.50
9 3824 15G 16S C N 112 114 -111.77 -136.60 28.67 0.87 -64.10 178.34 11.05
9 16S 16S N CA 114 115 136.85 151.20 -35.00
10 3844 35F 36E C N 274 276 52.87 54.60 4.00 0.44 -63.60 140.79 24.21
10 36E 36E N CA 276 277 38.79 42.40 -40.30
11 3859 50E 51S C N 405 407 -138.32 -64.10 83.82 8.59 -64.10 83.82 8.59
11 51S 51S N CA 407 408 3.96 -35.00 -35.00
12 3860 51S 52S C N 411 413 59.98 56.90 6.16 0.26 -64.10 140.57 18.61
12 52S 52S N CA 413 414 31.07 36.40 -35.00
13 3896 87K 88D C N 695 697 175.19 -96.50 94.37 3.84 -63.30 171.42 19.38
13 88D 88D N CA 697 698 80.92 114.20 -40.00
14 3923 114R 115H C N 904 906 -79.63 -125.60 68.20 1.71 -63.20 131.74 15.51
14 115H 115H N CA 906 907 88.41 138.80 -42.30
15 3924 115H 116R C N 914 916 -55.71 -63.00 43.20 5.38 -125.20 152.49 8.39
15 116R 116R N CA 916 917 -83.67 -41.10 140.60
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 16 60 78 119 128 117 173 177 176
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sequence.B99990001.pdb 1047.86523
sequence.B99990002.pdb 1057.48938
Посмотрим на них: розовым - созданная модель, желтым - референсная
оба лиганда на месте - слились
In [50]:
! rm sequence.rsr # удаляем рестрейны
In [64]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:14','O6:138')]: #вносим ограничение на расстоянии до 1 ангстрема N - 14 остатка и О6 - лиганда
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=1.0, stdev=0.01))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='1lmp_bommo_lig.ali', knowns=alignm[1].code, sequence=alignm[0].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()
In [65]:
a.name = 'mod' + alignm[0].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
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: 13095 12135
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 : 12135 12135
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2991
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 : 3882.2852
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 14 17 0.033 0.033 369.74 1.000
2 Bond angle potential : 1504 11 45 3.815 3.815 442.80 1.000
3 Stereochemical cosine torsion poten: 713 0 40 49.851 49.851 276.24 1.000
4 Stereochemical improper torsion pot: 461 1 4 2.301 2.301 51.052 1.000
5 Soft-sphere overlap restraints : 2991 5 6 0.034 0.034 406.74 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 31 62 0.732 0.732 859.49 1.000
10 Distance restraints 2 (N-O) : 2371 24 57 0.648 0.648 707.41 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 4 6.042 6.042 58.557 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 6 75.529 75.529 52.784 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 77.034 77.034 41.522 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 70.226 70.226 23.186 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 63.942 63.942 11.946 1.000
18 Disulfide distance restraints : 3 0 0 0.020 0.020 0.20735 1.000
19 Disulfide angle restraints : 6 0 1 5.843 5.843 4.5230 1.000
20 Disulfide dihedral angle restraints: 3 0 0 28.703 28.703 2.4671 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 0.394 0.394 33.488 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 22 28 38.051 69.691 146.78 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 4 8 1.317 1.317 130.99 1.000
27 Distance restraints 5 (X-Y) : 1390 1 24 0.122 0.122 262.37 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: sequence.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: 22063.8926
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
1 103 13C 14V C N 101 103 1.54 1.35 0.19 6.86 1.35 0.19 6.86
2 107 14V 14V N CA 103 104 1.76 1.43 0.33 10.95 1.43 0.33 10.95
3 109 14V 14V C CA 108 104 1.94 1.49 0.45 12.94 1.49 0.45 12.94
4 110 14V 15G C N 108 110 1.62 1.35 0.27 9.70 1.35 0.27 9.70
5 111 15G 15G N CA 110 111 1.76 1.43 0.33 11.00 1.43 0.33 11.00
6 113 15G 15G C CA 112 111 1.91 1.49 0.42 12.07 1.49 0.42 12.07
7 114 15G 16S C N 112 114 1.63 1.35 0.28 10.07 1.35 0.28 10.07
8 117 16S 16S N CA 114 115 1.71 1.43 0.28 9.26 1.43 0.28 9.26
9 119 16S 16S C CA 118 115 1.77 1.49 0.28 8.11 1.49 0.28 8.11
10 120 16S 17E C N 118 120 1.51 1.35 0.16 5.76 1.35 0.16 5.76
11 126 17E 17E N CA 120 121 1.61 1.43 0.18 5.84 1.43 0.18 5.84
12 128 17E 17E C CA 127 121 1.67 1.49 0.18 5.33 1.49 0.18 5.33
13 129 17E 18A C N 127 129 1.49 1.35 0.14 5.00 1.35 0.14 5.00
14 131 18A 18A N CA 129 130 1.57 1.43 0.14 4.70 1.43 0.14 4.70
-------------------------------------------------------------------------------------------------
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 1263 14V 14V N CA 103 104 136.78 107.00 29.78 8.56 107.00 29.78 8.56
2 1267 14V 14V CA C 104 108 137.49 116.50 20.99 6.04 116.50 20.99 6.04
3 1270 14V 15G C N 108 110 142.88 120.00 22.88 5.20 120.00 22.88 5.20
4 1272 15G 15G N CA 110 111 138.19 107.00 31.19 8.97 107.00 31.19 8.97
5 1274 15G 15G CA C 111 112 137.20 116.50 20.71 5.95 116.50 20.71 5.95
6 1275 15G 16S C N 112 114 141.73 120.00 21.73 4.94 120.00 21.73 4.94
7 1278 16S 16S N CA 114 115 135.61 107.00 28.61 8.23 107.00 28.61 8.23
8 1286 17E 17E N CA 120 121 130.01 107.00 23.01 6.61 107.00 23.01 6.61
9 2080 88D 88D N CA 697 698 126.99 107.00 19.99 5.75 107.00 19.99 5.75
-------------------------------------------------------------------------------------------------
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 4357 16S 54D CA CA 115 431 10.04 5.80 4.24 8.73 5.80 4.24 8.73
2 4358 16S 55T CA CA 115 439 8.12 5.51 2.61 6.01 5.51 2.61 6.01
3 4359 16S 56S CA CA 115 446 11.18 6.77 4.41 8.10 6.77 4.41 8.10
4 4370 16S 98T CA CA 115 772 10.66 7.38 3.29 4.73 7.38 3.29 4.73
5 4371 16S 99D CA CA 115 779 10.62 4.93 5.70 10.40 4.93 5.70 10.40
6 4391 17E 54D CA CA 121 431 6.83 4.29 2.54 5.83 4.29 2.54 5.83
-------------------------------------------------------------------------------------------------
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 6563 16S 52S N O 114 418 12.85 9.40 3.45 4.66 9.40 3.45 4.66
2 6564 16S 53R N O 114 429 10.38 6.35 4.04 7.36 6.35 4.04 7.36
3 6566 16S 55T N O 114 444 9.18 6.09 3.08 5.88 6.09 3.08 5.88
4 6567 16S 56S N O 114 450 12.58 7.78 4.81 7.07 7.78 4.81 7.07
5 6573 16S 97L N O 114 770 11.11 5.18 5.93 9.46 5.18 5.93 9.46
6 6574 16S 98T N O 114 777 10.14 5.41 4.73 6.85 5.41 4.73 6.85
7 6575 16S 99D N O 114 785 11.21 6.03 5.19 7.13 6.03 5.19 7.13
8 6581 17E 52S N O 120 418 10.10 6.94 3.17 4.55 6.94 3.17 4.55
9 6582 17E 53R N O 120 429 6.85 4.43 2.42 4.60 4.43 2.42 4.60
10 7316 54D 16S N O 430 119 7.38 4.59 2.79 5.05 4.59 2.79 5.05
11 7342 55T 16S N O 438 119 6.31 3.07 3.24 6.97 3.07 3.24 6.97
12 7369 56S 16S N O 445 119 7.64 4.83 2.81 4.73 4.83 2.81 4.73
13 8023 86G 63N N O 684 508 10.64 7.27 3.36 4.75 7.27 3.36 4.75
14 8033 87K 63N N O 688 508 12.14 8.66 3.48 5.81 8.66 3.48 5.81
-------------------------------------------------------------------------------------------------
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 -82.92 -73.00 10.85 0.68 -63.80 175.65 26.84
1 2Q 2Q N CA 9 10 145.09 140.70 -40.30
2 3811 2Q 3K C N 16 18 -71.27 -70.20 12.14 0.90 -62.90 169.31 21.54
2 3K 3K N CA 18 19 128.30 140.40 -40.80
3 3812 3K 4L C N 25 27 -99.40 -108.50 20.47 0.99 -63.50 159.46 20.38
3 4L 4L N CA 27 28 114.16 132.50 -41.20
4 3815 6I 7F C N 49 51 -64.45 -71.40 20.41 1.43 -63.20 165.81 22.94
4 7F 7F N CA 51 52 121.51 140.70 -44.30
5 3816 7F 8A C N 60 62 -121.89 -134.00 15.37 0.40 -62.50 -171.94 28.56
5 8A 8A N CA 62 63 137.54 147.00 -40.90
6 3817 8A 9L C N 65 67 -137.47 -108.50 52.42 2.98 -63.50 149.59 18.33
6 9L 9L N CA 67 68 88.82 132.50 -41.20
7 3820 11V 12L C N 87 89 -176.13 -108.50 119.72 5.60 -63.50 142.63 26.10
7 12L 12L N CA 89 90 -128.71 132.50 -41.20
8 3823 14V 15G C N 108 110 172.16 -167.20 23.26 0.73 82.20 179.53 12.72
8 15G 15G N CA 110 111 163.86 174.60 8.50
9 3824 15G 16S C N 112 114 -164.04 -136.60 81.52 3.47 -64.10 139.29 17.23
9 16S 16S N CA 114 115 -132.04 151.20 -35.00
10 3826 17E 18A C N 127 129 150.07 -134.00 84.65 1.93 -68.20 147.03 11.07
10 18A 18A N CA 129 130 -175.59 147.00 145.30
11 3841 32K 33H C N 249 251 -57.84 -63.20 10.50 1.12 -125.60 -177.11 8.00
11 33H 33H N CA 251 252 -51.33 -42.30 138.80
12 3842 33H 34G C N 259 261 -86.23 -62.40 29.96 4.38 82.20 171.37 12.50
12 34G 34G N CA 261 262 -23.05 -41.20 8.50
13 3844 35F 36E C N 274 276 56.99 54.60 9.40 0.55 -63.60 141.28 24.31
13 36E 36E N CA 276 277 33.30 42.40 -40.30
14 3859 50E 51S C N 405 407 -149.53 -64.10 99.23 9.82 -64.10 99.23 9.82
14 51S 51S N CA 407 408 15.49 -35.00 -35.00
15 3860 51S 52S C N 411 413 54.27 56.90 8.16 0.34 -64.10 142.38 18.54
15 52S 52S N CA 413 414 44.12 36.40 -35.00
16 3871 62R 63N C N 499 501 -72.47 -119.90 70.66 3.84 -63.20 129.85 16.75
16 63N 63N N CA 501 502 -170.62 137.00 -41.10
17 3872 63N 64G C N 507 509 -68.93 -62.40 22.91 3.17 82.20 153.65 11.19
17 64G 64G N CA 509 510 -19.24 -41.20 8.50
18 3896 87K 88D C N 695 697 169.63 -96.50 96.65 3.93 -63.30 -177.34 20.51
18 88D 88D N CA 697 698 91.21 114.20 -40.00
19 3920 111I 112Y C N 872 874 -48.24 -98.40 56.05 3.47 -63.50 147.60 24.21
19 112Y 112Y N CA 874 875 103.41 128.40 -43.40
20 3922 113K 114R C N 893 895 -78.10 -125.20 63.18 1.89 -63.00 140.41 18.00
20 114R 114R N CA 895 896 98.49 140.60 -41.10
21 3923 114R 115H C N 904 906 175.06 -63.20 122.04 18.92 -63.20 122.04 18.92
21 115H 115H N CA 906 907 -33.72 -42.30 -42.30
22 3944 135S 136S C N 1082 1084 -83.68 -72.40 87.01 4.74 -64.10 88.52 7.74
22 136S 136S N CA 1084 1085 -121.33 152.40 -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 10251 16S 99D CB CB 116 780 12.06 3.64 8.42 4.98 3.64 8.42 4.98
2 10252 16S 99D CB CG 116 781 12.39 3.52 8.88 5.29 3.52 8.88 5.29
3 10253 16S 99D CB OD1 116 782 11.53 3.36 8.16 4.92 3.36 8.16 4.92
4 10254 16S 99D CB OD2 116 783 13.62 4.26 9.36 5.32 4.26 9.36 5.32
-------------------------------------------------------------------------------------------------
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 12135 14V 138. N O6 103 1109 1.14 1.00 0.14 14.48 1.00 0.14 14.48
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 103 1102 2.247
serious non-bonded atom clash: 103 1109 1.145
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: 1 0 1 0 2 17 28 105 108 149 161 173 210 199 240
<< 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.
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 : 12135 12135
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2929
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 : 3908.7000
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 14 23 0.034 0.034 395.00 1.000
2 Bond angle potential : 1504 13 43 3.903 3.903 461.50 1.000
3 Stereochemical cosine torsion poten: 713 0 40 50.325 50.325 281.53 1.000
4 Stereochemical improper torsion pot: 461 1 5 2.600 2.600 61.319 1.000
5 Soft-sphere overlap restraints : 2929 5 6 0.034 0.034 396.77 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 29 59 0.720 0.720 812.44 1.000
10 Distance restraints 2 (N-O) : 2371 24 51 0.625 0.625 636.30 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 6.477 6.477 67.278 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 78.393 78.393 54.000 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 83.896 83.896 44.822 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 75.471 75.471 20.521 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 82.028 82.028 13.721 1.000
18 Disulfide distance restraints : 3 0 0 0.041 0.041 0.86805 1.000
19 Disulfide angle restraints : 6 0 0 4.187 4.187 2.3222 1.000
20 Disulfide dihedral angle restraints: 3 0 0 12.296 12.296 0.52349 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 0.446 0.446 46.921 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 21 24 33.693 65.627 136.72 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 4 16 1.395 1.395 150.51 1.000
27 Distance restraints 5 (X-Y) : 1390 7 30 0.145 0.145 325.64 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: sequence.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: 22645.0957
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
1 103 13C 14V C N 101 103 1.55 1.35 0.21 7.28 1.35 0.21 7.28
2 107 14V 14V N CA 103 104 1.77 1.43 0.34 11.29 1.43 0.34 11.29
3 109 14V 14V C CA 108 104 1.94 1.49 0.45 12.95 1.49 0.45 12.95
4 110 14V 15G C N 108 110 1.63 1.35 0.28 10.05 1.35 0.28 10.05
5 111 15G 15G N CA 110 111 1.77 1.43 0.34 11.16 1.43 0.34 11.16
6 113 15G 15G C CA 112 111 1.90 1.49 0.41 12.03 1.49 0.41 12.03
7 114 15G 16S C N 112 114 1.63 1.35 0.29 10.18 1.35 0.29 10.18
8 117 16S 16S N CA 114 115 1.72 1.43 0.29 9.40 1.43 0.29 9.40
9 119 16S 16S C CA 118 115 1.78 1.49 0.29 8.41 1.49 0.29 8.41
10 120 16S 17E C N 118 120 1.51 1.35 0.16 5.85 1.35 0.16 5.85
11 126 17E 17E N CA 120 121 1.61 1.43 0.18 6.05 1.43 0.18 6.05
12 128 17E 17E C CA 127 121 1.67 1.49 0.18 5.11 1.49 0.18 5.11
13 129 17E 18A C N 127 129 1.48 1.35 0.14 4.85 1.35 0.14 4.85
14 131 18A 18A N CA 129 130 1.57 1.43 0.14 4.63 1.43 0.14 4.63
-------------------------------------------------------------------------------------------------
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 1234 11V 11V N CA 82 83 125.22 107.00 18.22 5.24 107.00 18.22 5.24
2 1263 14V 14V N CA 103 104 137.09 107.00 30.09 8.65 107.00 30.09 8.65
3 1267 14V 14V CA C 104 108 136.89 116.50 20.39 5.86 116.50 20.39 5.86
4 1270 14V 15G C N 108 110 143.32 120.00 23.32 5.30 120.00 23.32 5.30
5 1272 15G 15G N CA 110 111 138.74 107.00 31.74 9.13 107.00 31.74 9.13
6 1274 15G 15G CA C 111 112 137.97 116.50 21.47 6.17 116.50 21.47 6.17
7 1275 15G 16S C N 112 114 141.68 120.00 21.68 4.93 120.00 21.68 4.93
8 1278 16S 16S N CA 114 115 134.82 107.00 27.82 8.00 107.00 27.82 8.00
9 1286 17E 17E N CA 120 121 129.32 107.00 22.32 6.42 107.00 22.32 6.42
10 1981 78W 78W N CA 627 628 123.10 107.00 16.10 4.63 107.00 16.10 4.63
11 2080 88D 88D N CA 697 698 127.69 107.00 20.69 5.95 107.00 20.69 5.95
-------------------------------------------------------------------------------------------------
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 4357 16S 54D CA CA 115 431 9.92 5.80 4.12 8.49 5.80 4.12 8.49
2 4358 16S 55T CA CA 115 439 7.91 5.51 2.40 5.53 5.51 2.40 5.53
3 4359 16S 56S CA CA 115 446 11.04 6.77 4.27 7.85 6.77 4.27 7.85
4 4371 16S 99D CA CA 115 779 10.35 4.93 5.42 9.90 4.93 5.42 9.90
5 4391 17E 54D CA CA 121 431 6.72 4.29 2.43 5.58 4.29 2.43 5.58
-------------------------------------------------------------------------------------------------
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 6563 16S 52S N O 114 418 12.74 9.40 3.34 4.51 9.40 3.34 4.51
2 6564 16S 53R N O 114 429 10.17 6.35 3.82 6.97 6.35 3.82 6.97
3 6566 16S 55T N O 114 444 9.02 6.09 2.93 5.59 6.09 2.93 5.59
4 6567 16S 56S N O 114 450 12.41 7.78 4.64 6.82 7.78 4.64 6.82
5 6573 16S 97L N O 114 770 10.90 5.18 5.72 9.12 5.18 5.72 9.12
6 6574 16S 98T N O 114 777 9.81 5.41 4.40 6.36 5.41 4.40 6.36
7 6575 16S 99D N O 114 785 10.88 6.03 4.85 6.67 6.03 4.85 6.67
8 7316 54D 16S N O 430 119 7.25 4.59 2.65 4.80 4.59 2.65 4.80
9 7342 55T 16S N O 438 119 6.07 3.07 3.01 6.46 3.07 3.01 6.46
10 7369 56S 16S N O 445 119 7.54 4.83 2.71 4.56 4.83 2.71 4.56
11 8023 86G 63N N O 684 508 10.58 7.27 3.31 4.67 7.27 3.31 4.67
12 8033 87K 63N N O 688 508 11.90 8.66 3.24 5.41 8.66 3.24 5.41
-------------------------------------------------------------------------------------------------
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 -103.97 -121.10 20.21 0.62 -63.80 173.98 23.66
1 2Q 2Q N CA 9 10 128.98 139.70 -40.30
2 3811 2Q 3K C N 16 18 -117.37 -118.00 20.06 0.98 -62.90 169.06 25.20
2 3K 3K N CA 18 19 159.15 139.10 -40.80
3 3812 3K 4L C N 25 27 -83.55 -108.50 38.70 1.77 -63.50 145.50 19.14
3 4L 4L N CA 27 28 102.91 132.50 -41.20
4 3815 6I 7F C N 49 51 -143.65 -124.20 28.54 1.58 -63.20 -174.88 21.31
4 7F 7F N CA 51 52 122.42 143.30 -44.30
5 3816 7F 8A C N 60 62 172.53 -134.00 55.29 1.37 -62.50 -158.50 39.55
5 8A 8A N CA 62 63 161.04 147.00 -40.90
6 3817 8A 9L C N 65 67 -122.61 -108.50 31.92 1.82 -63.50 156.65 19.33
6 9L 9L N CA 67 68 103.87 132.50 -41.20
7 3820 11V 12L C N 87 89 -177.59 -108.50 106.44 4.87 -63.50 155.27 28.14
7 12L 12L N CA 89 90 -146.53 132.50 -41.20
8 3823 14V 15G C N 108 110 167.12 -167.20 27.84 0.82 82.20 177.03 12.41
8 15G 15G N CA 110 111 163.83 174.60 8.50
9 3824 15G 16S C N 112 114 -162.07 -136.60 79.11 3.40 -64.10 139.21 17.10
9 16S 16S N CA 114 115 -133.90 151.20 -35.00
10 3826 17E 18A C N 127 129 142.17 -134.00 90.11 2.07 -68.20 153.61 11.78
10 18A 18A N CA 129 130 -179.95 147.00 145.30
11 3844 35F 36E C N 274 276 48.36 54.60 6.43 0.66 -63.60 140.13 24.05
11 36E 36E N CA 276 277 43.97 42.40 -40.30
12 3859 50E 51S C N 405 407 -153.47 -64.10 106.96 10.22 -64.10 106.96 10.22
12 51S 51S N CA 407 408 23.78 -35.00 -35.00
13 3860 51S 52S C N 411 413 52.49 56.90 5.07 0.42 -64.10 138.04 18.06
13 52S 52S N CA 413 414 38.90 36.40 -35.00
14 3871 62R 63N C N 499 501 -77.30 -119.90 55.66 2.99 -63.20 146.76 19.14
14 63N 63N N CA 501 502 172.82 137.00 -41.10
15 3872 63N 64G C N 507 509 -58.23 -62.40 25.74 4.06 82.20 142.52 10.34
15 64G 64G N CA 509 510 -15.80 -41.20 8.50
16 3896 87K 88D C N 695 697 161.12 -96.50 102.99 4.20 -63.30 -162.88 22.04
16 88D 88D N CA 697 698 103.09 114.20 -40.00
17 3920 111I 112Y C N 872 874 -54.40 -98.40 50.54 3.31 -63.50 147.22 23.83
17 112Y 112Y N CA 874 875 103.54 128.40 -43.40
18 3923 114R 115H C N 904 906 -86.30 -125.60 66.46 1.73 -63.20 129.58 14.90
18 115H 115H N CA 906 907 85.20 138.80 -42.30
19 3924 115H 116R C N 914 916 -54.36 -63.00 41.24 5.05 -125.20 155.10 8.54
19 116R 116R N CA 916 917 -81.43 -41.10 140.60
20 3935 126H 127C C N 1020 1022 -126.13 -63.00 74.99 9.60 -63.00 74.99 9.60
20 127C 127C N CA 1022 1023 -0.63 -41.10 -41.10
21 3942 133D 134I C N 1068 1070 -86.18 -63.40 62.63 9.63 -63.40 62.63 9.63
21 134I 134I N CA 1070 1071 14.73 -43.60 -43.60
-------------------------------------------------------------------------------------------------
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 10251 16S 99D CB CB 116 780 11.87 3.64 8.24 4.87 3.64 8.24 4.87
2 10252 16S 99D CB CG 116 781 12.31 3.52 8.79 5.24 3.52 8.79 5.24
3 10253 16S 99D CB OD1 116 782 11.51 3.36 8.14 4.91 3.36 8.14 4.91
4 10254 16S 99D CB OD2 116 783 13.54 4.26 9.28 5.27 4.26 9.28 5.27
-------------------------------------------------------------------------------------------------
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 11112 114R 138. CA O6 896 1109 7.78 6.81 0.96 4.82 6.81 0.96 4.82
2 12135 14V 138. N O6 103 1109 1.14 1.00 0.14 13.86 1.00 0.14 13.86
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 103 1102 2.243
serious non-bonded atom clash: 103 1109 1.139
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: 1 0 1 0 1 22 22 102 90 163 165 159 189 218 221
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sequence.B99990001.pdb 3882.28516
sequence.B99990002.pdb 3908.69995
Видим сдвиг лиганда правда не очень значительный, но по скорам различие существенно
Аланиновый вариант
In [74]:
alignm=modeller.alignment(env)
In [70]:
print(len(st))
144
In [76]:
ala = 'A' * 144 + '...'
alignm.append_sequence(ala)
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'sequence'
alignm[1].code = '3D'
In [77]:
alignm.salign()
alignm.write(file='ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [79]:
cat! ala.ali
cat: '!': No such file or directory >P1;sequence sequence::1 : :+147 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...* >P1;3D structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------------- --WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
In [80]:
a = modeller.automodel.automodel(env, alnfile='ala.ali', knowns = alignm[1].code, sequence = alignm[0].code )
a.name='mod'+alignm[0].code
a.starting_model = 1
a.ending_model = 2
a.make()
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: 1 144
atom names : C +N
atom indices : 719 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 144
atom names : C CA +N O
atom indices : 719 717 0 720
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: 10460 9747
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 764 764
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9747 9747
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1439
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 : 905.8965
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 : 720 0 0 0.008 0.008 12.384 1.000
2 Bond angle potential : 1007 2 10 2.653 2.653 147.85 1.000
3 Stereochemical cosine torsion poten: 292 0 40 78.597 78.597 294.60 1.000
4 Stereochemical improper torsion pot: 288 0 0 1.101 1.101 8.8700 1.000
5 Soft-sphere overlap restraints : 1439 2 3 0.012 0.012 24.840 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 1 0.277 0.277 71.617 1.000
10 Distance restraints 2 (N-O) : 2564 0 8 0.405 0.405 157.82 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: 143 3 6 6.482 6.482 70.862 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) : 722 0 0 0.267 0.267 5.7916 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: 142 35 23 34.761 85.530 85.275 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.481 0.481 1.2453 1.000
27 Distance restraints 5 (X-Y) : 1401 0 2 0.046 0.046 24.739 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: sequence.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: 15746.2129
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 1156 63A 63A N CA 311 312 123.44 107.00 16.44 4.73 107.00 16.44 4.73
-------------------------------------------------------------------------------------------------
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 2485 36A 36A CA C 177 179 -155.18 -180.00 24.82 4.96 -180.00 24.82 4.96
-------------------------------------------------------------------------------------------------
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 2309 2A 3A C N 9 11 -66.70 -62.50 4.37 0.88 -68.20 172.63 13.98
1 3A 3A N CA 11 12 -42.07 -40.90 145.30
2 2310 3A 4A C N 14 16 70.96 -68.20 139.76 11.40 -68.20 139.76 11.40
2 4A 4A N CA 16 17 132.36 145.30 145.30
3 2322 15A 16A C N 74 76 78.40 55.40 26.60 1.96 -62.50 155.47 31.59
3 16A 16A N CA 76 77 24.84 38.20 -40.90
4 2325 18A 19A C N 89 91 66.13 55.40 23.70 0.86 -62.50 141.09 28.65
4 19A 19A N CA 91 92 17.07 38.20 -40.90
5 2327 20A 21A C N 99 101 53.79 55.40 4.30 0.39 -62.50 138.43 28.12
5 21A 21A N CA 101 102 34.21 38.20 -40.90
6 2328 21A 22A C N 104 106 61.76 55.40 8.76 0.48 -62.50 144.16 29.31
6 22A 22A N CA 106 107 32.17 38.20 -40.90
7 2343 36A 37A C N 179 181 81.22 55.40 149.74 11.16 -62.50 -163.91 30.56
7 37A 37A N CA 181 182 -174.30 38.20 -40.90
8 2355 48A 49A C N 239 241 84.47 55.40 39.13 2.22 -62.50 156.21 31.59
8 49A 49A N CA 241 242 12.02 38.20 -40.90
9 2360 53A 54A C N 264 266 90.78 -134.00 140.60 3.43 -62.50 -156.67 31.93
9 54A 54A N CA 266 267 -174.50 147.00 -40.90
10 2363 56A 57A C N 279 281 59.75 55.40 15.12 1.27 -62.50 153.95 31.15
10 57A 57A N CA 281 282 52.68 38.20 -40.90
11 2368 61A 62A C N 304 306 -66.58 -62.50 41.69 6.64 -62.50 41.69 6.64
11 62A 62A N CA 306 307 0.59 -40.90 -40.90
12 2369 62A 63A C N 309 311 -116.58 -62.50 91.14 17.78 -62.50 91.14 17.78
12 63A 63A N CA 311 312 -114.26 -40.90 -40.90
13 2370 63A 64A C N 314 316 -57.48 -68.20 10.88 0.86 -62.50 175.74 28.56
13 64A 64A N CA 316 317 143.44 145.30 -40.90
14 2371 64A 65A C N 319 321 -167.78 -134.00 34.84 0.87 -62.50 -165.45 37.47
14 65A 65A N CA 321 322 155.50 147.00 -40.90
15 2372 65A 66A C N 324 326 -107.02 -134.00 35.76 0.99 -62.50 170.34 26.12
15 66A 66A N CA 326 327 123.52 147.00 -40.90
16 2373 66A 67A C N 329 331 -161.05 -134.00 28.51 1.29 -62.50 -155.73 30.60
16 67A 67A N CA 331 332 138.02 147.00 -40.90
17 2374 67A 68A C N 334 336 155.52 -134.00 74.33 1.75 -62.50 -154.56 40.92
17 68A 68A N CA 336 337 170.62 147.00 -40.90
18 2375 68A 69A C N 339 341 -69.85 -68.20 11.63 0.88 -62.50 162.46 26.99
18 69A 69A N CA 341 342 156.81 145.30 -40.90
19 2376 69A 70A C N 344 346 -58.30 -68.20 25.66 1.73 -62.50 162.58 26.85
19 70A 70A N CA 346 347 121.63 145.30 -40.90
20 2377 70A 71A C N 349 351 162.32 -134.00 68.83 1.57 -62.50 -161.02 39.54
20 71A 71A N CA 351 352 173.10 147.00 -40.90
21 2378 71A 72A C N 354 356 -124.49 -134.00 16.21 0.59 -62.50 -174.56 28.09
21 72A 72A N CA 356 357 133.87 147.00 -40.90
22 2379 72A 73A C N 359 361 175.46 -134.00 55.32 1.26 -62.50 -166.92 38.00
22 73A 73A N CA 361 362 169.48 147.00 -40.90
23 2380 73A 74A C N 364 366 89.71 -134.00 136.97 4.04 -62.50 -140.28 33.83
23 74A 74A N CA 366 367 160.64 147.00 -40.90
24 2381 74A 75A C N 369 371 -124.45 -134.00 9.55 0.31 -62.50 -176.91 33.32
24 75A 75A N CA 371 372 146.81 147.00 -40.90
25 2382 75A 76A C N 374 376 -122.73 -134.00 14.87 0.85 -62.50 173.21 31.61
25 76A 76A N CA 376 377 156.70 147.00 -40.90
26 2383 76A 77A C N 379 381 168.70 -134.00 61.46 2.90 -62.50 -150.16 31.76
26 77A 77A N CA 381 382 124.77 147.00 -40.90
27 2388 81A 82A C N 404 406 79.83 55.40 54.31 1.97 -62.50 145.58 29.04
27 82A 82A N CA 406 407 -10.31 38.20 -40.90
28 2392 85A 86A C N 424 426 50.92 55.40 15.62 0.62 -62.50 147.35 29.73
28 86A 86A N CA 426 427 53.16 38.20 -40.90
29 2395 88A 89A C N 439 441 72.97 55.40 18.19 2.13 -62.50 159.30 32.38
29 89A 89A N CA 441 442 42.92 38.20 -40.90
30 2398 91A 92A C N 454 456 60.66 55.40 12.39 1.17 -62.50 152.73 30.94
30 92A 92A N CA 456 457 49.42 38.20 -40.90
31 2425 118A 119A C N 589 591 82.14 -134.00 158.23 3.59 -62.50 179.45 28.81
31 119A 119A N CA 591 592 -147.11 147.00 -40.90
32 2438 131A 132A C N 654 656 43.62 55.40 29.98 1.09 -62.50 150.46 30.05
32 132A 132A N CA 656 657 65.76 38.20 -40.90
33 2440 133A 134A C N 664 666 -63.81 -62.50 36.75 5.96 -134.00 166.67 7.25
33 134A 134A N CA 666 667 -4.17 -40.90 147.00
34 2447 140A 141A C N 699 701 72.39 55.40 43.58 1.59 -62.50 140.40 28.23
34 141A 141A N CA 701 702 -1.94 38.20 -40.90
35 2449 142A 143A C N 709 711 62.49 55.40 8.81 0.57 -62.50 145.19 29.52
35 143A 143A N CA 711 712 32.98 38.20 -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 8 7 51 60 84 80 81 132 124 90
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 764 764
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9747 9747
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1352
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 : 843.9468
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 : 720 0 0 0.006 0.006 6.8799 1.000
2 Bond angle potential : 1007 1 9 2.454 2.454 125.60 1.000
3 Stereochemical cosine torsion poten: 292 0 38 76.648 76.648 281.57 1.000
4 Stereochemical improper torsion pot: 288 0 2 1.670 1.670 16.417 1.000
5 Soft-sphere overlap restraints : 1352 2 2 0.011 0.011 18.740 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 0.259 0.259 60.590 1.000
10 Distance restraints 2 (N-O) : 2564 0 5 0.376 0.376 139.29 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: 143 1 7 5.463 5.463 50.322 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) : 722 0 0 0.267 0.267 6.3935 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: 142 33 20 34.789 80.652 108.40 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.556 0.556 1.8087 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.049 0.049 27.924 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: sequence.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: 14922.2266
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 1149 62A 62A N CA 306 307 134.57 107.00 27.57 7.93 107.00 27.57 7.93
-------------------------------------------------------------------------------------------------
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 2510 61A 61A CA C 302 304 -152.43 -180.00 27.57 5.51 -180.00 27.57 5.51
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2322 15A 16A C N 74 76 78.76 55.40 27.05 1.99 -62.50 155.70 31.63
1 16A 16A N CA 76 77 24.58 38.20 -40.90
2 2325 18A 19A C N 89 91 95.88 55.40 149.67 6.09 -62.50 171.20 29.59
2 19A 19A N CA 91 92 -105.90 38.20 -40.90
3 2326 19A 20A C N 94 96 69.42 -68.20 159.03 15.50 -68.20 159.03 15.50
3 20A 20A N CA 96 97 -135.00 145.30 145.30
4 2328 21A 22A C N 104 106 92.53 55.40 41.31 3.29 -62.50 166.59 33.75
4 22A 22A N CA 106 107 20.10 38.20 -40.90
5 2343 36A 37A C N 179 181 66.34 55.40 13.18 0.90 -62.50 147.47 29.99
5 37A 37A N CA 181 182 30.85 38.20 -40.90
6 2344 37A 38A C N 184 186 63.26 55.40 10.95 0.59 -62.50 144.65 29.42
6 38A 38A N CA 186 187 30.58 38.20 -40.90
7 2356 49A 50A C N 244 246 174.33 -134.00 75.53 2.36 -68.20 130.47 9.05
7 50A 50A N CA 246 247 -157.92 147.00 145.30
8 2360 53A 54A C N 264 266 92.24 -134.00 139.42 3.38 -62.50 -156.09 32.08
8 54A 54A N CA 266 267 -173.70 147.00 -40.90
9 2363 56A 57A C N 279 281 61.74 55.40 11.28 1.17 -62.50 152.49 30.92
9 57A 57A N CA 281 282 47.53 38.20 -40.90
10 2369 62A 63A C N 309 311 -80.55 -68.20 17.52 1.10 -62.50 162.37 27.53
10 63A 63A N CA 311 312 157.73 145.30 -40.90
11 2370 63A 64A C N 314 316 -125.40 -134.00 15.37 0.57 -62.50 -173.90 28.17
11 64A 64A N CA 316 317 134.25 147.00 -40.90
12 2371 64A 65A C N 319 321 62.71 -68.20 134.61 12.37 -62.50 -170.34 28.96
12 65A 65A N CA 321 322 176.65 145.30 -40.90
13 2372 65A 66A C N 324 326 -130.37 -134.00 5.92 0.36 -62.50 -179.34 33.24
13 66A 66A N CA 326 327 151.67 147.00 -40.90
14 2373 66A 67A C N 329 331 -115.15 -134.00 19.72 0.47 -62.50 -174.46 33.20
14 67A 67A N CA 331 332 141.19 147.00 -40.90
15 2374 67A 68A C N 334 336 -74.79 -68.20 10.64 0.67 -62.50 165.89 27.81
15 68A 68A N CA 336 337 153.66 145.30 -40.90
16 2375 68A 69A C N 339 341 -75.14 -68.20 8.53 0.84 -62.50 179.20 30.00
16 69A 69A N CA 341 342 140.35 145.30 -40.90
17 2376 69A 70A C N 344 346 -156.51 -134.00 32.91 1.03 -62.50 175.42 33.74
17 70A 70A N CA 346 347 171.00 147.00 -40.90
18 2377 70A 71A C N 349 351 -86.92 -68.20 38.29 3.66 -62.50 154.74 24.28
18 71A 71A N CA 351 352 111.91 145.30 -40.90
19 2378 71A 72A C N 354 356 170.41 -134.00 61.72 1.40 -62.50 -166.97 38.20
19 72A 72A N CA 356 357 173.81 147.00 -40.90
20 2379 72A 73A C N 359 361 -65.09 -68.20 3.20 0.24 -62.50 174.56 28.73
20 73A 73A N CA 361 362 144.56 145.30 -40.90
21 2380 73A 74A C N 364 366 -99.73 -68.20 34.95 3.37 -62.50 175.13 27.12
21 74A 74A N CA 366 367 130.23 145.30 -40.90
22 2381 74A 75A C N 369 371 -71.05 -68.20 7.54 0.51 -62.50 167.04 27.80
22 75A 75A N CA 371 372 152.28 145.30 -40.90
23 2382 75A 76A C N 374 376 -137.19 -134.00 16.93 0.88 -62.50 172.49 32.27
23 76A 76A N CA 376 377 163.63 147.00 -40.90
24 2383 76A 77A C N 379 381 -142.29 -134.00 63.85 3.42 -62.50 134.91 26.31
24 77A 77A N CA 381 382 -149.69 147.00 -40.90
25 2384 77A 78A C N 384 386 -62.34 -62.50 47.65 7.80 -62.50 47.65 7.80
25 78A 78A N CA 386 387 -88.55 -40.90 -40.90
26 2388 81A 82A C N 404 406 81.07 55.40 57.90 2.09 -62.50 146.12 29.05
26 82A 82A N CA 406 407 -13.71 38.20 -40.90
27 2392 85A 86A C N 424 426 52.43 55.40 8.09 0.30 -62.50 143.92 29.14
27 86A 86A N CA 426 427 45.72 38.20 -40.90
28 2395 88A 89A C N 439 441 53.59 55.40 30.61 1.70 -62.50 159.69 32.01
28 89A 89A N CA 441 442 68.76 38.20 -40.90
29 2398 91A 92A C N 454 456 64.68 55.40 9.78 1.16 -62.50 151.42 30.76
29 92A 92A N CA 456 457 41.27 38.20 -40.90
30 2425 118A 119A C N 589 591 82.13 -134.00 157.98 3.59 -62.50 179.82 28.85
30 119A 119A N CA 591 592 -147.76 147.00 -40.90
31 2438 131A 132A C N 654 656 47.43 55.40 14.33 0.57 -62.50 142.71 28.79
31 132A 132A N CA 656 657 50.11 38.20 -40.90
32 2447 140A 141A C N 699 701 69.72 55.40 35.10 1.27 -62.50 140.34 28.37
32 141A 141A N CA 701 702 6.15 38.20 -40.90
33 2449 142A 143A C N 709 711 65.55 55.40 14.01 0.77 -62.50 145.66 29.62
33 143A 143A N CA 711 712 28.53 38.20 -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 9 41 56 72 70 83 113 109 101
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sequence.B99990001.pdb 905.89648
sequence.B99990002.pdb 843.94678
Скоры в данном случае оказались меньше, чем в нативном варианте, однако не очень сильно
И структуры получились очень похожи (голубым - дикий тип, зеленым - гомолог).
In [ ]: