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): 2021/05/28 00:55:57
Выбрала белок LYS_HYPCU из осенней паутинной моли (Fall webworm moth).
# скачаем белок заготовку
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2021-05-28 00:58:31-- 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]
--2021-05-28 00:58:31-- 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]
--2021-05-28 00:58:32-- 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'
[ <=> ] 128,871 340K/s in 0.4s
2021-05-28 00:58:34 (340 KB/s) - `1lmp.pdb' saved [128871]
# скачаем последовательность
! wget https://www.uniprot.org/uniprot/P50717.fasta
--2021-05-28 00:58:34-- https://www.uniprot.org/uniprot/P50717.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: 214 [text/plain] Saving to: `P50717.fasta' 100%[======================================>] 214 --.-K/s in 0s 2021-05-28 00:58:35 (112 MB/s) - `P50717.fasta' saved [214/214]
# создадим объект выравнивание
alignm=modeller.alignment(env)
alignm
Empty alignment
alignm.append(file='P50717.fasta', align_codes='all',alignment_format='FASTA')
# создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'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.
alignm
Alignment of Sequence 'seq', Structure 'pdb'
# 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 MQKLAVFLFAIAAVCIHCEAKYYSTRCDLVRELRKQGFPENQMGDWVCLVENESGRKTDKVGPVNKNGSKDYGLF QINDKYWCSNTRTPGKD--CNVTCADLLLDDITKASTCAKKI-FKRHNFRAWYGWRNHCDGKTLPDTSNC----- --* >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 KVYDRCELAR------------------ALKASGMDGYAGNSLPNWVCLSKWESSYNTQATN-RNTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/. ..*
Выравнивание выглядит нормально.
# 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
----------------------------------------------
92 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: 11929 10925
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 142
Number of all, selected real atoms : 1136 1136
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10925 10925
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2262
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 : 965.0159
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 0 1 0.007 0.007 17.004 1.000
2 Bond angle potential : 1566 1 7 2.159 2.159 143.94 1.000
3 Stereochemical cosine torsion poten: 750 0 24 47.192 47.192 259.50 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.160 1.160 14.437 1.000
5 Soft-sphere overlap restraints : 2262 0 0 0.003 0.003 2.2212 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2232 0 2 0.386 0.386 106.99 1.000
10 Distance restraints 2 (N-O) : 2390 0 6 0.454 0.454 151.75 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: 141 1 3 4.935 4.935 40.493 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 71.881 71.881 24.238 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 0 70.984 70.984 34.773 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 68.828 68.828 21.653 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 107.665 107.665 17.001 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.25900 1.000
19 Disulfide angle restraints : 6 0 0 2.071 2.071 0.56807 1.000
20 Disulfide dihedral angle restraints: 3 0 0 27.782 27.782 2.2039 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1269 0 0 0.325 0.325 16.662 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 19 19 27.245 62.716 91.297 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 0 0.509 0.509 20.034 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: 15683.9990
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2170 92D 92D N CA 729 730 123.75 107.00 16.75 4.82 107.00 16.75 4.82
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 38F 38F CA C 299 307 -157.05 -180.00 22.95 4.59 -180.00 22.95 4.59
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3979 9F 10A C N 75 77 43.51 -68.20 114.16 8.84 -62.50 -165.82 37.45
1 10A 10A N CA 77 78 121.80 145.30 -40.90
2 3981 11I 12A C N 88 90 -61.76 -68.20 10.06 0.63 -62.50 178.46 29.28
2 12A 12A N CA 90 91 137.56 145.30 -40.90
3 3982 12A 13A C N 93 95 -162.54 -134.00 35.86 0.93 -62.50 -179.37 34.90
3 13A 13A N CA 95 96 168.71 147.00 -40.90
4 3986 16I 17H C N 119 121 55.89 56.30 0.68 0.10 -63.20 144.90 24.82
4 17H 17H N CA 121 122 40.25 40.80 -42.30
5 3988 18C 19E C N 135 137 -94.06 -117.80 29.47 0.88 -63.60 162.53 20.15
5 19E 19E N CA 137 138 119.34 136.80 -40.30
6 3989 19E 20A C N 144 146 -123.10 -134.00 11.44 0.27 -62.50 -174.26 33.67
6 20A 20A N CA 146 147 143.52 147.00 -40.90
7 3990 20A 21K C N 149 151 -122.45 -118.00 5.79 0.29 -62.90 -174.01 21.68
7 21K 21K N CA 151 152 135.40 139.10 -40.80
8 3993 23Y 24S C N 182 184 -50.44 -72.40 24.56 1.97 -64.10 162.17 11.01
8 24S 24S N CA 184 185 163.41 152.40 -35.00
9 3994 24S 25T C N 188 190 -76.49 -78.10 37.41 1.65 -63.20 131.40 17.73
9 25T 25T N CA 190 191 -172.82 149.80 -42.10
10 3995 25T 26R C N 195 197 -59.73 -72.10 18.64 1.21 -63.00 169.08 23.06
10 26R 26R N CA 197 198 127.95 141.90 -41.10
11 3996 26R 27C C N 206 208 -66.30 -63.00 4.44 0.77 -117.90 -177.72 7.82
11 27C 27C N CA 208 209 -44.08 -41.10 141.10
12 3997 27C 28D C N 212 214 -95.50 -96.50 7.13 0.30 -63.30 164.44 18.57
12 28D 28D N CA 214 215 121.26 114.20 -40.00
13 4061 91K 92D C N 727 729 -137.99 -63.30 81.75 13.94 -63.30 81.75 13.94
13 92D 92D N CA 729 730 -73.22 -40.00 -40.00
14 4085 115I 116F C N 901 903 -37.84 -124.20 98.14 2.63 -63.20 143.25 21.60
14 116F 116F N CA 903 904 96.69 143.30 -44.30
15 4088 118R 119H C N 932 934 -99.47 -125.60 57.72 1.65 -63.20 134.61 14.93
15 119H 119H N CA 934 935 87.33 138.80 -42.30
16 4089 119H 120N C N 942 944 -58.60 -63.20 34.04 4.02 -119.90 160.35 8.41
16 120N 120N N CA 944 945 -74.83 -41.10 137.00
17 4100 130H 131C C N 1050 1052 -112.23 -63.00 50.23 7.78 -63.00 50.23 7.78
17 131C 131C N CA 1052 1053 -31.12 -41.10 -41.10
18 4109 139T 140S C N 1114 1116 -88.31 -72.40 63.86 4.30 -64.10 127.87 8.14
18 140S 140S N CA 1116 1117 90.56 152.40 -35.00
19 4110 140S 141N C N 1120 1122 -59.19 -63.20 5.49 0.62 -119.90 -171.80 9.72
19 141N 141N N CA 1122 1123 -44.86 -41.10 137.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 16 68 81 100 120 130 157 180 165
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 142
Number of all, selected real atoms : 1136 1136
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10925 10925
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2334
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 : 1126.6823
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 0 1 0.007 0.007 17.819 1.000
2 Bond angle potential : 1566 1 8 2.216 2.216 154.53 1.000
3 Stereochemical cosine torsion poten: 750 0 33 48.247 48.247 274.01 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.235 1.235 16.242 1.000
5 Soft-sphere overlap restraints : 2334 0 0 0.003 0.003 2.5116 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2232 0 1 0.391 0.391 109.38 1.000
10 Distance restraints 2 (N-O) : 2390 0 10 0.496 0.496 192.16 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 141 1 2 5.058 5.058 42.534 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 1 74.510 74.510 36.457 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 1 76.097 76.097 38.708 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 75.045 75.045 23.508 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 77.290 77.290 14.328 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.24116 1.000
19 Disulfide angle restraints : 6 0 0 2.240 2.240 0.66499 1.000
20 Disulfide dihedral angle restraints: 3 0 0 29.968 29.968 2.5056 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1269 0 0 0.413 0.413 32.162 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 22 19 36.434 67.275 135.68 1.000
26 Distance restraints 4 (SDCH-SDCH) : 509 0 0 0.636 0.636 33.242 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: 17061.3301
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2170 92D 92D N CA 729 730 123.73 107.00 16.73 4.81 107.00 16.73 4.81
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 38F 38F CA C 299 307 -155.97 -180.00 24.03 4.80 -180.00 24.03 4.80
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3979 9F 10A C N 75 77 -99.94 -134.00 59.06 3.59 -62.50 129.39 23.20
1 10A 10A N CA 77 78 -164.76 147.00 -40.90
2 3981 11I 12A C N 88 90 -130.31 -134.00 6.18 0.22 -62.50 -170.39 34.70
2 12A 12A N CA 90 91 142.04 147.00 -40.90
3 3982 12A 13A C N 93 95 -132.94 -134.00 14.25 0.78 -62.50 -172.57 28.24
3 13A 13A N CA 95 96 132.78 147.00 -40.90
4 3986 16I 17H C N 119 121 -166.96 -125.60 54.61 1.34 -63.20 176.88 28.67
4 17H 17H N CA 121 122 174.45 138.80 -42.30
5 3988 18C 19E C N 135 137 -121.10 -117.80 24.45 1.16 -63.60 168.77 25.75
5 19E 19E N CA 137 138 161.03 136.80 -40.30
6 3989 19E 20A C N 144 146 -113.08 -134.00 29.52 0.89 -62.50 174.55 26.62
6 20A 20A N CA 146 147 126.17 147.00 -40.90
7 3990 20A 21K C N 149 151 50.45 -70.20 129.94 10.47 -62.90 172.90 20.56
7 21K 21K N CA 151 152 -171.35 140.40 -40.80
8 3991 21K 22Y C N 158 160 -115.95 -124.30 8.92 0.74 -63.50 -174.39 32.12
8 22Y 22Y N CA 160 161 138.55 135.40 -43.40
9 3993 23Y 24S C N 182 184 -117.54 -136.60 37.02 1.39 -64.10 163.44 10.07
9 24S 24S N CA 184 185 119.46 151.20 -35.00
10 3995 25T 26R C N 195 197 -92.11 -72.10 28.16 2.45 -63.00 165.76 20.58
10 26R 26R N CA 197 198 122.09 141.90 -41.10
11 3996 26R 27C C N 206 208 -65.17 -63.00 6.53 0.96 -117.90 179.55 7.72
11 27C 27C N CA 208 209 -47.26 -41.10 141.10
12 3997 27C 28D C N 212 214 47.17 54.50 19.41 0.97 -63.30 148.25 24.88
12 28D 28D N CA 214 215 58.87 40.90 -40.00
13 3999 29L 30V C N 228 230 -149.81 -62.40 87.60 14.15 -62.40 87.60 14.15
13 30V 30V N CA 230 231 -48.21 -42.40 -42.40
14 4023 53E 54S C N 428 430 -137.57 -64.10 80.31 8.59 -64.10 80.31 8.59
14 54S 54S N CA 430 431 -2.55 -35.00 -35.00
15 4054 84S 85N C N 674 676 -108.16 -119.90 36.69 1.89 -63.20 153.86 21.80
15 85N 85N N CA 676 677 171.76 137.00 -41.10
16 4055 85N 86T C N 682 684 -72.77 -63.20 14.37 1.55 55.90 146.90 18.12
16 86T 86T N CA 684 685 -31.39 -42.10 39.50
17 4061 91K 92D C N 727 729 -137.93 -63.30 82.38 14.05 -63.30 82.38 14.05
17 92D 92D N CA 729 730 -74.87 -40.00 -40.00
18 4085 115I 116F C N 901 903 -53.03 -124.20 82.02 2.18 -63.20 147.18 21.12
18 116F 116F N CA 903 904 102.53 143.30 -44.30
19 4087 117K 118R C N 921 923 -77.88 -125.20 72.53 2.29 -63.00 127.61 16.28
19 118R 118R N CA 923 924 85.64 140.60 -41.10
20 4088 118R 119H C N 932 934 -172.25 -63.20 109.06 17.24 -63.20 109.06 17.24
20 119H 119H N CA 934 935 -41.01 -42.30 -42.30
21 4106 136L 137P C N 1092 1094 -63.09 -64.50 9.70 0.65 -58.70 168.15 13.54
21 137P 137P N CA 1094 1095 137.60 147.20 -30.50
22 4107 137P 138D C N 1099 1101 126.98 -63.30 169.76 26.75 -63.30 169.76 26.75
22 138D 138D N CA 1101 1102 -36.21 -40.00 -40.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 17 72 74 102 108 125 168 164 176
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 965.01593
seq.B99990002.pdb 1126.68225
# первая модель
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
# вторая модель
w2 = nglview.show_structure_file('seq.B99990002.pdb')
w2.clear_representations()
w2.add_cartoon('protein', color_scheme='residueindex')
w2.add_ball_and_stick('ligand', opacity=0.5)
w2
Модели в первом приближении одинаковые, но скор меньше у первой, поэтому будет рассматривать ее. Теперь посмотри на 1lmp.pdb.
lmp = nglview.show_structure_file('1lmp.pdb')
lmp.clear_representations()
lmp.add_cartoon('protein', color_scheme='residueindex')
lmp.add_ball_and_stick('ligand', opacity=0.5)
lmp
В 1lmp.pdb есть лиганд, а в полученных нами моделях - нет. Кажется, структуры довольно разные. Но это понятно, учитывая, что эти лизоцимы получены из форели и моли - далеких организмов.
with_lig = ''
for res in alignm[0].residues:
with_lig += res.code
for lig in alignm[1].residues[-3:]:
with_lig += lig.code
alignm.append_sequence(with_lig)
alignm[2].code = 'with_lig'
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 KVYDRCELAR------------------ALKASGMDGYAGNSLPNWVCLSKWESSYNTQATN-RNTDGSTDYGIF QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/. ..* >P1;with_lig sequence::1 : :+145 : :undefined:undefined:-1.00:-1.00 MQKLAVFLFAIAAVCIHCEAKYYSTRCDLVRELRKQGFPENQMGDWVCLVENESGRKTDKVGPVNKNGSKDYGLF QINDKYWCSNTRTPGKD--CNVTCADLLLDDITKASTCAKKI-FKRHNFRAWYGWRNHCDGKTLPDTS---NC-. ..*
Теперь в конце последовательности целевого белка тоже есть лиганд.
alignm
Alignment of Structure 'pdb', Sequence 'with_lig'
# Выбираем объект для моделирования.
s = alignm[1] # поменялись местами
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()
with_lig 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
----------------------------------------------
92 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C +N
atom indices : 1134 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C CA +N O
atom indices : 1134 1131 0 1135
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13323 12319
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12319 12319
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2591
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 : 1307.0881
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 0 1 0.008 0.008 22.467 1.000
2 Bond angle potential : 1566 1 11 2.389 2.389 177.20 1.000
3 Stereochemical cosine torsion poten: 750 0 26 47.197 47.197 265.55 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.299 1.299 17.551 1.000
5 Soft-sphere overlap restraints : 2591 1 2 0.008 0.008 20.199 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) : 2238 0 5 0.456 0.456 137.42 1.000
10 Distance restraints 2 (N-O) : 2391 1 22 0.541 0.541 238.03 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: 141 1 6 5.756 5.756 55.083 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 79.777 79.777 37.003 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 0 81.770 81.770 43.433 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 70.574 70.574 23.599 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 85.438 85.438 15.234 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.37154 1.000
19 Disulfide angle restraints : 6 0 0 4.100 4.100 2.2274 1.000
20 Disulfide dihedral angle restraints: 3 0 0 23.885 23.885 1.5548 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) : 1265 0 0 0.464 0.464 40.426 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 27 26 33.242 69.441 142.01 1.000
26 Distance restraints 4 (SDCH-SDCH) : 511 0 1 0.719 0.719 41.079 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 26.648 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: with_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 18251.4688
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2170 92D 92D N CA 729 730 124.91 107.00 17.91 5.15 107.00 17.91 5.15
-------------------------------------------------------------------------------------------------
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 8517 105I 10A N O 824 81 14.62 10.92 3.70 4.55 10.92 3.70 4.55
-------------------------------------------------------------------------------------------------
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 4119 9F 9F CA C 67 75 -150.28 -180.00 29.72 5.94 -180.00 29.72 5.94
-------------------------------------------------------------------------------------------------
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 3980 10A 11I C N 80 82 64.63 -97.30 162.03 6.84 -120.60 174.99 12.42
1 11I 11I N CA 82 83 121.61 127.20 130.30
2 3981 11I 12A C N 88 90 -144.61 -134.00 12.34 0.29 -62.50 -174.97 34.72
2 12A 12A N CA 90 91 153.29 147.00 -40.90
3 3986 16I 17H C N 119 121 -154.29 -125.60 63.88 1.83 -63.20 152.11 24.76
3 17H 17H N CA 121 122 -164.13 138.80 -42.30
4 3988 18C 19E C N 135 137 -81.64 -69.30 43.17 3.69 -63.60 142.58 18.08
4 19E 19E N CA 137 138 101.13 142.50 -40.30
5 3989 19E 20A C N 144 146 -145.09 -134.00 15.51 0.90 -62.50 -164.63 29.32
5 20A 20A N CA 146 147 136.15 147.00 -40.90
6 3990 20A 21K C N 149 151 -131.15 -118.00 28.41 1.47 -62.90 169.11 19.47
6 21K 21K N CA 151 152 113.92 139.10 -40.80
7 3992 22Y 23Y C N 170 172 -147.67 -124.30 84.33 3.59 -63.50 130.84 24.50
7 23Y 23Y N CA 172 173 -143.58 135.40 -43.40
8 3993 23Y 24S C N 182 184 -55.21 -72.40 17.22 1.26 -64.10 171.74 11.94
8 24S 24S N CA 184 185 153.49 152.40 -35.00
9 3994 24S 25T C N 188 190 -66.81 -78.10 37.29 1.28 -63.20 156.40 19.82
9 25T 25T N CA 190 191 114.26 149.80 -42.10
10 3995 25T 26R C N 195 197 -158.73 -125.20 33.53 1.35 -63.00 -157.45 33.84
10 26R 26R N CA 197 198 140.40 140.60 -41.10
11 3997 27C 28D C N 212 214 -131.40 -96.50 34.90 1.42 -63.30 168.02 17.90
11 28D 28D N CA 214 215 113.61 114.20 -40.00
12 4007 37G 38F C N 296 298 -60.10 -63.20 25.24 3.30 -124.20 160.69 8.74
12 38F 38F N CA 298 299 -69.35 -44.30 143.30
13 4008 38F 39P C N 307 309 -87.13 -58.70 65.68 3.84 -64.50 120.63 10.23
13 39P 39P N CA 309 310 28.71 -30.50 147.20
14 4023 53E 54S C N 428 430 -137.35 -64.10 79.05 8.61 -64.10 79.05 8.61
14 54S 54S N CA 430 431 -5.28 -35.00 -35.00
15 4054 84S 85N C N 674 676 -113.80 -119.90 31.52 1.56 -63.20 159.23 22.79
15 85N 85N N CA 676 677 167.92 137.00 -41.10
16 4055 85N 86T C N 682 684 -74.06 -63.20 14.75 1.64 55.90 148.38 18.31
16 86T 86T N CA 684 685 -32.11 -42.10 39.50
17 4061 91K 92D C N 727 729 -141.06 -63.30 83.54 14.20 -63.30 83.54 14.20
17 92D 92D N CA 729 730 -70.53 -40.00 -40.00
18 4074 104D 105I C N 822 824 -106.43 -63.40 79.38 12.07 -63.40 79.38 12.07
18 105I 105I N CA 824 825 23.10 -43.60 -43.60
19 4085 115I 116F C N 901 903 -53.73 -124.20 83.78 2.19 -63.20 142.60 20.44
19 116F 116F N CA 903 904 97.98 143.30 -44.30
20 4088 118R 119H C N 932 934 -88.97 -125.60 51.82 1.28 -63.20 146.73 16.89
20 119H 119H N CA 934 935 102.15 138.80 -42.30
21 4089 119H 120N C N 942 944 -58.50 -63.20 75.87 9.23 -119.90 122.65 6.58
21 120N 120N N CA 944 945 -116.82 -41.10 137.00
22 4099 129N 130H C N 1040 1042 -125.07 -63.20 77.42 9.25 -63.20 77.42 9.25
22 130H 130H N CA 1042 1043 4.23 -42.30 -42.30
23 4100 130H 131C C N 1050 1052 -125.63 -63.00 64.63 9.80 -63.00 64.63 9.80
23 131C 131C N CA 1052 1053 -25.17 -41.10 -41.10
24 4101 131C 132D C N 1056 1058 -54.51 -63.30 26.73 2.89 -70.90 145.39 7.99
24 132D 132D N CA 1058 1059 -65.24 -40.00 150.30
25 4102 132D 133G C N 1064 1066 -73.10 -62.40 13.77 2.00 82.20 160.63 11.99
25 133G 133G N CA 1066 1067 -32.54 -41.20 8.50
26 4109 139T 140S C N 1114 1116 -91.80 -72.40 26.71 1.28 -64.10 156.71 13.20
26 140S 140S N CA 1116 1117 170.76 152.40 -35.00
27 4110 140S 141N C N 1120 1122 -144.05 -63.20 98.94 16.24 55.90 -148.92 13.68
27 141N 141N N CA 1122 1123 -98.12 -41.10 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 11 17 84 84 135 114 144 163 180 200
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12319 12319
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2524
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 : 1257.4076
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 0 1 0.009 0.009 25.043 1.000
2 Bond angle potential : 1566 1 13 2.426 2.426 180.41 1.000
3 Stereochemical cosine torsion poten: 750 0 28 47.769 47.769 268.31 1.000
4 Stereochemical improper torsion pot: 481 0 0 1.376 1.376 21.225 1.000
5 Soft-sphere overlap restraints : 2524 2 2 0.009 0.009 21.621 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) : 2238 0 5 0.421 0.421 117.43 1.000
10 Distance restraints 2 (N-O) : 2391 0 13 0.485 0.485 191.04 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 141 1 4 5.575 5.575 51.672 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 2 75.251 75.251 42.665 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 0 64.613 64.613 40.614 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 84.097 84.097 26.063 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 91.393 91.393 15.201 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.30032 1.000
19 Disulfide angle restraints : 6 0 0 4.101 4.101 2.2278 1.000
20 Disulfide dihedral angle restraints: 3 0 0 23.837 23.837 1.6047 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) : 1265 0 0 0.402 0.402 25.704 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 25 30 34.839 69.127 160.48 1.000
26 Distance restraints 4 (SDCH-SDCH) : 511 0 0 0.727 0.727 40.183 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 25.609 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: with_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 17911.7793
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2170 92D 92D N CA 729 730 124.46 107.00 17.46 5.02 107.00 17.46 5.02
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 38F 38F CA C 299 307 -149.49 -180.00 30.51 6.10 -180.00 30.51 6.10
-------------------------------------------------------------------------------------------------
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 3978 8L 9F C N 64 66 -71.38 -63.20 80.85 11.78 -63.20 80.85 11.78
1 9F 9F N CA 66 67 -124.73 -44.30 -44.30
2 3980 10A 11I C N 80 82 27.98 -97.30 125.66 5.19 -120.60 148.73 10.54
2 11I 11I N CA 82 83 136.98 127.20 130.30
3 3981 11I 12A C N 88 90 -89.21 -68.20 21.01 1.78 -62.50 175.76 30.18
3 12A 12A N CA 90 91 145.39 145.30 -40.90
4 3982 12A 13A C N 93 95 -72.61 -68.20 5.65 0.36 -62.50 170.57 28.46
4 13A 13A N CA 95 96 148.83 145.30 -40.90
5 3986 16I 17H C N 119 121 -163.20 -125.60 58.46 1.48 -63.20 167.32 27.22
5 17H 17H N CA 121 122 -176.45 138.80 -42.30
6 3988 18C 19E C N 135 137 -65.62 -69.30 3.70 0.29 -63.60 176.87 23.69
6 19E 19E N CA 137 138 142.84 142.50 -40.30
7 3990 20A 21K C N 149 151 -165.79 -118.00 66.09 2.31 -62.90 169.30 28.02
7 21K 21K N CA 151 152 -175.25 139.10 -40.80
8 3993 23Y 24S C N 182 184 -49.38 -72.40 31.84 1.52 -64.10 166.05 12.96
8 24S 24S N CA 184 185 130.40 152.40 -35.00
9 3994 24S 25T C N 188 190 -134.97 -124.80 17.79 0.55 -63.20 175.19 27.17
9 25T 25T N CA 190 191 158.09 143.50 -42.10
10 3995 25T 26R C N 195 197 -75.95 -72.10 5.47 0.48 -63.00 179.57 23.41
10 26R 26R N CA 197 198 138.01 141.90 -41.10
11 3997 27C 28D C N 212 214 -109.80 -96.50 15.36 0.64 -63.30 168.42 18.48
11 28D 28D N CA 214 215 121.87 114.20 -40.00
12 4008 38F 39P C N 307 309 -13.22 -58.70 53.28 4.73 -64.50 162.83 14.93
12 39P 39P N CA 309 310 -58.26 -30.50 147.20
13 4009 39P 40E C N 314 316 -155.08 -117.80 96.80 5.29 54.60 150.41 17.95
13 40E 40E N CA 316 317 47.47 136.80 42.40
14 4023 53E 54S C N 428 430 -138.81 -64.10 85.00 8.63 -64.10 85.00 8.63
14 54S 54S N CA 430 431 5.54 -35.00 -35.00
15 4032 62G 63P C N 493 495 -51.06 -58.70 7.71 0.93 -64.50 179.27 12.68
15 63P 63P N CA 495 496 -31.56 -30.50 147.20
16 4033 63P 64V C N 500 502 168.67 -125.40 73.33 2.01 -73.50 123.27 8.36
16 64V 64V N CA 502 503 175.39 143.30 139.20
17 4054 84S 85N C N 674 676 -121.16 -63.20 71.63 8.46 -63.20 71.63 8.46
17 85N 85N N CA 676 677 0.99 -41.10 -41.10
18 4061 91K 92D C N 727 729 -139.81 -63.30 83.78 14.28 -63.30 83.78 14.28
18 92D 92D N CA 729 730 -74.13 -40.00 -40.00
19 4074 104D 105I C N 822 824 -107.87 -63.40 79.61 12.10 -63.40 79.61 12.10
19 105I 105I N CA 824 825 22.44 -43.60 -43.60
20 4085 115I 116F C N 901 903 -41.55 -124.20 97.22 2.55 -63.20 138.12 20.64
20 116F 116F N CA 903 904 92.11 143.30 -44.30
21 4087 117K 118R C N 921 923 -61.66 -125.20 65.04 2.26 -63.00 167.85 22.76
21 118R 118R N CA 923 924 126.75 140.60 -41.10
22 4088 118R 119H C N 932 934 97.35 -125.60 151.82 6.48 -63.20 -162.05 33.86
22 119H 119H N CA 934 935 73.49 138.80 -42.30
23 4089 119H 120N C N 942 944 -61.87 -63.20 73.02 9.06 -119.90 123.39 6.59
23 120N 120N N CA 944 945 -114.10 -41.10 137.00
24 4109 139T 140S C N 1114 1116 -149.68 -136.60 41.18 1.77 -64.10 159.63 17.74
24 140S 140S N CA 1116 1117 -169.76 151.20 -35.00
25 4110 140S 141N C N 1120 1122 -124.49 -119.90 53.61 2.33 55.90 -125.40 28.30
25 141N 141N N CA 1122 1123 -169.58 137.00 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 10 17 86 87 123 120 157 183 174 200
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
with_lig.B99990001.pdb 1307.08813
with_lig.B99990002.pdb 1257.40759
with_ligand = nglview.show_structure_file('with_lig.B99990001.pdb')
with_ligand.clear_representations()
with_ligand.add_cartoon('protein', color_scheme='residueindex')
with_ligand.add_ball_and_stick('ligand', opacity=0.5)
with_ligand
Белок стал компактнее и, в целом, более похожим на 1lmp.
! rm with_lig.rsr
alignm
Alignment of Structure 'pdb', Sequence 'with_lig'
print ('длина белка 1lmp', len(list(alignm[0].residues)))
print ('длина нашего белка', len(list(alignm[1].residues)))
длина белка 1lmp 132 длина нашего белка 145
Попробуем переместить лиганд в какое-нибудь совсем другое место, например, между аминокислотами 28 и 104.
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:28','O6:143'), ('N:104', 'O6:145')]:
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()
Опять моделируем.
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
----------------------------------------------
92 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C +N
atom indices : 1134 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 142
atom names : C CA +N O
atom indices : 1134 1131 0 1135
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/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: 13325 12321
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12321 12321
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3325
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 : 5936.1323
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 10 18 0.024 0.024 198.82 1.000
2 Bond angle potential : 1566 16 44 4.140 4.140 544.68 1.000
3 Stereochemical cosine torsion poten: 750 0 33 48.175 48.175 279.84 1.000
4 Stereochemical improper torsion pot: 481 1 4 2.320 2.320 54.355 1.000
5 Soft-sphere overlap restraints : 3325 2 6 0.012 0.012 59.071 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) : 2238 47 143 1.081 1.081 1439.4 1.000
10 Distance restraints 2 (N-O) : 2391 32 116 1.001 1.001 1022.6 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: 141 6 17 9.498 9.498 150.02 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 8 80.298 80.298 68.153 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 6 75.238 75.238 59.675 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 79.358 79.358 26.480 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 88.552 88.552 16.914 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.33474 1.000
19 Disulfide angle restraints : 6 0 0 4.891 4.891 3.1697 1.000
20 Disulfide dihedral angle restraints: 3 0 0 38.957 38.957 2.7955 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) : 1265 0 2 0.652 0.652 71.137 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 31 35 37.298 77.871 241.82 1.000
26 Distance restraints 4 (SDCH-SDCH) : 511 1 23 1.585 1.585 194.24 1.000
27 Distance restraints 5 (X-Y) : 1391 9 31 0.237 0.237 1502.6 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: with_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 27569.2832
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
1 223 28D 28D N CA 214 215 1.63 1.43 0.20 6.48 1.43 0.20 6.48
2 225 28D 28D C CA 220 215 1.79 1.49 0.30 8.83 1.49 0.30 8.83
3 226 28D 29L C N 220 222 1.49 1.35 0.14 4.98 1.35 0.14 4.98
4 231 29L 29L N CA 222 223 1.61 1.43 0.18 5.89 1.43 0.18 5.89
5 233 29L 29L C CA 228 223 1.65 1.49 0.16 4.79 1.49 0.16 4.79
6 822 102L 102L C CA 806 801 1.65 1.49 0.16 4.74 1.49 0.16 4.74
7 831 103D 104D C N 814 816 1.53 1.35 0.19 6.69 1.35 0.19 6.69
8 836 104D 104D N CA 816 817 1.67 1.43 0.24 7.97 1.43 0.24 7.97
9 838 104D 104D C CA 822 817 1.74 1.49 0.25 7.32 1.49 0.25 7.32
10 844 105I 105I N CA 824 825 1.60 1.43 0.17 5.69 1.43 0.17 5.69
-------------------------------------------------------------------------------------------------
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 1460 28D 28D N CA 214 215 130.35 107.00 23.35 6.72 107.00 23.35 6.72
2 1468 28D 29L C N 220 222 147.17 120.00 27.17 6.17 120.00 27.17 6.17
3 1471 29L 29L N CA 222 223 150.48 107.00 43.48 12.50 107.00 43.48 12.50
4 1482 30V 30V N CA 230 231 130.45 107.00 23.45 6.74 107.00 23.45 6.74
5 1492 31R 31R N CA 237 238 123.01 107.00 16.01 4.60 107.00 16.01 4.60
6 2170 92D 92D N CA 729 730 124.96 107.00 17.96 5.16 107.00 17.96 5.16
7 2273 102L 102L CA C 801 806 132.95 116.50 16.45 4.73 116.50 16.45 4.73
8 2284 103D 103D CA C 809 814 143.54 116.50 27.04 7.78 116.50 27.04 7.78
9 2292 104D 104D N CA 816 817 132.29 107.00 25.29 7.27 107.00 25.29 7.27
10 2295 104D 104D CA C 817 822 137.82 116.50 21.32 6.13 116.50 21.32 6.13
11 2303 105I 105I N CA 824 825 134.81 107.00 27.81 8.00 107.00 27.81 8.00
12 2307 105I 105I CA C 825 830 134.16 116.50 17.66 5.08 116.50 17.66 5.08
-------------------------------------------------------------------------------------------------
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 4551 1M 103D CA CA 2 809 9.76 4.93 4.83 8.46 4.93 4.83 8.46
2 4584 2Q 103D CA CA 10 809 12.19 8.13 4.06 5.20 8.13 4.06 5.20
3 4615 3K 103D CA CA 19 809 13.47 8.67 4.80 7.32 8.67 4.80 7.32
4 4725 7F 103D CA CA 48 809 16.51 12.15 4.36 5.03 12.15 4.36 5.03
5 6020 74L 108A CA CA 578 849 9.70 7.84 1.86 5.05 7.84 1.86 5.05
-------------------------------------------------------------------------------------------------
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 6794 2Q 103D N O 9 815 11.59 7.61 3.98 4.64 7.61 3.98 4.64
2 6813 3K 103D N O 18 815 12.18 7.74 4.44 6.40 7.74 4.44 6.40
3 6826 4L 103D N O 27 815 14.96 9.90 5.06 5.05 9.90 5.06 5.05
4 6887 8L 103D N O 58 815 13.47 9.53 3.94 5.31 9.53 3.94 5.31
5 6934 29L 6V N O 222 46 11.98 5.08 6.89 4.88 5.08 6.89 4.88
6 7921 75F 108A N O 585 852 9.09 7.13 1.96 4.86 7.13 1.96 4.86
7 8462 101L 104D N O 792 823 9.44 6.38 3.06 5.06 6.38 3.06 5.06
8 8500 104D 1M N O 816 8 12.09 7.84 4.25 4.92 7.84 4.25 4.92
9 8501 104D 2Q N O 816 17 15.62 10.68 4.94 4.80 10.68 4.94 4.80
10 8509 104D 101L N O 816 799 9.93 6.43 3.50 5.77 6.43 3.50 5.77
11 8510 104D 102L N O 816 807 5.72 3.30 2.43 4.62 3.30 2.43 4.62
-------------------------------------------------------------------------------------------------
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 4138 28D 28D CA C 215 220 -148.88 -180.00 31.12 6.22 -180.00 31.12 6.22
2 4139 29L 29L CA C 223 228 -153.81 -180.00 26.19 5.24 -180.00 26.19 5.24
3 4144 34R 34R CA C 266 274 -155.54 -180.00 24.46 4.89 -180.00 24.46 4.89
4 4148 38F 38F CA C 299 307 -151.38 -180.00 28.62 5.72 -180.00 28.62 5.72
5 4213 103D 103D CA C 809 814 -138.05 -180.00 41.95 8.39 -180.00 41.95 8.39
-------------------------------------------------------------------------------------------------
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 3973 3K 4L C N 25 27 -68.03 -63.50 8.44 1.45 -70.70 170.10 12.99
1 4L 4L N CA 27 28 -48.32 -41.20 141.60
2 3974 4L 5A C N 33 35 159.11 -62.50 143.22 28.74 -62.50 143.22 28.74
2 5A 5A N CA 35 36 -77.77 -40.90 -40.90
3 3981 11I 12A C N 88 90 -78.48 -68.20 19.77 1.27 -62.50 157.72 26.66
3 12A 12A N CA 90 91 162.19 145.30 -40.90
4 3982 12A 13A C N 93 95 -61.73 -68.20 6.55 0.59 -62.50 172.73 28.27
4 13A 13A N CA 95 96 146.37 145.30 -40.90
5 3986 16I 17H C N 119 121 -66.49 -67.60 20.80 1.57 -63.20 161.56 20.00
5 17H 17H N CA 121 122 119.23 140.00 -42.30
6 3988 18C 19E C N 135 137 -91.29 -69.30 21.99 1.68 -63.60 179.84 25.53
6 19E 19E N CA 137 138 142.00 142.50 -40.30
7 3989 19E 20A C N 144 146 -122.97 -134.00 17.27 0.58 -62.50 -175.22 28.02
7 20A 20A N CA 146 147 133.71 147.00 -40.90
8 3991 21K 22Y C N 158 160 -47.36 -98.40 54.14 2.58 -63.50 170.92 26.31
8 22Y 22Y N CA 160 161 146.44 128.40 -43.40
9 3992 22Y 23Y C N 170 172 -120.21 -124.30 51.46 2.90 -63.50 141.74 25.30
9 23Y 23Y N CA 172 173 -173.30 135.40 -43.40
10 3993 23Y 24S C N 182 184 -56.47 -72.40 16.57 1.04 -64.10 177.32 12.41
10 24S 24S N CA 184 185 147.84 152.40 -35.00
11 3994 24S 25T C N 188 190 -144.28 -124.80 41.03 1.29 -63.20 160.31 25.75
11 25T 25T N CA 190 191 179.61 143.50 -42.10
12 3995 25T 26R C N 195 197 163.50 -125.20 71.81 3.11 -63.00 -141.43 24.98
12 26R 26R N CA 197 198 131.97 140.60 -41.10
13 3997 27C 28D C N 212 214 -33.85 -70.90 68.52 5.14 -63.30 115.86 12.81
13 28D 28D N CA 214 215 -152.06 150.30 -40.00
14 3999 29L 30V C N 228 230 -45.70 -125.40 79.74 3.04 -62.40 177.60 21.55
14 30V 30V N CA 230 231 140.79 143.30 -42.40
15 4003 33L 34R C N 263 265 -159.44 -63.00 105.99 19.25 57.30 -171.14 13.28
15 34R 34R N CA 265 266 -85.08 -41.10 38.00
16 4023 53E 54S C N 428 430 -144.71 -64.10 89.25 9.38 -64.10 89.25 9.38
16 54S 54S N CA 430 431 3.33 -35.00 -35.00
17 4061 91K 92D C N 727 729 -145.68 -63.30 87.92 14.93 -63.30 87.92 14.93
17 92D 92D N CA 729 730 -70.71 -40.00 -40.00
18 4070 100L 101L C N 790 792 -63.64 -63.50 47.68 6.61 -63.50 47.68 6.61
18 101L 101L N CA 792 793 6.48 -41.20 -41.20
19 4072 102L 103D C N 806 808 -170.98 -96.50 80.13 3.31 -63.30 -153.46 32.37
19 103D 103D N CA 808 809 143.75 114.20 -40.00
20 4073 103D 104D C N 814 816 53.81 -63.30 130.35 17.19 -70.90 167.94 13.74
20 104D 104D N CA 816 817 -97.23 -40.00 150.30
21 4075 105I 106T C N 830 832 -114.14 -63.20 57.17 9.83 -63.20 57.17 9.83
21 106T 106T N CA 832 833 -68.06 -42.10 -42.10
22 4085 115I 116F C N 901 903 -68.65 -124.20 81.18 2.22 -63.20 128.51 17.48
22 116F 116F N CA 903 904 84.10 143.30 -44.30
23 4088 118R 119H C N 932 934 -84.68 -125.60 63.62 1.61 -63.20 134.11 15.54
23 119H 119H N CA 934 935 90.08 138.80 -42.30
24 4089 119H 120N C N 942 944 -58.85 -63.20 40.12 4.79 -119.90 154.58 8.13
24 120N 120N N CA 944 945 -80.98 -41.10 137.00
25 4099 129N 130H C N 1040 1042 -119.55 -63.20 58.03 8.42 -63.20 58.03 8.42
25 130H 130H N CA 1042 1043 -28.48 -42.30 -42.30
26 4101 131C 132D C N 1056 1058 -53.58 -63.30 26.43 2.83 -70.90 146.16 8.07
26 132D 132D N CA 1058 1059 -64.57 -40.00 150.30
27 4102 132D 133G C N 1064 1066 -72.63 -62.40 12.80 1.88 82.20 160.44 12.00
27 133G 133G N CA 1066 1067 -33.51 -41.20 8.50
28 4106 136L 137P C N 1092 1094 -59.36 -64.50 16.34 1.50 -58.70 166.79 13.84
28 137P 137P N CA 1094 1095 162.71 147.20 -30.50
29 4107 137P 138D C N 1099 1101 79.25 54.50 50.27 2.46 -63.30 147.31 24.73
29 138D 138D N CA 1101 1102 -2.86 40.90 -40.00
30 4109 139T 140S C N 1114 1116 -158.64 -136.60 36.80 1.29 -64.10 172.54 19.32
30 140S 140S N CA 1116 1117 -179.33 151.20 -35.00
31 4110 140S 141N C N 1120 1122 -135.05 -119.90 19.52 1.05 55.90 -170.69 23.37
31 141N 141N N CA 1122 1123 124.71 137.00 39.50
-------------------------------------------------------------------------------------------------
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 10477 35K 75F CE CZ 281 593 10.83 4.64 6.19 5.62 4.64 6.19 5.62
-------------------------------------------------------------------------------------------------
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 12320 28D 143. N O6 214 1148 5.97 3.00 2.97 29.68 3.00 2.97 29.68
2 12321 104D 145. N O6 816 1178 8.59 3.00 5.59 55.90 3.00 5.59 55.90
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 2 27 42 149 126 192 176 186 199 234 270
<< 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 : 145
Number of all, selected real atoms : 1179 1179
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12321 12321
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3392
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 : 5931.5073
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1161 11 17 0.025 0.025 204.58 1.000
2 Bond angle potential : 1566 13 50 4.526 4.526 625.52 1.000
3 Stereochemical cosine torsion poten: 750 0 36 49.244 49.244 290.60 1.000
4 Stereochemical improper torsion pot: 481 2 7 2.769 2.769 76.237 1.000
5 Soft-sphere overlap restraints : 3392 3 8 0.013 0.013 65.790 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) : 2238 49 129 1.061 1.061 1396.6 1.000
10 Distance restraints 2 (N-O) : 2391 37 122 0.975 0.975 1038.9 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 141 2 12 10.159 10.159 171.62 1.000
14 Sidechain Chi_1 dihedral restraints: 124 0 7 76.343 76.343 70.833 1.000
15 Sidechain Chi_2 dihedral restraints: 91 0 4 72.182 72.182 57.549 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 66.351 66.351 23.056 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 1 97.947 97.947 17.317 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32196 1.000
19 Disulfide angle restraints : 6 0 0 3.120 3.120 1.2899 1.000
20 Disulfide dihedral angle restraints: 3 0 0 20.943 20.943 1.4627 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) : 1265 0 0 0.598 0.598 69.639 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 140 31 35 40.819 79.923 195.69 1.000
26 Distance restraints 4 (SDCH-SDCH) : 511 0 23 1.478 1.478 165.63 1.000
27 Distance restraints 5 (X-Y) : 1391 7 30 0.230 0.230 1458.8 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: with_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 26805.3340
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
1 223 28D 28D N CA 214 215 1.68 1.43 0.25 8.13 1.43 0.25 8.13
2 225 28D 28D C CA 220 215 1.76 1.49 0.27 7.88 1.49 0.27 7.88
3 226 28D 29L C N 220 222 1.50 1.35 0.15 5.40 1.35 0.15 5.40
4 231 29L 29L N CA 222 223 1.60 1.43 0.17 5.75 1.43 0.17 5.75
5 822 102L 102L C CA 806 801 1.69 1.49 0.20 5.74 1.49 0.20 5.74
6 828 103D 103D N CA 808 809 1.60 1.43 0.17 5.56 1.43 0.17 5.56
7 830 103D 103D C CA 814 809 1.65 1.49 0.16 4.66 1.49 0.16 4.66
8 831 103D 104D C N 814 816 1.50 1.35 0.16 5.65 1.35 0.16 5.65
9 836 104D 104D N CA 816 817 1.65 1.43 0.22 7.38 1.43 0.22 7.38
10 838 104D 104D C CA 822 817 1.79 1.49 0.30 8.68 1.49 0.30 8.68
11 844 105I 105I N CA 824 825 1.58 1.43 0.15 4.99 1.43 0.15 4.99
-------------------------------------------------------------------------------------------------
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 1449 26R 27C C N 206 208 143.17 120.00 23.17 5.27 120.00 23.17 5.27
2 1460 28D 28D N CA 214 215 140.42 107.00 33.42 9.61 107.00 33.42 9.61
3 1468 28D 29L C N 220 222 149.57 120.00 29.57 6.72 120.00 29.57 6.72
4 1471 29L 29L N CA 222 223 147.23 107.00 40.23 11.57 107.00 40.23 11.57
5 1474 29L 29L CA C 223 228 133.27 116.50 16.78 4.82 116.50 16.78 4.82
6 2170 92D 92D N CA 729 730 125.81 107.00 18.81 5.41 107.00 18.81 5.41
7 2284 103D 103D CA C 809 814 144.50 116.50 28.00 8.05 116.50 28.00 8.05
8 2292 104D 104D N CA 816 817 149.37 107.00 42.37 12.18 107.00 42.37 12.18
9 2303 105I 105I N CA 824 825 127.63 107.00 20.63 5.93 107.00 20.63 5.93
-------------------------------------------------------------------------------------------------
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 4551 1M 103D CA CA 2 809 10.00 4.93 5.08 8.89 4.93 5.08 8.89
2 4584 2Q 103D CA CA 10 809 12.72 8.13 4.59 5.88 8.13 4.59 5.88
3 4615 3K 103D CA CA 19 809 12.96 8.67 4.29 6.54 8.67 4.29 6.54
4 4725 7F 103D CA CA 48 809 16.37 12.15 4.22 4.86 12.15 4.22 4.86
5 4726 7F 104D CA CA 48 817 16.50 12.38 4.12 4.62 12.38 4.12 4.62
6 6020 74L 108A CA CA 578 849 9.96 7.84 2.12 5.75 7.84 2.12 5.75
-------------------------------------------------------------------------------------------------
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 6778 1M 103D N O 1 815 9.52 6.03 3.50 4.61 6.03 3.50 4.61
2 6794 2Q 103D N O 9 815 12.44 7.61 4.83 5.63 7.61 4.83 5.63
3 6813 3K 103D N O 18 815 12.82 7.74 5.08 7.33 7.74 5.08 7.33
4 6826 4L 103D N O 27 815 14.95 9.90 5.06 5.05 9.90 5.06 5.05
5 6887 8L 103D N O 58 815 13.52 9.53 3.98 5.36 9.53 3.98 5.36
6 6934 29L 6V N O 222 46 11.50 5.08 6.42 4.54 5.08 6.42 4.54
7 7582 58T 103D N O 460 815 10.05 7.13 2.91 4.80 7.13 2.91 4.80
8 7888 74L 108A N O 577 852 10.19 8.11 2.07 4.76 8.11 2.07 4.76
9 7921 75F 108A N O 585 852 9.40 7.13 2.26 5.62 7.13 2.26 5.62
10 8462 101L 104D N O 792 823 9.61 6.38 3.22 5.33 6.38 3.22 5.33
11 8500 104D 1M N O 816 8 12.50 7.84 4.65 5.39 7.84 4.65 5.39
12 8501 104D 2Q N O 816 17 15.63 10.68 4.95 4.81 10.68 4.95 4.81
13 8503 104D 56R N O 816 450 13.77 10.15 3.62 4.80 10.15 3.62 4.80
14 8509 104D 101L N O 816 799 10.04 6.43 3.62 5.96 6.43 3.62 5.96
15 8510 104D 102L N O 816 807 5.77 3.30 2.47 4.71 3.30 2.47 4.71
16 8517 105I 10A N O 824 81 14.98 10.92 4.06 4.98 10.92 4.06 4.98
-------------------------------------------------------------------------------------------------
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 4213 103D 103D CA C 809 814 -109.66 -180.00 70.34 14.06 -180.00 70.34 14.06
-------------------------------------------------------------------------------------------------
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 3971 1M 2Q C N 7 9 -59.57 -63.80 14.07 2.29 -121.10 177.58 7.23
1 2Q 2Q N CA 9 10 -26.88 -40.30 139.70
2 3978 8L 9F C N 64 66 -85.65 -124.20 88.43 3.05 -63.20 110.33 13.89
2 9F 9F N CA 66 67 63.72 143.30 -44.30
3 3980 10A 11I C N 80 82 70.95 -97.30 168.58 6.96 -120.60 168.61 11.47
3 11I 11I N CA 82 83 137.68 127.20 130.30
4 3981 11I 12A C N 88 90 -55.87 -68.20 12.58 0.98 -62.50 176.44 28.60
4 12A 12A N CA 90 91 142.79 145.30 -40.90
5 3982 12A 13A C N 93 95 -153.30 -134.00 28.37 0.89 -62.50 176.47 33.76
5 13A 13A N CA 95 96 167.79 147.00 -40.90
6 3985 15C 16I C N 111 113 -59.11 -63.40 4.51 0.76 -120.60 -174.24 8.41
6 16I 16I N CA 113 114 -44.99 -43.60 130.30
7 3986 16I 17H C N 119 121 -75.69 -67.60 15.65 0.97 -63.20 164.77 21.39
7 17H 17H N CA 121 122 153.40 140.00 -42.30
8 3988 18C 19E C N 135 137 -79.78 -69.30 15.36 0.86 -63.60 166.76 23.14
8 19E 19E N CA 137 138 153.72 142.50 -40.30
9 3989 19E 20A C N 144 146 -87.54 -68.20 19.61 1.55 -62.50 172.43 29.55
9 20A 20A N CA 146 147 148.50 145.30 -40.90
10 3991 21K 22Y C N 158 160 -115.29 -124.30 9.88 0.82 -63.50 -175.45 31.92
10 22Y 22Y N CA 160 161 139.46 135.40 -43.40
11 3992 22Y 23Y C N 170 172 -133.46 -124.30 21.54 0.85 -63.50 176.19 31.43
11 23Y 23Y N CA 172 173 154.89 135.40 -43.40
12 3993 23Y 24S C N 182 184 -85.56 -72.40 36.70 1.76 -64.10 139.99 11.55
12 24S 24S N CA 184 185 -173.34 152.40 -35.00
13 3994 24S 25T C N 188 190 -147.48 -124.80 104.73 3.84 -63.20 110.95 19.00
13 25T 25T N CA 190 191 -114.25 143.50 -42.10
14 3995 25T 26R C N 195 197 -144.96 -125.20 35.23 1.19 -63.00 170.17 28.52
14 26R 26R N CA 197 198 169.77 140.60 -41.10
15 3997 27C 28D C N 212 214 64.70 -70.90 141.80 11.72 -63.30 -178.81 20.46
15 28D 28D N CA 214 215 -168.24 150.30 -40.00
16 3999 29L 30V C N 228 230 -149.00 -125.40 23.95 0.81 -62.40 -169.00 29.47
16 30V 30V N CA 230 231 147.36 143.30 -42.40
17 4023 53E 54S C N 428 430 -146.23 -64.10 92.74 9.50 -64.10 92.74 9.50
17 54S 54S N CA 430 431 8.08 -35.00 -35.00
18 4032 62G 63P C N 493 495 -49.84 -58.70 10.56 0.92 -64.50 177.18 14.01
18 63P 63P N CA 495 496 -36.23 -30.50 147.20
19 4033 63P 64V C N 500 502 172.22 -125.40 68.74 1.90 -73.50 118.94 8.07
19 64V 64V N CA 502 503 172.17 143.30 139.20
20 4054 84S 85N C N 674 676 -114.76 -119.90 22.97 1.15 -63.20 167.64 23.89
20 85N 85N N CA 676 677 159.39 137.00 -41.10
21 4055 85N 86T C N 682 684 -73.76 -63.20 13.93 1.57 55.90 148.55 18.32
21 86T 86T N CA 684 685 -33.01 -42.10 39.50
22 4061 91K 92D C N 727 729 156.55 -96.50 108.43 4.41 -63.30 -164.46 22.21
22 92D 92D N CA 729 730 96.35 114.20 -40.00
23 4069 99D 100L C N 782 784 -70.91 -63.50 54.30 7.15 -63.50 54.30 7.15
23 100L 100L N CA 784 785 12.59 -41.20 -41.20
24 4070 100L 101L C N 790 792 -62.81 -63.50 46.96 6.56 -63.50 46.96 6.56
24 101L 101L N CA 792 793 5.76 -41.20 -41.20
25 4072 102L 103D C N 806 808 -154.01 -96.50 59.93 2.47 -63.30 -166.37 20.54
25 103D 103D N CA 808 809 131.07 114.20 -40.00
26 4075 105I 106T C N 830 832 -119.24 -63.20 64.03 11.02 -63.20 64.03 11.02
26 106T 106T N CA 832 833 -73.06 -42.10 -42.10
27 4085 115I 116F C N 901 903 -65.91 -124.20 78.46 2.07 -63.20 135.12 18.58
27 116F 116F N CA 903 904 90.79 143.30 -44.30
28 4099 129N 130H C N 1040 1042 -122.96 -63.20 84.35 9.49 -63.20 84.35 9.49
28 130H 130H N CA 1042 1043 17.22 -42.30 -42.30
29 4100 130H 131C C N 1050 1052 -127.96 -63.00 64.98 10.92 -63.00 64.98 10.92
29 131C 131C N CA 1052 1053 -42.84 -41.10 -41.10
30 4109 139T 140S C N 1114 1116 -149.84 -136.60 37.04 1.55 -64.10 163.49 18.03
30 140S 140S N CA 1116 1117 -174.21 151.20 -35.00
31 4110 140S 141N C N 1120 1122 -121.83 -119.90 52.76 2.35 55.90 -127.28 15.22
31 141N 141N N CA 1122 1123 -170.27 137.00 39.50
-------------------------------------------------------------------------------------------------
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 12320 28D 143. N O6 214 1148 6.46 3.00 3.46 34.63 3.00 3.46 34.63
2 12321 104D 145. N O6 816 1178 8.26 3.00 5.26 52.61 3.00 5.26 52.61
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 28 36 117 122 179 180 205 220 244 264
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
with_lig.B99990001.pdb 5936.13232
with_lig.B99990002.pdb 5931.50732
move_lig = nglview.show_structure_file('with_lig.B99990001.pdb')
move_lig.clear_representations()
move_lig.add_cartoon('protein', color_scheme='residueindex')
move_lig.add_ball_and_stick('ligand', opacity=0.5)
move_lig
Лиганд не поместился, но структура белка чуть-чуть поменялась.
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' * 145 + '...'
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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------------- ---WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...* >P1;seq_ala sequence::1 : :+148 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-...*
Действительно, аланиновый, с лигандом.
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: 1 145
atom names : C +N
atom indices : 724 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 145
atom names : C CA +N O
atom indices : 724 722 0 725
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: 10483 9765
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 769 769
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9765 9765
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1435
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 : 873.9680
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 : 725 0 0 0.007 0.007 11.404 1.000
2 Bond angle potential : 1014 1 6 2.349 2.349 115.83 1.000
3 Stereochemical cosine torsion poten: 294 0 40 77.753 77.753 292.29 1.000
4 Stereochemical improper torsion pot: 290 0 0 1.102 1.102 9.4873 1.000
5 Soft-sphere overlap restraints : 1435 2 2 0.012 0.012 25.377 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 73.246 1.000
10 Distance restraints 2 (N-O) : 2564 0 12 0.435 0.435 181.82 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: 144 0 6 5.280 5.280 47.342 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 0.275 0.275 6.3456 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: 143 36 21 34.668 86.493 85.651 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.561 0.561 1.6614 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.044 0.044 23.517 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: 15906.9307
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2325 2A 3A C N 9 11 -67.12 -62.50 4.80 0.97 -68.20 172.48 13.95
1 3A 3A N CA 11 12 -42.22 -40.90 145.30
2 2326 3A 4A C N 14 16 69.14 -68.20 137.86 11.27 -68.20 137.86 11.27
2 4A 4A N CA 16 17 133.31 145.30 145.30
3 2338 15A 16A C N 74 76 78.74 55.40 27.29 1.97 -62.50 155.46 31.58
3 16A 16A N CA 76 77 24.05 38.20 -40.90
4 2341 18A 19A C N 89 91 51.93 55.40 16.63 0.74 -62.50 148.96 30.05
4 19A 19A N CA 91 92 54.46 38.20 -40.90
5 2344 21A 22A C N 104 106 179.91 -134.00 111.40 6.87 -62.50 145.97 23.43
5 22A 22A N CA 106 107 45.58 147.00 -40.90
6 2359 36A 37A C N 179 181 66.82 55.40 13.07 0.99 -62.50 148.38 30.18
6 37A 37A N CA 181 182 31.85 38.20 -40.90
7 2360 37A 38A C N 184 186 62.76 55.40 12.36 0.52 -62.50 143.08 29.10
7 38A 38A N CA 186 187 28.27 38.20 -40.90
8 2371 48A 49A C N 239 241 85.99 55.40 41.74 2.32 -62.50 156.91 31.69
8 49A 49A N CA 241 242 9.81 38.20 -40.90
9 2376 53A 54A C N 264 266 91.67 -134.00 139.34 3.42 -62.50 -155.02 32.17
9 54A 54A N CA 266 267 -175.99 147.00 -40.90
10 2379 56A 57A C N 279 281 60.58 55.40 11.51 1.11 -62.50 152.11 30.83
10 57A 57A N CA 281 282 48.48 38.20 -40.90
11 2385 62A 63A C N 309 311 -98.26 -68.20 32.97 2.31 -62.50 164.19 28.79
11 63A 63A N CA 311 312 158.85 145.30 -40.90
12 2386 63A 64A C N 314 316 -117.93 -134.00 19.95 0.51 -62.50 -175.42 28.10
12 64A 64A N CA 316 317 135.17 147.00 -40.90
13 2387 64A 65A C N 319 321 175.83 -134.00 51.26 2.11 -62.50 -144.89 32.35
13 65A 65A N CA 321 322 136.49 147.00 -40.90
14 2388 65A 66A C N 324 326 159.87 -134.00 67.17 1.81 -62.50 -148.68 41.76
14 66A 66A N CA 326 327 158.75 147.00 -40.90
15 2389 66A 67A C N 329 331 -141.83 -134.00 22.56 1.39 -62.50 -175.36 27.70
15 67A 67A N CA 331 332 125.84 147.00 -40.90
16 2390 67A 68A C N 334 336 -118.16 -134.00 30.19 1.18 -62.50 171.48 26.01
16 68A 68A N CA 336 337 121.30 147.00 -40.90
17 2391 68A 69A C N 339 341 66.03 -68.20 136.53 12.36 -62.50 -163.32 29.99
17 69A 69A N CA 341 342 170.23 145.30 -40.90
18 2392 69A 70A C N 344 346 -64.81 -68.20 15.08 1.10 -62.50 171.53 28.00
18 70A 70A N CA 346 347 130.61 145.30 -40.90
19 2393 70A 71A C N 349 351 -148.58 -134.00 18.64 0.49 -62.50 -177.87 34.45
19 71A 71A N CA 351 352 158.60 147.00 -40.90
20 2394 71A 72A C N 354 356 -67.55 -68.20 11.41 0.94 -62.50 162.48 26.88
20 72A 72A N CA 356 357 156.70 145.30 -40.90
21 2395 72A 73A C N 359 361 -60.30 -68.20 8.78 0.85 -62.50 169.98 27.75
21 73A 73A N CA 361 362 149.13 145.30 -40.90
22 2396 73A 74A C N 364 366 -123.46 -134.00 16.53 0.99 -62.50 170.62 31.22
22 74A 74A N CA 366 367 159.74 147.00 -40.90
23 2397 74A 75A C N 369 371 -67.95 -68.20 8.70 0.71 -62.50 165.19 27.34
23 75A 75A N CA 371 372 154.00 145.30 -40.90
24 2398 75A 76A C N 374 376 -121.56 -134.00 12.45 0.39 -62.50 -177.60 33.04
24 76A 76A N CA 376 377 146.53 147.00 -40.90
25 2399 76A 77A C N 379 381 -173.45 -134.00 49.90 1.30 -62.50 179.84 35.27
25 77A 77A N CA 381 382 177.56 147.00 -40.90
26 2400 77A 78A C N 384 386 -179.98 -134.00 46.09 1.65 -62.50 -149.03 40.80
26 78A 78A N CA 386 387 143.87 147.00 -40.90
27 2405 82A 83A C N 409 411 80.22 55.40 53.58 1.95 -62.50 146.18 29.18
27 83A 83A N CA 411 412 -9.28 38.20 -40.90
28 2409 86A 87A C N 429 431 53.85 55.40 12.62 0.64 -62.50 148.09 29.94
28 87A 87A N CA 431 432 50.73 38.20 -40.90
29 2412 89A 90A C N 444 446 74.28 55.40 18.89 2.07 -62.50 158.18 32.17
29 90A 90A N CA 446 447 38.55 38.20 -40.90
30 2415 92A 93A C N 459 461 64.25 55.40 15.82 1.64 -62.50 156.74 31.77
30 93A 93A N CA 461 462 51.31 38.20 -40.90
31 2442 119A 120A C N 594 596 79.66 -134.00 160.12 3.64 -62.50 178.00 28.48
31 120A 120A N CA 596 597 -148.02 147.00 -40.90
32 2454 131A 132A C N 654 656 -54.28 -62.50 16.07 2.41 -68.20 160.60 13.44
32 132A 132A N CA 656 657 -54.71 -40.90 145.30
33 2455 132A 133A C N 659 661 -119.15 -134.00 53.63 2.63 -62.50 147.66 22.23
33 133A 133A N CA 661 662 95.46 147.00 -40.90
34 2456 133A 134A C N 664 666 -161.70 -134.00 32.72 0.78 -68.20 95.44 7.41
34 134A 134A N CA 666 667 164.42 147.00 145.30
35 2464 141A 142A C N 704 706 67.50 55.40 38.12 1.47 -62.50 136.90 27.63
35 142A 142A N CA 706 707 2.05 38.20 -40.90
36 2466 143A 144A C N 714 716 129.16 -134.00 133.52 3.90 -62.50 -173.53 37.89
36 144A 144A N CA 716 717 -121.09 147.00 -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 5 14 47 62 91 71 71 132 112 99
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 148
Number of all, selected real atoms : 769 769
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9765 9765
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1400
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 : 826.9249
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 : 725 0 0 0.005 0.005 6.1549 1.000
2 Bond angle potential : 1014 0 5 2.172 2.172 96.962 1.000
3 Stereochemical cosine torsion poten: 294 0 37 76.746 76.746 286.58 1.000
4 Stereochemical improper torsion pot: 290 0 0 1.024 1.024 8.3183 1.000
5 Soft-sphere overlap restraints : 1400 2 2 0.011 0.011 19.223 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 4 0.301 0.301 79.123 1.000
10 Distance restraints 2 (N-O) : 2564 1 7 0.420 0.420 157.80 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: 144 1 5 5.331 5.331 48.253 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 0.268 0.268 6.1606 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: 143 36 21 32.763 82.268 93.888 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.498 0.498 1.3276 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.044 0.044 23.141 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: 15172.2080
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6608 92A 79A N O 456 395 5.05 2.92 2.13 5.33 2.92 2.13 5.33
-------------------------------------------------------------------------------------------------
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 2486 20A 20A CA C 97 99 -156.85 -180.00 23.14 4.63 -180.00 23.14 4.63
-------------------------------------------------------------------------------------------------
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 2338 15A 16A C N 74 76 79.28 55.40 27.56 2.04 -62.50 156.11 31.71
1 16A 16A N CA 76 77 24.45 38.20 -40.90
2 2341 18A 19A C N 89 91 62.24 55.40 15.38 0.56 -62.50 140.80 28.63
2 19A 19A N CA 91 92 24.42 38.20 -40.90
3 2359 36A 37A C N 179 181 67.62 55.40 14.55 1.02 -62.50 148.32 30.16
3 37A 37A N CA 181 182 30.29 38.20 -40.90
4 2360 37A 38A C N 184 186 62.03 55.40 10.54 0.47 -62.50 143.29 29.14
4 38A 38A N CA 186 187 30.00 38.20 -40.90
5 2371 48A 49A C N 239 241 84.13 55.40 39.84 2.16 -62.50 155.40 31.41
5 49A 49A N CA 241 242 10.59 38.20 -40.90
6 2376 53A 54A C N 264 266 91.27 -134.00 140.05 3.42 -62.50 -156.11 32.02
6 54A 54A N CA 266 267 -174.79 147.00 -40.90
7 2379 56A 57A C N 279 281 61.41 55.40 11.32 1.15 -62.50 152.38 30.89
7 57A 57A N CA 281 282 47.80 38.20 -40.90
8 2383 60A 61A C N 299 301 -60.61 -62.50 43.65 7.06 -62.50 43.65 7.06
8 61A 61A N CA 301 302 -84.51 -40.90 -40.90
9 2384 61A 62A C N 304 306 -106.08 -62.50 43.68 8.27 -62.50 43.68 8.27
9 62A 62A N CA 306 307 -37.98 -40.90 -40.90
10 2385 62A 63A C N 309 311 19.51 -68.20 99.06 6.77 -62.50 162.39 30.99
10 63A 63A N CA 311 312 99.26 145.30 -40.90
11 2386 63A 64A C N 314 316 -132.53 -134.00 30.25 1.75 -62.50 158.23 29.68
11 64A 64A N CA 316 317 177.21 147.00 -40.90
12 2387 64A 65A C N 319 321 -154.45 -134.00 24.83 0.61 -62.50 -177.17 34.87
12 65A 65A N CA 321 322 161.08 147.00 -40.90
13 2388 65A 66A C N 324 326 -106.82 -134.00 27.98 0.71 -62.50 -175.84 32.52
13 66A 66A N CA 326 327 140.36 147.00 -40.90
14 2389 66A 67A C N 329 331 -67.64 -68.20 7.09 0.55 -62.50 179.21 29.12
14 67A 67A N CA 331 332 138.23 145.30 -40.90
15 2390 67A 68A C N 334 336 -80.43 -68.20 17.92 1.13 -62.50 161.70 27.42
15 68A 68A N CA 336 337 158.40 145.30 -40.90
16 2391 68A 69A C N 339 341 -62.31 -68.20 17.97 1.24 -62.50 169.23 27.74
16 69A 69A N CA 341 342 128.33 145.30 -40.90
17 2392 69A 70A C N 344 346 -166.09 -134.00 44.64 1.32 -62.50 175.03 34.13
17 70A 70A N CA 346 347 178.02 147.00 -40.90
18 2393 70A 71A C N 349 351 -62.20 -68.20 13.61 1.28 -62.50 161.59 26.47
18 71A 71A N CA 351 352 157.52 145.30 -40.90
19 2394 71A 72A C N 354 356 -56.87 -68.20 18.35 1.16 -62.50 171.85 28.44
19 72A 72A N CA 356 357 130.86 145.30 -40.90
20 2395 72A 73A C N 359 361 -164.05 -134.00 36.52 0.90 -62.50 -177.74 35.25
20 73A 73A N CA 361 362 167.76 147.00 -40.90
21 2396 73A 74A C N 364 366 -67.15 -68.20 1.29 0.13 -62.50 173.11 28.60
21 74A 74A N CA 366 367 146.05 145.30 -40.90
22 2397 74A 75A C N 369 371 -75.21 -68.20 9.41 0.60 -62.50 168.00 28.17
22 75A 75A N CA 371 372 151.58 145.30 -40.90
23 2398 75A 76A C N 374 376 -112.67 -134.00 23.15 0.53 -62.50 -174.20 28.44
23 76A 76A N CA 376 377 138.00 147.00 -40.90
24 2399 76A 77A C N 379 381 -175.54 -134.00 43.02 1.06 -62.50 -163.35 38.19
24 77A 77A N CA 381 382 158.19 147.00 -40.90
25 2400 77A 78A C N 384 386 -149.89 -134.00 62.68 3.82 -62.50 154.38 23.22
25 78A 78A N CA 386 387 86.37 147.00 -40.90
26 2401 78A 79A C N 389 391 -66.68 -62.50 39.28 6.65 -62.50 39.28 6.65
26 79A 79A N CA 391 392 -79.96 -40.90 -40.90
27 2405 82A 83A C N 409 411 82.28 55.40 60.57 2.19 -62.50 146.88 29.13
27 83A 83A N CA 411 412 -16.09 38.20 -40.90
28 2407 84A 85A C N 419 421 -63.50 -62.50 2.43 0.45 -134.00 -176.06 11.34
28 85A 85A N CA 421 422 -43.11 -40.90 147.00
29 2408 85A 86A C N 424 426 67.76 -68.20 136.03 11.68 -68.20 136.03 11.68
29 86A 86A N CA 426 427 149.64 145.30 145.30
30 2409 86A 87A C N 429 431 58.48 55.40 11.76 0.48 -62.50 138.66 28.20
30 87A 87A N CA 431 432 26.85 38.20 -40.90
31 2412 89A 90A C N 444 446 55.10 55.40 22.76 1.35 -62.50 155.57 31.33
31 90A 90A N CA 446 447 60.95 38.20 -40.90
32 2415 92A 93A C N 459 461 65.93 55.40 10.62 1.21 -62.50 151.57 30.80
32 93A 93A N CA 461 462 39.60 38.20 -40.90
33 2442 119A 120A C N 594 596 80.33 -134.00 159.90 3.63 -62.50 177.96 28.52
33 120A 120A N CA 596 597 -147.06 147.00 -40.90
34 2455 132A 133A C N 659 661 53.16 55.40 2.25 0.25 -62.50 140.03 28.42
34 133A 133A N CA 661 662 38.05 38.20 -40.90
35 2464 141A 142A C N 704 706 69.34 55.40 43.80 1.68 -62.50 137.09 27.56
35 142A 142A N CA 706 707 -3.32 38.20 -40.90
36 2466 143A 144A C N 714 716 80.12 55.40 131.61 9.97 -62.50 -151.83 31.98
36 144A 144A N CA 716 717 167.46 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 7 8 42 57 80 76 99 114 107 88
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 873.96802
seq_ala.B99990002.pdb 826.92493
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
lmp
Что-то общее в них есть. Но то, что они не слишком уж похожими получились, радуемт, иначе это слишком удивительно было бы.
Сравним скоры аланинового и нативного лизоцимов: для аланинового лизоцима 873.96802 и 826.92493 (для первой и второй моделей), а для нативного лизоцима 965.01593 и 1126.68225. И это довольно странно: было бы гораздо понятнее, если бы скор у нативного лизоцима, наоборот, был бы меньше. Но такой результат говорит о том, что намоделировать можно все, что угодно, но скору нельзя просто так верить. Наверное, нужно набрать выборку из скоров и получить статистически значимые скоры для двух моделей, чтобы их можно было сравнивать. Возможно, мы бы не получили такой странный результат, если бы сравнивали лизоцимы из более близких видов, если причина этой странности в том, что белки просто уже слишком сильно различаются, и modeller не видит особой разницы, даже если все аминокислоты заменить на аланин.