Будем работать с лизоцимом LYS_BPPS1
import sys
sys.path.append('/usr/lib/modeller9v7/modlib/')
sys.path.append('/usr/lib/modeller9v7/lib/x86_64-intel8/python2.5/')
import modeller
import _modeller
import modeller.automodel
env=modeller.environ()
env.io.hetatm=True
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo.fbb.msu.ru 3.8-2-amd64 x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/05/25 15:13:43
Загрузим белок-заготовку и белок, с которым будем работать - LYS_BPPS1
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-05-25 15:13:51-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 132.249.231.77
Connecting to www.pdb.org|132.249.231.77|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-05-25 15:13:51-- http://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 132.249.231.10
Connecting to www.rcsb.org|132.249.231.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-05-25 15:13:52-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 128.6.244.231
Connecting to files.rcsb.org|128.6.244.231|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb'
[ <=> ] 131,301 254K/s in 0.5s
2017-05-25 15:13:53 (254 KB/s) - `1lmp.pdb' saved [131301]
! wget http://www.uniprot.org/uniprot/O80292.fasta
--2017-05-25 15:13:58-- http://www.uniprot.org/uniprot/O80292.fasta Resolving www.uniprot.org... 128.175.240.211, 193.62.193.81 Connecting to www.uniprot.org|128.175.240.211|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 239 [text/plain] Saving to: `O80292.fasta' 100%[======================================>] 239 --.-K/s in 0s 2017-05-25 15:13:58 (21.2 MB/s) - `O80292.fasta' saved [239/239]
Создадим выравнивание целевого белка с заготовкой
alignm2=modeller.alignment(env)
alignm2.append(file='O80292.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm2.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm2[0].code=alignm2[0].code[3:9] #переименовываем идентификатор
alignm2.salign()
alignm2.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2 SALIGN_____> adding the next group to the alignment; iteration 3
Строим модель:
## Выбираем объект для моделирования
s = alignm2[0]
pdb = alignm2[1]
print s.code, pdb.code
O80292 1lmp
## 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()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 167
atom names : C +N
atom indices : 1276 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 167
atom names : C CA +N O
atom indices : 1276 1270 0 1277
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.)
transfe_404W> At least one template is aligned with model residue 165:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 166:
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
irestab_402W> ires, irestp: 131 69
irestab_402W> ires, irestp: 132 70
irestab_402W> ires, irestp: 131 69
irestab_402W> ires, irestp: 132 70
irestab_402W> ires, irestp: 131 69
irestab_402W> ires, irestp: 132 70
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
0 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12074 10916
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 : 167
Number of all, selected real atoms : 1278 1278
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10916 10916
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3010
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 : 1680.5909
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 : 1300 0 0 0.007 0.007 17.618 1.000
2 Bond angle potential : 1756 0 9 2.348 2.348 182.55 1.000
3 Stereochemical cosine torsion poten: 794 0 33 48.152 48.152 294.76 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.459 1.459 22.096 1.000
5 Soft-sphere overlap restraints : 3010 0 0 0.005 0.005 7.8810 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) : 2408 2 17 0.829 0.829 239.78 1.000
10 Distance restraints 2 (N-O) : 2597 11 52 0.993 0.993 498.89 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: 166 1 3 5.483 5.483 58.855 1.000
14 Sidechain Chi_1 dihedral restraints: 133 0 0 82.371 82.371 45.796 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 1 91.149 91.149 47.417 1.000
16 Sidechain Chi_3 dihedral restraints: 45 0 0 81.050 81.050 32.128 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 96.780 96.780 15.480 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) : 809 0 0 0.573 0.573 19.431 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: 165 55 32 35.309 99.760 174.06 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 1 1.810 1.810 23.845 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: O80292.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: 25644.3027
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 8363 52T 167Q N O 355 1277 13.54 8.62 4.92 5.55 8.62 4.92 5.55
2 8377 53V 167Q N O 362 1277 14.34 8.17 6.17 8.39 8.17 6.17 8.39
3 8385 54C 167Q N O 369 1277 16.97 9.76 7.21 6.40 9.76 7.21 6.40
4 8394 55Y 167Q N O 375 1277 17.37 10.84 6.53 6.41 10.84 6.53 6.41
5 8423 57H 167Q N O 391 1277 14.64 9.99 4.65 6.11 9.99 4.65 6.11
6 8447 58T 167Q N O 401 1277 11.54 8.19 3.35 4.99 8.19 3.35 4.99
7 8473 59G 167Q N O 408 1277 9.07 6.08 2.99 5.43 6.08 2.99 5.43
8 9968 162C 139R N O 1228 1040 16.32 10.23 6.10 4.93 10.23 6.10 4.93
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4593 63M 63M CA C 438 443 -143.29 -180.00 36.71 7.34 -180.00 36.71 7.34
-------------------------------------------------------------------------------------------------
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 4380 15I 16S C N 104 106 128.27 -136.60 96.75 3.40 -64.10 -130.89 28.55
1 16S 16S N CA 106 107 168.82 151.20 -35.00
2 4381 16S 17G C N 110 112 128.53 82.20 58.40 2.14 -62.40 169.66 29.70
2 17G 17G N CA 112 113 -27.05 8.50 -41.20
3 4383 18G 19A C N 118 120 65.88 55.40 17.61 0.75 -62.50 143.87 29.25
3 19A 19A N CA 120 121 24.04 38.20 -40.90
4 4385 20I 21A C N 131 133 55.43 55.40 2.32 0.14 -62.50 140.72 28.59
4 21A 21A N CA 133 134 35.88 38.20 -40.90
5 4386 21A 22I C N 136 138 33.24 -97.30 133.33 6.43 -120.60 156.78 9.82
5 22I 22I N CA 138 139 100.06 127.20 130.30
6 4389 24S 25V C N 155 157 -86.65 -125.40 42.98 2.21 -62.40 157.59 21.41
6 25V 25V N CA 157 158 161.89 143.30 -42.40
7 4390 25V 26L C N 162 164 -107.20 -108.50 2.38 0.11 -63.50 177.19 22.50
7 26L 26L N CA 164 165 130.51 132.50 -41.20
8 4392 27I 28T C N 178 180 -131.05 -124.80 17.63 0.93 -63.20 -177.78 19.76
8 28T 28T N CA 180 181 127.01 143.50 -42.10
9 4393 28T 29G C N 185 187 176.78 -167.20 17.17 0.25 82.20 -163.46 13.79
9 29G 29G N CA 187 188 -179.21 174.60 8.50
10 4394 29G 30P C N 189 191 -78.47 -58.70 29.17 1.97 -64.50 156.87 12.46
10 30P 30P N CA 191 192 -9.05 -30.50 147.20
11 4395 30P 31G C N 196 198 -94.48 -80.20 39.50 0.96 82.20 -123.26 18.32
11 31G 31G N CA 198 199 -149.07 174.10 8.50
12 4396 31G 32G C N 200 202 -68.87 -62.40 6.69 1.25 82.20 159.57 12.13
12 32G 32G N CA 202 203 -42.88 -41.20 8.50
13 4397 32G 33N C N 204 206 -58.96 -119.90 65.17 2.14 -63.20 155.06 19.62
13 33N 33N N CA 206 207 113.90 137.00 -41.10
14 4407 42K 43P C N 284 286 -115.47 -64.50 51.43 4.96 -58.70 -175.61 19.91
14 43P 43P N CA 286 287 154.07 147.20 -30.50
15 4408 43P 44Y C N 291 293 -82.12 -98.40 47.20 4.83 -63.50 128.85 19.52
15 44Y 44Y N CA 293 294 84.10 128.40 -43.40
16 4425 60K 61D C N 419 421 95.22 54.50 141.97 13.72 -63.30 -146.44 24.63
16 61D 61D N CA 421 422 176.90 40.90 -40.00
17 4427 62I 63M C N 435 437 -90.83 -63.40 67.33 8.43 -63.40 67.33 8.43
17 63M 63M N CA 437 438 20.99 -40.50 -40.50
18 4428 63M 64P C N 443 445 0.92 -58.70 87.48 5.95 -64.50 135.17 13.54
18 64P 64P N CA 445 446 -94.51 -30.50 147.20
19 4429 64P 65G C N 450 452 103.61 78.70 84.98 1.48 -80.20 -173.40 13.67
19 65G 65G N CA 452 453 112.65 -166.10 174.10
20 4445 80D 81L C N 573 575 54.30 60.20 23.61 0.95 -63.50 150.50 27.51
20 81L 81L N CA 575 576 52.46 29.60 -41.20
21 4447 82I 83T C N 589 591 -82.62 -78.10 17.88 0.92 -63.20 175.68 21.30
21 83T 83T N CA 591 592 132.50 149.80 -42.10
22 4448 83T 84V C N 596 598 -55.95 -62.40 23.50 3.37 -125.40 177.28 6.75
22 84V 84V N CA 598 599 -19.81 -42.40 143.30
23 4451 86R 87Q C N 619 621 -32.56 -73.00 40.48 2.92 -63.80 179.95 24.92
23 87Q 87Q N CA 621 622 142.48 140.70 -40.30
24 4484 119S 120T C N 880 882 -99.79 -124.80 39.35 1.23 -63.20 159.48 18.27
24 120T 120T N CA 882 883 113.12 143.50 -42.10
25 4486 121L 122L C N 895 897 -107.16 -108.50 39.12 2.13 -63.50 153.53 24.01
25 122L 122L N CA 897 898 171.60 132.50 -41.20
26 4487 122L 123R C N 903 905 -138.54 -125.20 65.67 2.85 -63.00 136.76 23.48
26 123R 123R N CA 905 906 -155.10 140.60 -41.10
27 4490 125I 126N C N 931 933 -91.41 -71.20 22.75 1.36 -63.20 168.04 22.60
27 126N 126N N CA 933 934 153.25 142.80 -41.10
28 4491 126N 127Q C N 939 941 -93.75 -73.00 52.78 3.09 -63.80 133.87 21.29
28 127Q 127Q N CA 941 942 -170.77 140.70 -40.30
29 4492 127Q 128G C N 948 950 -59.66 -62.40 3.96 0.56 82.20 151.28 11.56
29 128G 128G N CA 950 951 -44.05 -41.20 8.50
30 4493 128G 129D C N 952 954 -92.67 -70.90 24.58 1.35 -63.30 161.00 21.74
30 129D 129D N CA 954 955 161.71 150.30 -40.00
31 4495 130I 131K C N 968 970 -134.64 -118.00 24.00 0.85 -62.90 177.90 27.40
31 131K 131K N CA 970 971 156.41 139.10 -40.80
32 4496 131K 132G C N 977 979 -152.08 -167.20 45.39 1.52 82.20 176.09 13.53
32 132G 132G N CA 979 980 131.80 174.60 8.50
33 4498 133A 134C C N 986 988 -135.53 -63.00 74.04 11.46 -63.00 74.04 11.46
33 134C 134C N CA 988 989 -26.19 -41.10 -41.10
34 4499 134C 135D C N 992 994 -59.58 -63.30 6.37 0.68 -70.90 164.92 8.69
34 135D 135D N CA 994 995 -45.17 -40.00 150.30
35 4500 135D 136Q C N 1000 1002 -64.69 -63.80 4.62 0.73 -121.10 -175.69 9.48
35 136Q 136Q N CA 1002 1003 -44.83 -40.30 139.70
36 4503 138R 139R C N 1028 1030 -139.47 -125.20 41.32 2.23 -63.00 162.09 18.38
36 139R 139R N CA 1030 1031 101.82 140.60 -41.10
37 4509 144G 145G C N 1081 1083 -70.17 -62.40 9.35 1.39 82.20 158.74 11.94
37 145G 145G N CA 1083 1084 -36.00 -41.20 8.50
38 4511 146K 147Q C N 1094 1096 -67.92 -73.00 12.75 0.75 -63.80 169.36 24.69
38 147Q 147Q N CA 1096 1097 129.01 140.70 -40.30
39 4512 147Q 148W C N 1103 1105 -144.77 -124.90 50.48 1.94 -63.00 150.20 24.26
39 148W 148W N CA 1105 1106 -170.20 143.40 -44.20
40 4513 148W 149K C N 1117 1119 -92.03 -70.20 44.59 2.75 -62.90 142.92 20.26
40 149K 149K N CA 1119 1120 179.28 140.40 -40.80
41 4514 149K 150G C N 1126 1128 124.39 78.70 49.61 1.88 82.20 171.35 10.36
41 150G 150G N CA 1128 1129 174.57 -166.10 8.50
42 4515 150G 151L C N 1130 1132 -71.71 -70.70 5.45 0.38 -63.50 172.04 24.37
42 151L 151L N CA 1132 1133 146.96 141.60 -41.20
43 4516 151L 152M C N 1138 1140 -64.06 -73.00 33.41 2.13 -63.40 151.31 22.54
43 152M 152M N CA 1140 1141 110.81 143.00 -40.50
44 4517 152M 153T C N 1146 1148 -156.31 -124.80 56.00 1.73 -63.20 158.36 26.10
44 153T 153T N CA 1148 1149 -170.20 143.50 -42.10
45 4518 153T 154R C N 1153 1155 -64.24 -72.10 13.38 1.16 -63.00 166.17 22.53
45 154R 154R N CA 1155 1156 152.73 141.90 -41.10
46 4519 154R 155R C N 1164 1166 -65.57 -72.10 7.65 0.51 -63.00 179.03 24.01
46 155R 155R N CA 1166 1167 137.92 141.90 -41.10
47 4520 155R 156E C N 1175 1177 -112.87 -117.80 5.10 0.22 -63.60 -174.92 22.35
47 156E 156E N CA 1177 1178 138.10 136.80 -40.30
48 4521 156E 157V C N 1184 1186 -63.28 -62.40 2.53 0.37 -125.40 -177.19 10.25
48 157V 157V N CA 1186 1187 -44.77 -42.40 143.30
49 4522 157V 158E C N 1191 1193 -63.56 -69.30 8.54 0.78 -63.60 170.88 22.78
49 158E 158E N CA 1193 1194 148.82 142.50 -40.30
50 4523 158E 159R C N 1200 1202 67.40 57.30 20.25 1.02 -63.00 144.19 26.20
50 159R 159R N CA 1202 1203 20.45 38.00 -41.10
51 4524 159R 160D C N 1211 1213 -112.67 -96.50 19.06 0.78 -63.30 152.33 16.49
51 160D 160D N CA 1213 1214 104.11 114.20 -40.00
52 4526 161V 162C C N 1226 1228 -139.46 -117.90 22.51 0.66 -63.00 -172.37 28.62
52 162C 162C N CA 1228 1229 147.56 141.10 -41.10
53 4527 162C 163L C N 1232 1234 -174.21 -108.50 70.27 3.67 -63.50 -174.53 23.02
53 163L 163L N CA 1234 1235 107.61 132.50 -41.20
54 4528 163L 164W C N 1240 1242 105.56 58.80 119.47 9.78 -63.00 -118.56 28.62
54 164W 164W N CA 1242 1243 142.94 33.00 -44.20
55 4530 165G 166K C N 1258 1260 -163.22 -118.00 79.03 3.01 -62.90 152.81 25.66
55 166K 166K N CA 1260 1261 -156.08 139.10 -40.80
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 12 30 118 120 159 153 177 206 229 225
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 167
Number of all, selected real atoms : 1278 1278
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10916 10916
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3048
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 : 1576.4534
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 : 1300 0 0 0.007 0.007 18.205 1.000
2 Bond angle potential : 1756 2 9 2.332 2.332 178.26 1.000
3 Stereochemical cosine torsion poten: 794 0 38 49.357 49.357 305.13 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.341 1.341 18.806 1.000
5 Soft-sphere overlap restraints : 3048 0 0 0.005 0.005 7.4421 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) : 2408 3 19 0.881 0.881 238.22 1.000
10 Distance restraints 2 (N-O) : 2597 12 34 1.012 1.012 425.34 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: 166 1 5 5.480 5.480 58.787 1.000
14 Sidechain Chi_1 dihedral restraints: 133 0 0 80.194 80.194 37.146 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 1 77.300 77.300 36.755 1.000
16 Sidechain Chi_3 dihedral restraints: 45 0 0 82.198 82.198 29.592 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 106.097 106.097 13.842 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) : 809 0 0 0.449 0.449 10.789 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: 165 52 33 36.867 96.219 180.21 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 1 1.800 1.800 17.937 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: O80292.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: 23982.0918
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 3044 166K 167Q C N 1267 1269 139.91 120.00 19.91 4.53 120.00 19.91 4.53
2 3047 167Q 167Q N CA 1269 1270 127.83 107.00 20.83 4.73 107.00 20.83 4.73
-------------------------------------------------------------------------------------------------
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 8363 52T 167Q N O 355 1277 13.46 8.62 4.84 5.46 8.62 4.84 5.46
2 8377 53V 167Q N O 362 1277 14.31 8.17 6.14 8.34 8.17 6.14 8.34
3 8385 54C 167Q N O 369 1277 16.97 9.76 7.21 6.40 9.76 7.21 6.40
4 8394 55Y 167Q N O 375 1277 17.75 10.84 6.91 6.78 10.84 6.91 6.78
5 8423 57H 167Q N O 391 1277 14.67 9.99 4.69 6.16 9.99 4.69 6.16
6 8447 58T 167Q N O 401 1277 11.46 8.19 3.27 4.88 8.19 3.27 4.88
7 8473 59G 167Q N O 408 1277 8.97 6.08 2.88 5.24 6.08 2.88 5.24
-------------------------------------------------------------------------------------------------
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 4593 63M 63M CA C 438 443 -143.56 -180.00 36.44 7.29 -180.00 36.44 7.29
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4379 14A 15I C N 96 98 -105.02 -120.60 72.83 3.57 -63.40 110.87 17.02
1 15I 15I N CA 98 99 59.16 130.30 -43.60
2 4380 15I 16S C N 104 106 51.63 56.90 9.62 1.05 -64.10 131.94 17.44
2 16S 16S N CA 106 107 28.36 36.40 -35.00
3 4383 18G 19A C N 118 120 64.56 55.40 23.53 0.86 -62.50 139.43 28.32
3 19A 19A N CA 120 121 16.52 38.20 -40.90
4 4385 20I 21A C N 131 133 66.27 -68.20 142.93 13.51 -62.50 179.71 27.86
4 21A 21A N CA 133 134 -166.26 145.30 -40.90
5 4389 24S 25V C N 155 157 -119.76 -125.40 9.31 0.53 -62.40 176.47 25.87
5 25V 25V N CA 157 158 150.71 143.30 -42.40
6 4390 25V 26L C N 162 164 -131.57 -108.50 51.76 2.51 -63.50 155.64 25.82
6 26L 26L N CA 164 165 178.84 132.50 -41.20
7 4392 27I 28T C N 178 180 -147.18 -124.80 24.08 1.02 -63.20 -174.40 29.25
7 28T 28T N CA 180 181 152.39 143.50 -42.10
8 4393 28T 29G C N 185 187 101.19 78.70 55.20 0.83 82.20 136.32 7.56
8 29G 29G N CA 187 188 143.49 -166.10 8.50
9 4396 31G 32G C N 200 202 -151.97 -167.20 16.00 0.43 82.20 -147.71 15.67
9 32G 32G N CA 202 203 179.48 174.60 8.50
10 4397 32G 33N C N 204 206 98.08 55.90 102.56 10.31 -63.20 -122.69 38.13
10 33N 33N N CA 206 207 132.98 39.50 -41.10
11 4398 33N 34D C N 212 214 -127.76 -63.30 75.01 9.50 -63.30 75.01 9.50
11 34D 34D N CA 214 215 -1.63 -40.00 -40.00
12 4408 43P 44Y C N 291 293 63.66 55.90 7.81 0.83 -63.50 151.32 28.63
12 44Y 44Y N CA 293 294 38.62 39.50 -43.40
13 4419 54C 55Y C N 373 375 -104.72 -98.40 74.83 7.90 -63.50 105.62 14.95
13 55Y 55Y N CA 375 376 53.84 128.40 -43.40
14 4425 60K 61D C N 419 421 71.21 -70.90 152.39 12.71 -63.30 176.77 20.64
14 61D 61D N CA 421 422 -154.70 150.30 -40.00
15 4428 63M 64P C N 443 445 10.42 -64.50 95.70 6.56 -64.50 95.70 6.56
15 64P 64P N CA 445 446 87.65 147.20 147.20
16 4437 72E 73C C N 512 514 -124.20 -63.00 65.59 9.39 -63.00 65.59 9.39
16 73C 73C N CA 514 515 -17.49 -41.10 -41.10
17 4444 79K 80D C N 565 567 -130.88 -96.50 55.21 2.27 -63.30 129.95 13.82
17 80D 80D N CA 567 568 71.00 114.20 -40.00
18 4445 80D 81L C N 573 575 -47.93 -70.70 47.30 2.94 -63.50 142.19 20.67
18 81L 81L N CA 575 576 100.14 141.60 -41.20
19 4448 83T 84V C N 596 598 62.09 55.90 6.48 0.79 -125.40 -159.64 10.67
19 84V 84V N CA 598 599 41.39 39.50 143.30
20 4475 110N 111V C N 817 819 -97.90 -125.40 71.14 2.72 -62.40 125.23 14.16
20 111V 111V N CA 819 820 77.69 143.30 -42.40
21 4486 121L 122L C N 895 897 -66.18 -70.70 9.75 0.61 -63.50 174.18 24.03
21 122L 122L N CA 897 898 132.96 141.60 -41.20
22 4487 122L 123R C N 903 905 -104.51 -125.20 32.00 1.77 -63.00 159.40 24.40
22 123R 123R N CA 905 906 165.00 140.60 -41.10
23 4488 123R 124K C N 914 916 -62.44 -70.20 10.62 0.64 -62.90 173.94 22.61
23 124K 124K N CA 916 917 133.14 140.40 -40.80
24 4490 125I 126N C N 931 933 -85.58 -71.20 73.43 5.11 -63.20 114.10 13.15
24 126N 126N N CA 933 934 70.79 142.80 -41.10
25 4491 126N 127Q C N 939 941 -136.52 -121.10 29.80 1.56 -63.80 170.76 22.14
25 127Q 127Q N CA 941 942 114.20 139.70 -40.30
26 4492 127Q 128G C N 948 950 59.11 78.70 36.29 0.57 82.20 145.90 8.22
26 128G 128G N CA 950 951 -135.56 -166.10 8.50
27 4493 128G 129D C N 952 954 -78.07 -70.90 17.20 0.58 -63.30 154.77 20.03
27 129D 129D N CA 954 955 165.93 150.30 -40.00
28 4495 130I 131K C N 968 970 -128.83 -118.00 11.59 0.39 -62.90 -172.07 28.34
28 131K 131K N CA 970 971 143.21 139.10 -40.80
29 4496 131K 132G C N 977 979 -79.77 -80.20 3.94 0.13 82.20 -131.14 7.17
29 132G 132G N CA 979 980 170.19 174.10 8.50
30 4498 133A 134C C N 986 988 -150.92 -63.00 88.68 15.30 -63.00 88.68 15.30
30 134C 134C N CA 988 989 -52.75 -41.10 -41.10
31 4499 134C 135D C N 992 994 -59.76 -63.30 3.87 0.52 -70.90 168.50 8.86
31 135D 135D N CA 994 995 -41.57 -40.00 150.30
32 4500 135D 136Q C N 1000 1002 -62.41 -63.80 7.47 1.03 -121.10 -177.64 9.40
32 136Q 136Q N CA 1002 1003 -47.64 -40.30 139.70
33 4503 138R 139R C N 1028 1030 -129.10 -125.20 37.98 1.91 -63.00 158.37 18.10
33 139R 139R N CA 1030 1031 102.82 140.60 -41.10
34 4509 144G 145G C N 1081 1083 -80.89 -80.20 22.77 0.86 82.20 -123.23 18.07
34 145G 145G N CA 1083 1084 -163.14 174.10 8.50
35 4510 145G 146K C N 1085 1087 -63.61 -70.20 19.76 1.57 -62.90 160.18 20.84
35 146K 146K N CA 1087 1088 159.02 140.40 -40.80
36 4511 146K 147Q C N 1094 1096 -60.95 -73.00 14.76 1.15 -63.80 170.50 24.92
36 147Q 147Q N CA 1096 1097 149.23 140.70 -40.30
37 4512 147Q 148W C N 1103 1105 -100.24 -124.90 35.30 1.13 -63.00 166.55 18.97
37 148W 148W N CA 1105 1106 118.13 143.40 -44.20
38 4513 148W 149K C N 1117 1119 -166.45 -118.00 49.35 1.72 -62.90 -160.30 32.10
38 149K 149K N CA 1119 1120 148.44 139.10 -40.80
39 4514 149K 150G C N 1126 1128 75.89 78.70 8.93 0.37 82.20 177.03 8.28
39 150G 150G N CA 1128 1129 -174.58 -166.10 8.50
40 4515 150G 151L C N 1130 1132 -85.02 -70.70 26.08 1.61 -63.50 156.88 23.07
40 151L 151L N CA 1132 1133 163.40 141.60 -41.20
41 4516 151L 152M C N 1138 1140 -82.30 -73.00 37.39 2.39 -63.40 141.55 22.64
41 152M 152M N CA 1140 1141 179.21 143.00 -40.50
42 4517 152M 153T C N 1146 1148 -73.74 -78.10 35.85 1.68 -63.20 132.93 17.75
42 153T 153T N CA 1148 1149 -174.62 149.80 -42.10
43 4519 154R 155R C N 1164 1166 -153.89 -125.20 33.78 1.00 -63.00 -175.57 31.03
43 155R 155R N CA 1166 1167 158.43 140.60 -41.10
44 4520 155R 156E C N 1175 1177 -99.83 -117.80 32.32 1.18 -63.60 154.54 18.85
44 156E 156E N CA 1177 1178 109.93 136.80 -40.30
45 4521 156E 157V C N 1184 1186 -64.76 -62.40 2.88 0.49 -125.40 -177.00 10.24
45 157V 157V N CA 1186 1187 -44.04 -42.40 143.30
46 4522 157V 158E C N 1191 1193 -140.67 -117.80 56.22 2.29 -63.60 152.45 24.58
46 158E 158E N CA 1193 1194 -171.84 136.80 -40.30
47 4523 158E 159R C N 1200 1202 -60.34 -72.10 12.28 0.86 -63.00 179.46 24.42
47 159R 159R N CA 1202 1203 138.35 141.90 -41.10
48 4524 159R 160D C N 1211 1213 -68.37 -70.90 9.92 0.37 -63.30 179.36 22.45
48 160D 160D N CA 1213 1214 140.71 150.30 -40.00
49 4526 161V 162C C N 1226 1228 -99.33 -117.90 80.35 3.41 -63.00 106.04 15.65
49 162C 162C N CA 1228 1229 -140.72 141.10 -41.10
50 4527 162C 163L C N 1232 1234 178.00 -108.50 74.93 3.75 -63.50 -161.61 24.63
50 163L 163L N CA 1234 1235 117.91 132.50 -41.20
51 4528 163L 164W C N 1240 1242 -154.53 -124.90 65.70 2.43 -63.00 146.01 24.32
51 164W 164W N CA 1242 1243 -157.97 143.40 -44.20
52 4530 165G 166K C N 1258 1260 -155.27 -118.00 74.56 2.95 -62.90 147.91 24.60
52 166K 166K N CA 1260 1261 -156.32 139.10 -40.80
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 19 26 117 112 168 167 165 214 237 214
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
O80292.B99990001.pdb 1680.59094
O80292.B99990002.pdb 1576.45337
import nglview
import ipywidgets
w1 = nglview.show_structure_file('O80292.B99990001.pdb')
w1
Image(url="pr10_1.png")
w2 = nglview.show_structure_file('O80292.B99990002.pdb')
w2
Image(url="pr10_2.png")
В созданных моделях нет лиганда. Исправим:
seq=''
for i in alignm2[0].residues:
seq =seq + i.code
seql=seq + "..."
print seql
MAMSPALRNSVMAAISGGAIAIASVLITGPGGNDGLEGVRYKPYKDVVGVLTVCYGHTGKDIMPGKTYTEAECKALLNKDLITVARQINPYIKVDIPETTRGALYSFVYNVGAGNFRTSTLLRKINQGDIKGACDQLRRWTYAGGKQWKGLMTRREVERDVCLWGKQ...
with open('seql.fasta', 'w') as outfilea:
outfilea.write('>O80292_lig blabla' +'\n')
outfilea.write(seql+'\n')
alignm3=modeller.alignment(env)
alignm3.append(file='seql.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm3.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm3[0].code
'O80292_lig'
sl = alignm3[0]
pdb = alignm3[1]
print sl.code, pdb.code
O80292_lig 1lmp
alignm3.salign()
alignm3.write(file='all_in_one3.ali', alignment_format='PIR')
b = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns= pdb.code , sequence = sl.code)
b.name='mod'+sl.code
b.starting_model = 1
b.ending_model = 2
b.make()
SALIGN_____> adding the next group to the alignment; iteration 1
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 167
atom names : C +N
atom indices : 1276 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 14 167
atom names : C CA +N O
atom indices : 1276 1270 0 1277
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 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: 13455 12297
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 170
Number of all, selected real atoms : 1321 1321
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12297 12297
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3088
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 : 1248.1348
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 : 1300 0 0 0.006 0.006 11.327 1.000
2 Bond angle potential : 1756 2 10 2.932 2.932 204.00 1.000
3 Stereochemical cosine torsion poten: 794 0 50 51.488 51.488 324.72 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.505 1.505 23.067 1.000
5 Soft-sphere overlap restraints : 3088 1 2 0.008 0.008 22.110 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 0.331 0.331 82.468 1.000
10 Distance restraints 2 (N-O) : 2564 0 7 0.498 0.498 162.51 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: 166 0 4 4.658 4.658 42.469 1.000
14 Sidechain Chi_1 dihedral restraints: 133 0 2 81.819 81.819 51.198 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 0 78.859 78.859 41.154 1.000
16 Sidechain Chi_3 dihedral restraints: 45 0 0 67.316 67.316 23.395 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 94.244 94.244 15.854 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) : 818 0 0 0.337 0.337 10.667 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: 165 47 36 38.453 85.763 206.71 1.000
26 Distance restraints 4 (SDCH-SDCH) : 114 0 1 1.481 1.481 11.940 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.035 0.035 14.542 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: O80292_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: 22532.4824
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 4367 2A 3M C N 12 14 -91.50 -73.00 20.90 1.41 -63.40 169.11 27.49
1 3M 3M N CA 14 15 152.74 143.00 -40.50
2 4380 15I 16S C N 104 106 79.11 56.90 24.86 2.16 -64.10 155.37 20.75
2 16S 16S N CA 106 107 25.24 36.40 -35.00
3 4383 18G 19A C N 118 120 60.46 55.40 10.07 0.38 -62.50 141.68 28.81
3 19A 19A N CA 120 121 29.49 38.20 -40.90
4 4385 20I 21A C N 131 133 50.18 55.40 9.97 0.38 -62.50 142.72 28.86
4 21A 21A N CA 133 134 46.69 38.20 -40.90
5 4386 21A 22I C N 136 138 33.19 -97.30 134.19 6.67 -63.40 169.69 31.23
5 22I 22I N CA 138 139 95.92 127.20 -43.60
6 4389 24S 25V C N 155 157 -171.30 -125.40 98.04 3.48 -62.40 139.80 23.69
6 25V 25V N CA 157 158 -130.07 143.30 -42.40
7 4390 25V 26L C N 162 164 -23.63 -70.70 74.13 4.63 -63.50 131.71 20.75
7 26L 26L N CA 164 165 84.33 141.60 -41.20
8 4392 27I 28T C N 178 180 -112.81 -124.80 64.72 3.13 -63.20 121.40 18.82
8 28T 28T N CA 180 181 -152.90 143.50 -42.10
9 4395 30P 31G C N 196 198 -143.76 -167.20 29.56 0.56 82.20 -160.27 15.16
9 31G 31G N CA 198 199 156.58 174.60 8.50
10 4396 31G 32G C N 200 202 155.60 -167.20 46.91 1.65 82.20 155.88 10.88
10 32G 32G N CA 202 203 146.02 174.60 8.50
11 4397 32G 33N C N 204 206 -150.61 -119.90 38.23 1.11 -63.20 -178.44 27.59
11 33N 33N N CA 206 207 159.76 137.00 -41.10
12 4398 33N 34D C N 212 214 -69.93 -70.90 6.69 0.38 -63.30 163.22 20.55
12 34D 34D N CA 214 215 156.91 150.30 -40.00
13 4399 34D 35G C N 220 222 -125.88 -167.20 45.29 0.68 82.20 -148.22 16.28
13 35G 35G N CA 222 223 156.06 174.60 8.50
14 4400 35G 36L C N 224 226 -90.46 -70.70 32.35 2.01 -63.50 153.96 23.01
14 36L 36L N CA 226 227 167.21 141.60 -41.20
15 4401 36L 37E C N 232 234 -60.25 -69.30 9.34 0.62 -63.60 179.52 23.76
15 37E 37E N CA 234 235 140.21 142.50 -40.30
16 4402 37E 38G C N 241 243 160.94 -167.20 31.99 0.55 82.20 -173.57 12.67
16 38G 38G N CA 243 244 177.50 174.60 8.50
17 4404 39V 40R C N 252 254 -155.40 -125.20 38.49 1.14 -63.00 179.98 30.50
17 40R 40R N CA 254 255 164.46 140.60 -41.10
18 4405 40R 41Y C N 263 265 -122.25 -124.30 9.45 0.59 -63.50 -178.27 31.80
18 41Y 41Y N CA 265 266 144.63 135.40 -43.40
19 4406 41Y 42K C N 275 277 50.91 56.60 10.67 0.56 -62.90 144.12 24.94
19 42K 42K N CA 277 278 47.62 38.60 -40.80
20 4409 44Y 45K C N 303 305 -91.88 -70.20 26.78 2.23 -62.90 168.01 20.41
20 45K 45K N CA 305 306 124.69 140.40 -40.80
21 4410 45K 46D C N 312 314 -76.89 -70.90 11.57 0.86 -63.30 -179.88 23.07
21 46D 46D N CA 314 315 140.40 150.30 -40.00
22 4413 48V 49G C N 334 336 -62.92 -62.40 4.77 0.69 82.20 151.93 11.47
22 49G 49G N CA 336 337 -36.46 -41.20 8.50
23 4415 50V 51L C N 345 347 -49.95 -70.70 25.14 2.53 -63.50 163.57 21.97
23 51L 51L N CA 347 348 155.79 141.60 -41.20
24 4419 54C 55Y C N 373 375 -145.71 -124.30 35.61 1.45 -63.50 173.46 31.50
24 55Y 55Y N CA 375 376 163.86 135.40 -43.40
25 4420 55Y 56G C N 385 387 83.97 78.70 5.27 0.27 82.20 174.56 8.39
25 56G 56G N CA 387 388 -166.05 -166.10 8.50
26 4421 56G 57H C N 389 391 -96.68 -63.20 43.16 7.34 -63.20 43.16 7.34
26 57H 57H N CA 391 392 -69.53 -42.30 -42.30
27 4422 57H 58T C N 399 401 -82.90 -78.10 5.07 0.33 -63.20 170.86 23.22
27 58T 58T N CA 401 402 148.18 149.80 -42.10
28 4425 60K 61D C N 419 421 -130.61 -70.90 71.74 3.55 -63.30 146.33 22.39
28 61D 61D N CA 421 422 -169.93 150.30 -40.00
29 4427 62I 63M C N 435 437 -127.83 -125.60 43.72 2.14 -63.40 151.70 18.91
29 63M 63M N CA 437 438 96.84 140.50 -40.50
30 4429 64P 65G C N 450 452 99.88 82.20 71.14 2.57 -62.40 163.41 28.35
30 65G 65G N CA 452 453 -60.41 8.50 -41.20
31 4438 73C 74K C N 518 520 -147.99 -62.90 103.96 13.51 -62.90 103.96 13.51
31 74K 74K N CA 520 521 18.92 -40.80 -40.80
32 4439 74K 75A C N 527 529 53.34 55.40 4.63 0.17 -62.50 142.65 28.92
32 75A 75A N CA 529 530 42.35 38.20 -40.90
33 4440 75A 76L C N 532 534 68.40 60.20 14.62 0.58 -63.50 144.37 26.59
33 76L 76L N CA 534 535 17.50 29.60 -41.20
34 4443 78N 79K C N 556 558 -98.82 -62.90 76.29 8.76 -62.90 76.29 8.76
34 79K 79K N CA 558 559 26.50 -40.80 -40.80
35 4449 84V 85A C N 603 605 -87.06 -68.20 70.08 6.28 -62.50 121.22 18.82
35 85A 85A N CA 605 606 77.81 145.30 -40.90
36 4450 85A 86R C N 608 610 -173.35 -63.00 123.15 16.85 -63.00 123.15 16.85
36 86R 86R N CA 610 611 13.58 -41.10 -41.10
37 4451 86R 87Q C N 619 621 59.71 55.10 7.90 0.41 -63.80 144.08 26.15
37 87Q 87Q N CA 621 622 33.88 40.30 -40.30
38 4456 91Y 92I C N 663 665 65.60 -97.30 170.97 8.14 -120.60 -179.47 10.76
38 92I 92I N CA 665 666 179.11 127.20 130.30
39 4464 99T 100T C N 726 728 -115.05 -63.20 52.72 8.68 -63.20 52.72 8.68
39 100T 100T N CA 728 729 -51.62 -42.10 -42.10
40 4469 104L 105Y C N 761 763 73.93 55.90 24.51 1.53 -63.50 152.59 28.64
40 105Y 105Y N CA 763 764 22.89 39.50 -43.40
41 4470 105Y 106S C N 773 775 -135.47 -64.10 81.66 8.23 -64.10 81.66 8.23
41 106S 106S N CA 775 776 4.67 -35.00 -35.00
42 4473 108V 109Y C N 797 799 61.32 55.90 7.90 0.93 -124.30 -163.69 16.31
42 109Y 109Y N CA 799 800 45.24 39.50 135.40
43 4506 141T 142Y C N 1060 1062 71.99 55.90 163.34 12.64 -124.30 176.75 10.70
43 142Y 142Y N CA 1062 1063 -157.95 39.50 135.40
44 4508 143A 144G C N 1077 1079 -55.86 -62.40 20.85 3.46 82.20 141.26 10.40
44 144G 144G N CA 1079 1080 -21.40 -41.20 8.50
45 4526 161V 162C C N 1226 1228 -108.62 -63.00 81.60 8.61 -63.00 81.60 8.61
45 162C 162C N CA 1228 1229 26.56 -41.10 -41.10
46 4528 163L 164W C N 1240 1242 72.60 58.80 28.62 0.76 -63.00 145.27 25.68
46 164W 164W N CA 1242 1243 7.92 33.00 -44.20
47 4529 164W 165G C N 1254 1256 -118.16 -80.20 74.63 4.74 82.20 -170.91 14.77
47 165G 165G N CA 1256 1257 109.84 174.10 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 15 18 130 117 175 182 184 219 200 223
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 170
Number of all, selected real atoms : 1321 1321
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12297 12297
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3148
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 : 1423.5087
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 : 1300 0 0 0.006 0.006 12.963 1.000
2 Bond angle potential : 1756 4 17 3.615 3.615 263.04 1.000
3 Stereochemical cosine torsion poten: 794 0 42 51.014 51.014 319.61 1.000
4 Stereochemical improper torsion pot: 515 0 1 1.550 1.550 24.724 1.000
5 Soft-sphere overlap restraints : 3148 1 3 0.009 0.009 26.881 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 3 0.369 0.369 109.25 1.000
10 Distance restraints 2 (N-O) : 2564 0 21 0.564 0.564 238.38 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: 166 0 5 4.923 4.923 47.451 1.000
14 Sidechain Chi_1 dihedral restraints: 133 0 7 80.577 80.577 57.573 1.000
15 Sidechain Chi_2 dihedral restraints: 98 0 0 83.261 83.261 38.818 1.000
16 Sidechain Chi_3 dihedral restraints: 45 0 0 71.935 71.935 26.976 1.000
17 Sidechain Chi_4 dihedral restraints: 23 0 0 93.167 93.167 15.265 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) : 818 0 0 0.384 0.384 10.287 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: 165 49 34 38.090 93.368 201.99 1.000
26 Distance restraints 4 (SDCH-SDCH) : 114 0 0 1.474 1.474 7.7375 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.045 0.045 22.567 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: O80292_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: 23494.4512
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 2594 126N 126N ND2 CG 938 936 139.12 122.50 16.63 4.63 122.50 16.63 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 4367 2A 3M C N 12 14 -100.51 -125.60 26.53 1.26 -63.40 174.35 29.00
1 3M 3M N CA 14 15 149.15 140.50 -40.50
2 4380 15I 16S C N 104 106 121.07 -136.60 104.32 3.64 -64.10 -127.31 29.27
2 16S 16S N CA 106 107 171.44 151.20 -35.00
3 4381 16S 17G C N 110 112 121.33 82.20 46.58 1.88 -62.40 177.95 30.70
3 17G 17G N CA 112 113 -16.77 8.50 -41.20
4 4382 17G 18G C N 114 116 -59.24 -62.40 5.39 0.74 -167.20 176.66 6.92
4 18G 18G N CA 116 117 -45.57 -41.20 174.60
5 4383 18G 19A C N 118 120 -138.57 -134.00 67.57 3.93 -62.50 142.48 21.38
5 19A 19A N CA 120 121 79.58 147.00 -40.90
6 4385 20I 21A C N 131 133 54.89 55.40 1.76 0.07 -62.50 142.50 28.92
6 21A 21A N CA 133 134 39.89 38.20 -40.90
7 4386 21A 22I C N 136 138 32.33 -97.30 133.31 6.63 -63.40 169.37 31.15
7 22I 22I N CA 138 139 96.11 127.20 -43.60
8 4389 24S 25V C N 155 157 178.38 -125.40 95.29 2.99 -62.40 153.92 26.07
8 25V 25V N CA 157 158 -139.76 143.30 -42.40
9 4390 25V 26L C N 162 164 14.65 -70.70 89.20 7.15 -63.50 175.25 29.16
9 26L 26L N CA 164 165 115.66 141.60 -41.20
10 4392 27I 28T C N 178 180 -102.38 -124.80 34.10 1.07 -63.20 164.64 18.79
10 28T 28T N CA 180 181 117.81 143.50 -42.10
11 4393 28T 29G C N 185 187 105.90 78.70 73.51 1.14 82.20 119.48 6.96
11 29G 29G N CA 187 188 125.61 -166.10 8.50
12 4395 30P 31G C N 196 198 -128.61 -167.20 50.15 1.00 82.20 -159.43 15.51
12 31G 31G N CA 198 199 142.56 174.60 8.50
13 4396 31G 32G C N 200 202 165.89 -167.20 27.05 0.45 82.20 -171.48 12.97
13 32G 32G N CA 202 203 177.43 174.60 8.50
14 4397 32G 33N C N 204 206 -116.15 -119.90 4.24 0.22 -63.20 -172.45 26.46
14 33N 33N N CA 206 207 138.98 137.00 -41.10
15 4398 33N 34D C N 212 214 -125.31 -70.90 59.84 3.44 -63.30 157.54 23.45
15 34D 34D N CA 214 215 175.18 150.30 -40.00
16 4399 34D 35G C N 220 222 94.15 78.70 18.62 0.56 82.20 175.41 9.11
16 35G 35G N CA 222 223 -176.49 -166.10 8.50
17 4400 35G 36L C N 224 226 -71.19 -70.70 19.18 1.43 -63.50 158.21 22.42
17 36L 36L N CA 226 227 160.78 141.60 -41.20
18 4401 36L 37E C N 232 234 -60.80 -69.30 11.10 1.02 -63.60 170.09 22.53
18 37E 37E N CA 234 235 149.64 142.50 -40.30
19 4402 37E 38G C N 241 243 -134.25 -167.20 33.46 0.52 82.20 -144.87 16.31
19 38G 38G N CA 243 244 168.74 174.60 8.50
20 4404 39V 40R C N 252 254 -150.60 -125.20 35.61 1.08 -63.00 176.60 29.75
20 40R 40R N CA 254 255 165.55 140.60 -41.10
21 4405 40R 41Y C N 263 265 -113.28 -98.40 17.09 1.00 -63.50 170.80 24.77
21 41Y 41Y N CA 265 266 119.98 128.40 -43.40
22 4406 41Y 42K C N 275 277 141.94 -118.00 101.25 4.10 -62.90 -133.94 27.22
22 42K 42K N CA 277 278 123.60 139.10 -40.80
23 4408 43P 44Y C N 291 293 -153.06 -124.30 54.42 2.15 -63.50 162.01 29.90
23 44Y 44Y N CA 293 294 -178.40 135.40 -43.40
24 4410 45K 46D C N 312 314 -57.73 -70.90 18.10 0.75 -63.30 177.97 22.31
24 46D 46D N CA 314 315 137.88 150.30 -40.00
25 4413 48V 49G C N 334 336 83.72 78.70 21.60 0.82 82.20 153.60 7.38
25 49G 49G N CA 336 337 -145.09 -166.10 8.50
26 4416 51L 52T C N 353 355 -96.61 -78.10 39.88 2.32 -63.20 160.11 18.51
26 52T 52T N CA 355 356 114.48 149.80 -42.10
27 4420 55Y 56G C N 385 387 135.55 -167.20 58.55 1.43 82.20 162.84 10.43
27 56G 56G N CA 387 388 162.35 174.60 8.50
28 4421 56G 57H C N 389 391 56.61 56.30 2.08 0.16 -63.20 144.65 24.79
28 57H 57H N CA 391 392 38.75 40.80 -42.30
29 4422 57H 58T C N 399 401 -63.26 -78.10 15.25 0.99 -63.20 164.59 21.11
29 58T 58T N CA 401 402 153.31 149.80 -42.10
30 4424 59G 60K C N 410 412 -55.54 -70.20 21.73 1.30 -62.90 165.33 21.88
30 60K 60K N CA 412 413 124.36 140.40 -40.80
31 4425 60K 61D C N 419 421 -97.09 -70.90 47.69 1.63 -63.30 134.18 18.73
31 61D 61D N CA 421 422 -169.85 150.30 -40.00
32 4427 62I 63M C N 435 437 -154.80 -125.60 40.23 2.16 -63.40 178.50 22.04
32 63M 63M N CA 437 438 112.83 140.50 -40.50
33 4428 63M 64P C N 443 445 -71.62 -64.50 7.12 0.73 -58.70 178.09 13.69
33 64P 64P N CA 445 446 147.13 147.20 -30.50
34 4438 73C 74K C N 518 520 -120.68 -62.90 64.13 8.94 -62.90 64.13 8.94
34 74K 74K N CA 520 521 -12.98 -40.80 -40.80
35 4439 74K 75A C N 527 529 58.70 55.40 4.49 0.25 -62.50 143.09 29.08
35 75A 75A N CA 529 530 35.16 38.20 -40.90
36 4440 75A 76L C N 532 534 73.82 60.20 24.27 0.96 -63.50 146.39 26.85
36 76L 76L N CA 534 535 9.51 29.60 -41.20
37 4443 78N 79K C N 556 558 -96.58 -62.90 80.59 9.27 -62.90 80.59 9.27
37 79K 79K N CA 558 559 32.42 -40.80 -40.80
38 4451 86R 87Q C N 619 621 80.62 55.10 29.71 2.48 -63.80 158.54 28.59
38 87Q 87Q N CA 621 622 25.09 40.30 -40.30
39 4456 91Y 92I C N 663 665 87.07 -120.60 158.02 9.45 -120.60 158.02 9.45
39 92I 92I N CA 665 666 172.35 130.30 130.30
40 4469 104L 105Y C N 761 763 162.01 -63.50 137.14 24.79 -63.50 137.14 24.79
40 105Y 105Y N CA 763 764 -70.24 -43.40 -43.40
41 4472 107F 108V C N 790 792 -57.80 -62.40 32.73 3.89 -125.40 157.18 8.95
41 108V 108V N CA 792 793 -74.80 -42.40 143.30
42 4506 141T 142Y C N 1060 1062 70.44 55.90 159.95 12.28 -124.30 177.01 10.87
42 142Y 142Y N CA 1062 1063 -161.21 39.50 135.40
43 4508 143A 144G C N 1077 1079 -59.29 -80.20 31.25 2.17 82.20 -137.91 16.67
43 144G 144G N CA 1079 1080 -162.68 174.10 8.50
44 4509 144G 145G C N 1081 1083 91.79 82.20 51.56 2.02 -62.40 154.19 27.51
44 145G 145G N CA 1083 1084 -42.16 8.50 -41.20
45 4524 159R 160D C N 1211 1213 -80.26 -63.30 68.86 7.63 -63.30 68.86 7.63
45 160D 160D N CA 1213 1214 26.74 -40.00 -40.00
46 4526 161V 162C C N 1226 1228 -151.47 -117.90 84.16 3.69 -63.00 137.33 15.02
46 162C 162C N CA 1228 1229 63.93 141.10 -41.10
47 4527 162C 163L C N 1232 1234 -65.19 -63.50 3.40 0.42 -70.70 179.94 13.42
47 163L 163L N CA 1234 1235 -38.25 -41.20 141.60
48 4529 164W 165G C N 1254 1256 -96.14 -80.20 62.82 3.27 82.20 -153.13 8.80
48 165G 165G N CA 1256 1257 113.34 174.10 8.50
49 4530 165G 166K C N 1258 1260 -63.19 -70.20 20.61 1.33 -62.90 161.81 21.00
49 166K 166K N CA 1260 1261 121.01 140.40 -40.80
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 14 21 133 107 177 168 180 199 197 240
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
O80292_lig.B99990001.pdb 1248.13477
O80292_lig.B99990002.pdb 1423.50867
w3 = nglview.show_structure_file('O80292_lig.B99990002.pdb')
w3
Атомы лиганда показаны шариками.
Image(url="pr10_3.png")