Гомологичное моделирование комплекса белка с лигандом
Цель данного занятия ознакомится с возможностями гомологичного моделирования комплекса белка с лигандом.
Программе MODELLER для моделирования структуры белков, в качестве входных данных нужны: управляющий скрипт, файл pdb со структурой-образцом, файл выравнивания с дополнительной информацией.
In [2]:
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
In [3]:
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 18:23:37
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-05-25 18:23:42-- 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 18:23:42-- 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 18:23:43-- 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.2'
[ <=> ] 131,301 332K/s in 0.4s
2017-05-25 18:23:44 (332 KB/s) - `1lmp.pdb.2' saved [131301]
In [5]:
! wget http://www.uniprot.org/uniprot/P62693.fasta
--2017-05-25 18:23:45-- http://www.uniprot.org/uniprot/P62693.fasta Resolving www.uniprot.org... 193.62.193.81, 128.175.240.211 Connecting to www.uniprot.org|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 305 [text/plain] Saving to: `P62693.fasta.4' 100%[======================================>] 305 --.-K/s in 0s 2017-05-25 18:23:45 (22.5 MB/s) - `P62693.fasta.4' saved [305/305]
In [6]:
alignm=modeller.alignment(env)
In [7]:
alignm.append(file='P62693.fasta', align_codes='all',alignment_format='FASTA')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'LYS_BPPHV'
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.
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.
In [8]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [9]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
LYS_BPPHV 1lmp
In [10]:
## 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()
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: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
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 224:
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 225:
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: 130 69
irestab_402W> ires, irestp: 131 69
irestab_402W> ires, irestp: 132 70
irestab_402W> ires, irestp: 130 69
irestab_402W> ires, irestp: 132 70
irestab_402W> ires, irestp: 130 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: 14728 13139
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
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 : 226
Number of all, selected real atoms : 1784 1784
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13139 13139
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4162
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 : 2544.9226
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 : 1824 0 0 0.006 0.006 18.507 1.000
2 Bond angle potential : 2468 2 19 2.778 2.778 275.82 1.000
3 Stereochemical cosine torsion poten: 1168 0 53 49.917 49.917 451.98 1.000
4 Stereochemical improper torsion pot: 773 0 2 1.490 1.490 35.649 1.000
5 Soft-sphere overlap restraints : 4162 0 1 0.007 0.007 21.174 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) : 2407 19 61 0.906 0.906 611.78 1.000
10 Distance restraints 2 (N-O) : 2595 16 59 0.946 0.946 552.34 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: 225 2 11 5.921 5.921 93.019 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 6 87.436 87.436 79.406 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 83.057 83.057 71.597 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 91.290 91.290 45.756 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 90.353 90.353 15.498 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) : 905 0 0 0.592 0.592 21.983 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: 224 91 45 34.662 107.721 237.42 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 0 1.125 1.125 13.001 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_BPPHV.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: 37968.7617
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 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 7430 10L 223G CA CA 69 1756 12.86 6.74 6.12 7.74 6.74 6.12 7.74
2 7531 13E 223G CA CA 94 1756 12.39 7.45 4.94 6.77 7.45 4.94 6.77
3 7551 14F 223G CA CA 103 1756 15.97 9.62 6.35 6.47 9.62 6.35 6.47
4 8924 94F 129R CA CA 731 1003 10.25 7.73 2.52 5.15 7.73 2.52 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 9775 14F 223G N O 102 1758 14.81 9.07 5.74 5.65 9.07 5.74 5.65
2 10430 43G 226K N O 339 1783 15.94 10.35 5.60 5.23 10.35 5.60 5.23
3 10451 44T 226K N O 343 1783 15.19 8.18 7.01 6.90 8.18 7.01 6.90
4 10467 45T 226K N O 350 1783 16.42 8.62 7.79 7.47 8.62 7.79 7.47
5 10481 46W 226K N O 357 1783 16.31 8.17 8.14 8.93 8.17 8.14 8.93
6 10489 47T 226K N O 371 1783 17.81 9.76 8.04 5.46 9.76 8.04 5.46
7 10498 48Q 226K N O 378 1783 18.33 10.84 7.49 5.42 10.84 7.49 5.42
8 10527 50Q 226K N O 392 1783 17.54 9.99 7.55 5.16 9.99 7.55 5.16
9 10551 51A 226K N O 401 1783 15.87 8.19 7.69 4.51 8.19 7.69 4.51
10 10907 94F 129R N O 730 1012 13.13 9.70 3.44 4.90 9.70 3.44 4.90
11 10908 94F 138K N O 730 1087 16.17 10.64 5.53 5.80 10.64 5.53 5.80
-------------------------------------------------------------------------------------------------
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 6676 219D 219D CA C 1729 1734 -136.98 -180.00 43.02 8.60 -180.00 43.02 8.60
-------------------------------------------------------------------------------------------------
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 6251 18R 19L C N 141 143 61.45 60.20 2.38 0.24 -63.50 144.63 26.67
1 19L 19L N CA 143 144 31.63 29.60 -41.20
2 6253 20T 21A C N 156 158 53.89 55.40 2.81 0.29 -62.50 139.40 28.31
2 21A 21A N CA 158 159 35.83 38.20 -40.90
3 6254 21A 22Y C N 161 163 72.93 55.90 25.76 1.44 -63.50 150.51 28.22
3 22Y 22Y N CA 163 164 20.18 39.50 -43.40
4 6270 37H 38Y C N 302 304 63.08 55.90 11.58 0.61 -63.50 146.54 27.67
4 38Y 38Y N CA 304 305 30.42 39.50 -43.40
5 6281 48Q 49A C N 385 387 82.67 55.40 38.47 2.04 -62.50 154.19 31.18
5 49A 49A N CA 387 388 11.07 38.20 -40.90
6 6295 62K 63Y C N 493 495 -104.11 -98.40 37.42 3.91 -63.50 140.80 20.44
6 63Y 63Y N CA 495 496 91.42 128.40 -43.40
7 6296 63Y 64A C N 505 507 -139.24 -134.00 45.79 2.47 -62.50 148.06 28.35
7 64A 64A N CA 507 508 -167.52 147.00 -40.90
8 6298 65P 66M C N 517 519 -89.37 -73.00 16.54 1.22 -63.40 176.12 28.36
8 66M 66M N CA 519 520 145.31 143.00 -40.50
9 6300 67V 68D C N 532 534 -81.81 -70.90 34.81 1.25 -63.30 137.90 18.19
9 68D 68D N CA 534 535 -176.65 150.30 -40.00
10 6301 68D 69A C N 540 542 -63.63 -68.20 8.29 0.80 -62.50 166.89 27.41
10 69A 69A N CA 542 543 152.22 145.30 -40.90
11 6302 69A 70Y C N 545 547 -77.15 -98.40 21.28 0.81 -63.50 173.40 26.82
11 70Y 70Y N CA 547 548 129.47 128.40 -43.40
12 6304 71V 72K C N 564 566 -127.89 -118.00 18.48 0.72 -62.90 176.86 26.85
12 72K 72K N CA 566 567 154.71 139.10 -40.80
13 6305 72K 73G C N 573 575 -148.50 -167.20 34.22 0.95 82.20 -171.30 14.38
13 73G 73G N CA 575 576 145.94 174.60 8.50
14 6306 73G 74K C N 577 579 -118.48 -118.00 6.10 0.30 -62.90 -177.51 21.35
14 74K 74K N CA 579 580 133.02 139.10 -40.80
15 6307 74K 75A C N 586 588 -131.93 -134.00 6.04 0.37 -62.50 -179.67 33.27
15 75A 75A N CA 588 589 152.67 147.00 -40.90
16 6308 75A 76N C N 591 593 -103.11 -119.90 24.76 0.73 -63.20 164.81 18.69
16 76N 76N N CA 593 594 118.81 137.00 -41.10
17 6309 76N 77Q C N 599 601 -147.53 -121.10 33.19 1.03 -63.80 -179.49 30.88
17 77Q 77Q N CA 601 602 159.78 139.70 -40.30
18 6310 77Q 78N C N 608 610 -93.02 -119.90 39.43 1.16 -63.20 152.20 17.55
18 78N 78N N CA 610 611 108.16 137.00 -41.10
19 6311 78N 79E C N 616 618 -152.01 -117.80 38.96 1.14 -63.60 -173.46 29.78
19 79E 79E N CA 618 619 155.44 136.80 -40.30
20 6312 79E 80F C N 625 627 -95.77 -71.40 43.08 3.83 -63.20 152.99 19.17
20 80F 80F N CA 627 628 105.18 140.70 -44.30
21 6313 80F 81D C N 636 638 -118.08 -96.50 28.74 1.18 -63.30 145.89 15.61
21 81D 81D N CA 638 639 95.22 114.20 -40.00
22 6315 82A 83L C N 649 651 -137.07 -108.50 36.37 1.61 -63.50 179.56 29.49
22 83L 83L N CA 651 652 155.00 132.50 -41.20
23 6317 84V 85S C N 664 666 -125.67 -136.60 12.44 0.64 -64.10 178.79 17.29
23 85S 85S N CA 666 667 157.14 151.20 -35.00
24 6318 85S 86L C N 670 672 -113.30 -108.50 28.95 1.51 -63.50 165.42 26.04
24 86L 86L N CA 672 673 161.05 132.50 -41.20
25 6319 86L 87A C N 678 680 -67.99 -68.20 1.20 0.10 -62.50 172.70 28.57
25 87A 87A N CA 680 681 146.49 145.30 -40.90
26 6320 87A 88Y C N 683 685 -136.94 -124.30 36.53 1.49 -63.50 164.25 29.65
26 88Y 88Y N CA 685 686 169.68 135.40 -43.40
27 6321 88Y 89N C N 695 697 -75.66 -71.20 62.46 3.88 -63.20 114.48 15.01
27 89N 89N N CA 697 698 -154.90 142.80 -41.10
28 6323 90C 91G C N 709 711 -64.93 -62.40 6.14 0.83 82.20 153.61 11.57
28 91G 91G N CA 711 712 -35.61 -41.20 8.50
29 6324 91G 92N C N 713 715 -54.33 -71.20 19.07 1.13 -63.20 175.22 22.40
29 92N 92N N CA 715 716 133.89 142.80 -41.10
30 6326 93V 94F C N 728 730 -130.66 -63.20 100.98 11.52 -63.20 100.98 11.52
30 94F 94F N CA 730 731 30.83 -44.30 -44.30
31 6327 94F 95V C N 739 741 144.01 -125.40 117.44 6.55 -125.40 117.44 6.55
31 95V 95V N CA 741 742 68.56 143.30 143.30
32 6333 100A 101P C N 782 784 -65.51 -58.70 21.74 2.36 -64.50 161.66 12.01
32 101P 101P N CA 784 785 -51.15 -30.50 147.20
33 6334 101P 102F C N 789 791 -70.02 -63.20 17.19 2.00 58.10 142.08 21.84
33 102F 102F N CA 791 792 -28.52 -44.30 32.90
34 6336 103S 104H C N 806 808 -118.86 -63.20 59.52 8.17 -63.20 59.52 8.17
34 104H 104H N CA 808 809 -21.25 -42.30 -42.30
35 6337 104H 105A C N 816 818 50.66 55.40 43.20 2.22 -62.50 166.42 33.08
35 105A 105A N CA 818 819 81.14 38.20 -40.90
36 6340 107C 108A C N 839 841 70.10 55.40 14.72 1.56 -62.50 154.00 31.32
36 108A 108A N CA 841 842 37.43 38.20 -40.90
37 6366 133L 134N C N 1042 1044 -94.55 -119.90 59.77 2.07 -63.20 127.87 14.48
37 134N 134N N CA 1044 1045 82.87 137.00 -41.10
38 6367 134N 135L C N 1050 1052 -57.08 -63.50 63.56 8.48 -108.50 133.37 7.57
38 135L 135L N CA 1052 1053 -104.44 -41.20 132.50
39 6378 145N 146Q C N 1134 1136 -141.05 -121.10 99.99 5.04 -63.80 112.67 14.62
39 146Q 146Q N CA 1136 1137 41.72 139.70 -40.30
40 6380 147N 148N C N 1151 1153 -66.80 -63.20 6.00 0.65 55.90 144.23 17.75
40 148N 148N N CA 1153 1154 -36.31 -41.10 39.50
41 6382 149Q 150T C N 1168 1170 -136.02 -124.80 12.63 0.76 -63.20 -166.01 21.02
41 150T 150T N CA 1170 1171 137.70 143.50 -42.10
42 6385 152G 153M C N 1183 1185 -133.35 -125.60 7.79 0.33 -63.40 -167.05 34.36
42 153M 153M N CA 1185 1186 139.67 140.50 -40.50
43 6387 154I 155K C N 1199 1201 -110.28 -118.00 27.88 1.23 -62.90 160.28 18.78
43 155K 155K N CA 1201 1202 112.31 139.10 -40.80
44 6388 155K 156M C N 1208 1210 -179.52 -125.60 63.52 1.88 -63.40 -173.90 36.41
44 156M 156M N CA 1210 1211 174.07 140.50 -40.50
45 6389 156M 157Y C N 1216 1218 -83.89 -98.40 15.00 0.73 -63.50 169.25 25.83
45 157Y 157Y N CA 1218 1219 124.62 128.40 -43.40
46 6390 157Y 158L C N 1228 1230 -109.55 -108.50 16.42 0.88 -63.50 176.04 27.27
46 158L 158L N CA 1230 1231 148.89 132.50 -41.20
47 6393 160I 161G C N 1252 1254 -74.00 -80.20 22.70 0.61 82.20 -147.72 6.96
47 161G 161G N CA 1254 1255 152.26 174.10 8.50
48 6394 161G 162L C N 1256 1258 -104.68 -108.50 16.60 0.85 -63.50 162.85 20.64
48 162L 162L N CA 1258 1259 116.35 132.50 -41.20
49 6395 162L 163D C N 1264 1266 -80.89 -70.90 18.48 1.39 -63.30 175.64 20.67
49 163D 163D N CA 1266 1267 134.76 150.30 -40.00
50 6396 163D 164N C N 1272 1274 -122.50 -119.90 5.61 0.19 -63.20 -173.39 26.71
50 164N 164N N CA 1274 1275 141.96 137.00 -41.10
51 6397 164N 165S C N 1280 1282 -152.35 -136.60 23.29 0.77 -64.10 179.79 19.38
51 165S 165S N CA 1282 1283 168.35 151.20 -35.00
52 6398 165S 166G C N 1286 1288 -151.10 -167.20 38.49 1.21 82.20 -177.66 13.94
52 166G 166G N CA 1288 1289 139.63 174.60 8.50
53 6399 166G 167K C N 1290 1292 -154.62 -118.00 42.54 1.41 -62.90 -176.91 29.24
53 167K 167K N CA 1292 1293 160.75 139.10 -40.80
54 6400 167K 168A C N 1299 1301 -134.90 -134.00 5.77 0.34 -62.50 -168.02 35.34
54 168A 168A N CA 1301 1302 141.29 147.00 -40.90
55 6401 168A 169K C N 1304 1306 -144.58 -118.00 51.44 2.02 -62.90 158.69 25.47
55 169K 169K N CA 1306 1307 -176.86 139.10 -40.80
56 6402 169K 170H C N 1313 1315 -113.71 -125.60 66.88 2.30 -63.20 125.87 13.48
56 170H 170H N CA 1315 1316 72.99 138.80 -42.30
57 6403 170H 171W C N 1323 1325 -176.14 -124.90 76.41 2.48 -63.00 161.83 27.59
57 171W 171W N CA 1325 1326 -159.91 143.40 -44.20
58 6404 171W 172Y C N 1337 1339 -117.13 -124.30 27.44 1.77 -63.50 163.74 28.69
58 172Y 172Y N CA 1339 1340 161.89 135.40 -43.40
59 6406 173V 174S C N 1356 1358 -73.51 -72.40 5.04 0.26 -64.10 167.95 12.75
59 174S 174S N CA 1358 1359 157.32 152.40 -35.00
60 6410 177V 178S C N 1381 1383 -65.43 -72.40 31.50 2.09 -64.10 141.88 10.36
60 178S 178S N CA 1383 1384 -176.88 152.40 -35.00
61 6412 179V 180R C N 1394 1396 -161.30 -125.20 36.10 1.43 -63.00 -156.91 34.07
61 180R 180R N CA 1396 1397 141.18 140.60 -41.10
62 6413 180R 181H C N 1405 1407 -150.63 -63.20 111.81 19.05 -63.20 111.81 19.05
62 181H 181H N CA 1407 1408 -112.00 -42.30 -42.30
63 6415 182V 183R C N 1422 1424 -103.94 -125.20 43.27 1.54 -63.00 149.72 17.85
63 183R 183R N CA 1424 1425 102.92 140.60 -41.10
64 6416 183R 184T C N 1433 1435 -108.12 -124.80 26.73 0.83 -63.20 170.73 19.27
64 184T 184T N CA 1435 1436 122.62 143.50 -42.10
65 6418 185I 186R C N 1448 1450 -55.34 -72.10 20.58 1.35 -63.00 171.23 23.65
65 186R 186R N CA 1450 1451 129.96 141.90 -41.10
66 6420 187M 188L C N 1467 1469 79.27 -70.70 156.11 15.31 -63.50 -164.30 25.46
66 188L 188L N CA 1469 1470 -175.05 141.60 -41.20
67 6421 188L 189E C N 1475 1477 -58.28 -69.30 11.67 1.00 -63.60 173.44 22.84
67 189E 189E N CA 1477 1478 146.34 142.50 -40.30
68 6422 189E 190N C N 1484 1486 -107.62 -119.90 62.72 3.11 -63.20 128.33 18.57
68 190N 190N N CA 1486 1487 -161.49 137.00 -41.10
69 6423 190N 191Y C N 1492 1494 -66.15 -98.40 32.58 1.39 -63.50 167.21 26.39
69 191Y 191Y N CA 1494 1495 123.78 128.40 -43.40
70 6425 192Q 193N C N 1513 1515 52.05 55.90 11.28 1.08 -63.20 134.83 22.17
70 193N 193N N CA 1515 1516 28.89 39.50 -41.10
71 6426 193N 194K C N 1521 1523 -145.95 -118.00 41.55 1.49 -62.90 170.89 27.15
71 194K 194K N CA 1523 1524 169.85 139.10 -40.80
72 6428 195W 196A C N 1544 1546 150.41 -134.00 79.79 1.88 -62.50 -152.36 41.49
72 196A 196A N CA 1546 1547 172.55 147.00 -40.90
73 6429 196A 197K C N 1549 1551 -135.86 -118.00 17.86 0.67 -62.90 -165.83 29.58
73 197K 197K N CA 1551 1552 139.26 139.10 -40.80
74 6431 198L 199N C N 1566 1568 -60.92 -71.20 10.99 0.69 -63.20 -180.00 22.38
74 199N 199N N CA 1568 1569 138.92 142.80 -41.10
75 6432 199N 200L C N 1574 1576 -110.65 -108.50 30.55 1.63 -63.50 162.80 25.51
75 200L 200L N CA 1576 1577 162.97 132.50 -41.20
76 6435 202V 203D C N 1596 1598 -65.22 -70.90 8.97 0.70 -63.30 162.77 20.21
76 203D 203D N CA 1598 1599 157.24 150.30 -40.00
77 6436 203D 204T C N 1604 1606 -58.22 -78.10 39.82 1.30 -63.20 157.47 20.52
77 204T 204T N CA 1606 1607 115.30 149.80 -42.10
78 6438 205M 206F C N 1619 1621 -175.01 -124.20 55.94 2.81 -63.20 -161.34 22.42
78 206F 206F N CA 1621 1622 119.90 143.30 -44.30
79 6440 207I 208A C N 1638 1640 -161.67 -134.00 31.93 1.66 -62.50 -161.48 29.74
79 208A 208A N CA 1640 1641 131.07 147.00 -40.90
80 6441 208A 209E C N 1643 1645 -178.36 -117.80 65.15 1.94 -63.60 -164.00 32.32
80 209E 209E N CA 1645 1646 160.81 136.80 -40.30
81 6442 209E 210I C N 1652 1654 -66.46 -63.40 6.07 1.10 -120.60 -172.86 8.71
81 210I 210I N CA 1654 1655 -48.84 -43.60 130.30
82 6443 210I 211E C N 1660 1662 -149.99 -117.80 37.96 1.12 -63.60 -175.72 29.37
82 211E 211E N CA 1662 1663 156.92 136.80 -40.30
83 6444 211E 212A C N 1669 1671 -153.83 -134.00 34.51 2.10 -62.50 -176.08 27.55
83 212A 212A N CA 1671 1672 118.75 147.00 -40.90
84 6445 212A 213E C N 1674 1676 -76.35 -63.60 13.54 1.90 -117.80 177.46 8.04
84 213E 213E N CA 1676 1677 -35.75 -40.30 136.80
85 6446 213E 214F C N 1683 1685 -62.32 -124.20 64.25 2.01 -63.20 170.30 23.71
85 214F 214F N CA 1685 1686 126.00 143.30 -44.30
86 6447 214F 215G C N 1694 1696 163.74 82.20 85.13 4.64 -62.40 136.22 23.18
86 215G 215G N CA 1696 1697 -15.96 8.50 -41.20
87 6450 217K 218I C N 1718 1720 -171.29 -120.60 91.06 3.75 -63.40 154.41 28.92
87 218I 218I N CA 1720 1721 -154.06 130.30 -43.60
88 6452 219D 220M C N 1734 1736 -33.53 -73.00 54.67 3.48 56.30 114.11 12.25
88 220M 220M N CA 1736 1737 105.18 143.00 34.80
89 6454 221A 222S C N 1747 1749 -115.77 -136.60 67.37 3.74 -64.10 121.29 12.48
89 222S 222S N CA 1749 1750 -144.73 151.20 -35.00
90 6455 222S 223G C N 1753 1755 145.24 -167.20 57.96 1.98 82.20 147.16 10.03
90 223G 223G N CA 1755 1756 141.48 174.60 8.50
91 6456 223G 224E C N 1757 1759 -26.57 -69.30 50.73 2.93 -63.60 159.80 23.40
91 224E 224E N CA 1759 1760 115.15 142.50 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 29 45 174 180 234 224 253 272 273 292
<< 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 : 226
Number of all, selected real atoms : 1784 1784
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13139 13139
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3848
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 : 1916.6653
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 : 1824 0 0 0.006 0.006 19.986 1.000
2 Bond angle potential : 2468 2 14 2.305 2.305 243.03 1.000
3 Stereochemical cosine torsion poten: 1168 0 54 50.404 50.404 457.16 1.000
4 Stereochemical improper torsion pot: 773 0 0 1.244 1.244 24.407 1.000
5 Soft-sphere overlap restraints : 3848 0 0 0.005 0.005 11.006 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) : 2407 1 13 0.524 0.524 206.51 1.000
10 Distance restraints 2 (N-O) : 2595 14 28 0.926 0.926 454.78 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: 225 0 3 4.388 4.388 51.094 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 5 84.527 84.527 75.573 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 3 80.606 80.606 76.578 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 88.211 88.211 40.901 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 77.781 77.781 12.749 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) : 905 0 0 0.441 0.441 11.542 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: 224 89 36 36.605 109.070 216.61 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 1 1.137 1.137 14.744 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: LYS_BPPHV.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: 35868.8711
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 2164 31Y 31Y CA CB 246 247 127.33 107.50 19.83 4.58 107.50 19.83 4.58
2 2856 94F 95V C N 739 741 143.35 120.00 23.35 5.31 120.00 23.35 5.31
-------------------------------------------------------------------------------------------------
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 8924 94F 129R CA CA 731 1003 10.22 7.73 2.49 5.10 7.73 2.49 5.10
-------------------------------------------------------------------------------------------------
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 10451 44T 226K N O 343 1783 15.32 8.18 7.14 7.02 8.18 7.14 7.02
2 10467 45T 226K N O 350 1783 17.89 8.62 9.26 8.87 8.62 9.26 8.87
3 10481 46W 226K N O 357 1783 18.94 8.17 10.78 11.82 8.17 10.78 11.82
4 10489 47T 226K N O 371 1783 21.26 9.76 11.50 7.81 9.76 11.50 7.81
5 10498 48Q 226K N O 378 1783 22.09 10.84 11.25 8.14 10.84 11.25 8.14
6 10527 50Q 226K N O 392 1783 20.47 9.99 10.49 7.16 9.99 10.49 7.16
7 10551 51A 226K N O 401 1783 17.98 8.19 9.80 5.75 8.19 9.80 5.75
8 10577 52D 226K N O 406 1783 14.98 6.08 8.89 4.70 6.08 8.89 4.70
9 10908 94F 138K N O 730 1087 15.61 10.64 4.96 5.21 10.64 4.96 5.21
10 11792 140V 226K N O 1095 1783 11.13 5.60 5.53 7.35 5.60 5.53 7.35
11 11815 141S 226K N O 1102 1783 10.54 6.70 3.84 4.74 6.70 3.84 4.74
-------------------------------------------------------------------------------------------------
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 6251 18R 19L C N 141 143 51.25 60.20 24.92 0.88 -63.50 148.37 27.08
1 19L 19L N CA 143 144 52.85 29.60 -41.20
2 6253 20T 21A C N 156 158 -82.46 -68.20 64.95 5.72 -62.50 124.45 19.51
2 21A 21A N CA 158 159 81.94 145.30 -40.90
3 6254 21A 22Y C N 161 163 61.41 55.90 12.10 0.58 -63.50 144.24 27.23
3 22Y 22Y N CA 163 164 28.73 39.50 -43.40
4 6270 37H 38Y C N 302 304 67.05 55.90 19.70 0.99 -63.50 146.59 27.57
4 38Y 38Y N CA 304 305 23.27 39.50 -43.40
5 6281 48Q 49A C N 385 387 82.85 55.40 34.78 2.18 -62.50 156.40 31.69
5 49A 49A N CA 387 388 16.85 38.20 -40.90
6 6295 62K 63Y C N 493 495 -96.50 -98.40 55.89 5.95 -63.50 120.55 17.57
6 63Y 63Y N CA 495 496 72.54 128.40 -43.40
7 6296 63Y 64A C N 505 507 -122.87 -134.00 21.56 1.32 -62.50 165.08 30.28
7 64A 64A N CA 507 508 165.46 147.00 -40.90
8 6298 65P 66M C N 517 519 -159.69 -125.60 36.52 1.76 -63.40 -166.46 23.91
8 66M 66M N CA 519 520 127.39 140.50 -40.50
9 6300 67V 68D C N 532 534 -114.32 -96.50 43.72 1.81 -63.30 125.15 13.33
9 68D 68D N CA 534 535 74.28 114.20 -40.00
10 6301 68D 69A C N 540 542 -125.70 -134.00 12.37 0.39 -62.50 -170.43 28.72
10 69A 69A N CA 542 543 137.83 147.00 -40.90
11 6302 69A 70Y C N 545 547 -129.71 -124.30 6.17 0.34 -63.50 -169.87 33.49
11 70Y 70Y N CA 547 548 138.37 135.40 -43.40
12 6304 71V 72K C N 564 566 -134.83 -118.00 19.58 0.65 -62.90 -175.33 28.29
12 72K 72K N CA 566 567 149.11 139.10 -40.80
13 6305 72K 73G C N 573 575 160.65 -167.20 55.22 2.19 82.20 144.38 10.44
13 73G 73G N CA 575 576 129.71 174.60 8.50
14 6306 73G 74K C N 577 579 -146.40 -118.00 28.97 1.01 -62.90 -166.67 30.10
14 74K 74K N CA 579 580 144.83 139.10 -40.80
15 6307 74K 75A C N 586 588 -133.82 -134.00 6.99 0.39 -62.50 -167.23 35.41
15 75A 75A N CA 588 589 140.01 147.00 -40.90
16 6308 75A 76N C N 591 593 -124.43 -119.90 21.29 1.06 -63.20 168.80 18.48
16 76N 76N N CA 593 594 116.20 137.00 -41.10
17 6309 76N 77Q C N 599 601 -160.97 -121.10 44.36 1.38 -63.80 -172.33 32.55
17 77Q 77Q N CA 601 602 159.15 139.70 -40.30
18 6310 77Q 78N C N 608 610 -103.10 -119.90 22.77 0.66 -63.20 167.54 19.02
18 78N 78N N CA 610 611 121.62 137.00 -41.10
19 6311 78N 79E C N 616 618 -149.54 -117.80 37.74 1.11 -63.60 -176.19 29.29
19 79E 79E N CA 618 619 157.22 136.80 -40.30
20 6313 80F 81D C N 636 638 -79.03 -70.90 23.75 0.83 -63.30 148.23 19.28
20 81D 81D N CA 638 639 172.61 150.30 -40.00
21 6314 81D 82A C N 644 646 -119.29 -134.00 14.89 0.41 -62.50 -176.57 33.09
21 82A 82A N CA 646 647 144.69 147.00 -40.90
22 6315 82A 83L C N 649 651 -99.64 -108.50 9.30 0.48 -63.50 -179.82 23.20
22 83L 83L N CA 651 652 135.31 132.50 -41.20
23 6317 84V 85S C N 664 666 -77.16 -72.40 6.79 0.32 -64.10 168.26 13.01
23 85S 85S N CA 666 667 157.25 152.40 -35.00
24 6318 85S 86L C N 670 672 -76.19 -70.70 10.51 1.00 -63.50 174.31 23.50
24 86L 86L N CA 672 673 132.65 141.60 -41.20
25 6319 86L 87A C N 678 680 -76.87 -68.20 11.92 0.75 -62.50 166.25 27.97
25 87A 87A N CA 680 681 153.48 145.30 -40.90
26 6320 87A 88Y C N 683 685 -118.57 -124.30 7.48 0.35 -63.50 -177.51 26.39
26 88Y 88Y N CA 685 686 130.58 135.40 -43.40
27 6321 88Y 89N C N 695 697 -118.96 -119.90 3.15 0.16 -63.20 -172.61 26.60
27 89N 89N N CA 697 698 140.01 137.00 -41.10
28 6323 90C 91G C N 709 711 -74.77 -80.20 17.77 0.46 82.20 -143.79 6.97
28 91G 91G N CA 711 712 157.18 174.10 8.50
29 6324 91G 92N C N 713 715 -100.63 -119.90 22.30 0.67 -63.20 171.02 19.55
29 92N 92N N CA 715 716 125.77 137.00 -41.10
30 6326 93V 94F C N 728 730 -179.56 -124.20 78.90 2.13 -63.20 164.43 29.41
30 94F 94F N CA 730 731 -160.48 143.30 -44.30
31 6337 104H 105A C N 816 818 55.09 55.40 28.29 1.68 -62.50 159.24 31.98
31 105A 105A N CA 818 819 66.49 38.20 -40.90
32 6340 107C 108A C N 839 841 74.78 55.40 19.99 1.89 -62.50 156.05 31.74
32 108A 108A N CA 841 842 33.31 38.20 -40.90
33 6366 133L 134N C N 1042 1044 -89.91 -119.90 58.37 1.90 -63.20 130.78 15.03
33 134N 134N N CA 1044 1045 86.92 137.00 -41.10
34 6367 134N 135L C N 1050 1052 -46.50 -63.50 79.87 10.24 -108.50 124.76 7.11
34 135L 135L N CA 1052 1053 -119.24 -41.20 132.50
35 6382 149Q 150T C N 1168 1170 -80.35 -78.10 29.68 1.34 -63.20 163.21 19.84
35 150T 150T N CA 1170 1171 120.20 149.80 -42.10
36 6384 151G 152G C N 1179 1181 -166.73 -167.20 46.13 1.80 82.20 163.49 12.44
36 152G 152G N CA 1181 1182 128.47 174.60 8.50
37 6385 152G 153M C N 1183 1185 -63.70 -73.00 35.74 2.58 -63.40 141.99 21.22
37 153M 153M N CA 1185 1186 177.51 143.00 -40.50
38 6387 154I 155K C N 1199 1201 -55.37 -70.20 15.43 1.22 -62.90 174.72 22.29
38 155K 155K N CA 1201 1202 144.64 140.40 -40.80
39 6388 155K 156M C N 1208 1210 -83.85 -73.00 36.37 2.65 -63.40 150.19 20.91
39 156M 156M N CA 1210 1211 108.29 143.00 -40.50
40 6389 156M 157Y C N 1216 1218 -128.22 -124.30 4.34 0.36 -63.50 -171.58 26.96
40 157Y 157Y N CA 1218 1219 133.55 135.40 -43.40
41 6390 157Y 158L C N 1228 1230 -89.43 -108.50 30.06 1.38 -63.50 152.68 19.86
41 158L 158L N CA 1230 1231 109.26 132.50 -41.20
42 6393 160I 161G C N 1252 1254 76.62 78.70 3.27 0.17 82.20 177.21 8.88
42 161G 161G N CA 1254 1255 -168.62 -166.10 8.50
43 6394 161G 162L C N 1256 1258 -107.78 -108.50 7.07 0.39 -63.50 -175.34 28.35
43 162L 162L N CA 1258 1259 139.53 132.50 -41.20
44 6395 162L 163D C N 1264 1266 -91.93 -96.50 6.20 0.26 -63.30 152.71 17.31
44 163D 163D N CA 1266 1267 110.00 114.20 -40.00
45 6396 163D 164N C N 1272 1274 -76.83 -71.20 8.31 0.44 -63.20 170.53 22.08
45 164N 164N N CA 1274 1275 148.92 142.80 -41.10
46 6397 164N 165S C N 1280 1282 -124.23 -136.60 12.37 0.48 -64.10 -175.67 17.57
46 165S 165S N CA 1282 1283 150.75 151.20 -35.00
47 6398 165S 166G C N 1286 1288 93.43 78.70 45.34 0.75 82.20 142.95 7.50
47 166G 166G N CA 1288 1289 151.01 -166.10 8.50
48 6399 166G 167K C N 1290 1292 -135.66 -118.00 25.22 0.89 -62.90 177.67 27.43
48 167K 167K N CA 1292 1293 157.11 139.10 -40.80
49 6400 167K 168A C N 1299 1301 -119.14 -134.00 15.27 0.39 -62.50 -175.49 33.25
49 168A 168A N CA 1301 1302 143.50 147.00 -40.90
50 6401 168A 169K C N 1304 1306 -112.39 -118.00 6.39 0.30 -62.90 -176.17 26.80
50 169K 169K N CA 1306 1307 142.16 139.10 -40.80
51 6402 169K 170H C N 1313 1315 -116.67 -125.60 13.62 0.34 -63.20 178.99 19.66
51 170H 170H N CA 1315 1316 128.51 138.80 -42.30
52 6403 170H 171W C N 1323 1325 -120.81 -124.90 21.03 0.92 -63.00 176.70 19.59
52 171W 171W N CA 1325 1326 122.77 143.40 -44.20
53 6404 171W 172Y C N 1337 1339 -120.99 -124.30 22.68 1.07 -63.50 166.60 23.83
53 172Y 172Y N CA 1339 1340 112.96 135.40 -43.40
54 6406 173V 174S C N 1356 1358 -120.77 -136.60 35.60 1.40 -64.10 164.39 10.14
54 174S 174S N CA 1358 1359 119.32 151.20 -35.00
55 6407 174S 175D C N 1362 1364 -134.53 -96.50 39.22 1.61 -63.30 178.60 19.04
55 175D 175D N CA 1364 1365 123.79 114.20 -40.00
56 6408 175D 176G C N 1370 1372 -175.41 -167.20 44.90 1.83 82.20 159.23 11.98
56 176G 176G N CA 1372 1373 130.45 174.60 8.50
57 6410 177V 178S C N 1381 1383 -145.26 -136.60 11.05 0.60 -64.10 -163.16 12.34
57 178S 178S N CA 1383 1384 144.33 151.20 -35.00
58 6412 179V 180R C N 1394 1396 -136.58 -125.20 28.08 1.07 -63.00 169.44 27.90
58 180R 180R N CA 1396 1397 166.27 140.60 -41.10
59 6415 182V 183R C N 1422 1424 -156.80 -125.20 37.30 1.11 -63.00 -175.83 31.17
59 183R 183R N CA 1424 1425 160.41 140.60 -41.10
60 6416 183R 184T C N 1433 1435 -109.21 -124.80 18.60 0.68 -63.20 -178.61 20.56
60 184T 184T N CA 1435 1436 133.35 143.50 -42.10
61 6418 185I 186R C N 1448 1450 -143.72 -125.20 46.23 1.76 -63.00 158.10 26.77
61 186R 186R N CA 1450 1451 -177.04 140.60 -41.10
62 6419 186R 187M C N 1459 1461 -65.75 -73.00 18.66 1.39 -63.40 159.32 23.97
62 187M 187M N CA 1461 1462 160.19 143.00 -40.50
63 6420 187M 188L C N 1467 1469 73.11 -70.70 144.65 12.62 -63.50 -144.05 38.17
63 188L 188L N CA 1469 1470 126.04 141.60 -41.20
64 6421 188L 189E C N 1475 1477 -154.97 -117.80 57.15 1.92 -63.60 166.74 27.22
64 189E 189E N CA 1477 1478 -179.78 136.80 -40.30
65 6422 189E 190N C N 1484 1486 -64.39 -71.20 14.20 1.09 -63.20 163.65 20.53
65 190N 190N N CA 1486 1487 155.25 142.80 -41.10
66 6423 190N 191Y C N 1492 1494 -93.94 -98.40 5.06 0.32 -63.50 172.12 25.81
66 191Y 191Y N CA 1494 1495 126.00 128.40 -43.40
67 6424 191Y 192Q C N 1504 1506 -79.09 -73.00 9.17 0.53 -63.80 172.82 26.22
67 192Q 192Q N CA 1506 1507 147.56 140.70 -40.30
68 6425 192Q 193N C N 1513 1515 -75.46 -71.20 5.21 0.42 -63.20 179.54 23.13
68 193N 193N N CA 1515 1516 139.78 142.80 -41.10
69 6426 193N 194K C N 1521 1523 -80.58 -70.20 16.17 0.97 -62.90 167.34 22.74
69 194K 194K N CA 1523 1524 152.79 140.40 -40.80
70 6427 194K 195W C N 1530 1532 -68.41 -71.30 3.97 0.34 -63.00 174.17 22.11
70 195W 195W N CA 1532 1533 141.72 139.00 -44.20
71 6428 195W 196A C N 1544 1546 -110.51 -134.00 23.49 0.78 -62.50 178.56 31.81
71 196A 196A N CA 1546 1547 147.12 147.00 -40.90
72 6429 196A 197K C N 1549 1551 -67.18 -70.20 6.57 0.54 -62.90 173.02 22.70
72 197K 197K N CA 1551 1552 146.23 140.40 -40.80
73 6430 197K 198L C N 1558 1560 -64.61 -70.70 8.56 0.55 -63.50 176.78 24.48
73 198L 198L N CA 1560 1561 135.58 141.60 -41.20
74 6431 198L 199N C N 1566 1568 -84.64 -71.20 24.90 1.94 -63.20 164.34 19.44
74 199N 199N N CA 1568 1569 121.83 142.80 -41.10
75 6432 199N 200L C N 1574 1576 -91.54 -108.50 21.00 1.16 -63.50 176.16 26.15
75 200L 200L N CA 1576 1577 144.88 132.50 -41.20
76 6435 202V 203D C N 1596 1598 -134.35 -70.90 76.74 3.76 -63.30 145.13 22.47
76 203D 203D N CA 1598 1599 -166.55 150.30 -40.00
77 6436 203D 204T C N 1604 1606 -86.17 -63.20 69.69 10.46 -63.20 69.69 10.46
77 204T 204T N CA 1606 1607 -107.89 -42.10 -42.10
78 6437 204T 205M C N 1611 1613 -53.76 -73.00 19.46 1.43 -63.40 179.64 26.08
78 205M 205M N CA 1613 1614 140.12 143.00 -40.50
79 6438 205M 206F C N 1619 1621 -143.88 -124.20 42.56 1.43 -63.20 156.98 26.86
79 206F 206F N CA 1621 1622 -178.96 143.30 -44.30
80 6439 206F 207I C N 1630 1632 8.15 -97.30 105.69 4.54 -120.60 129.15 8.63
80 207I 207I N CA 1632 1633 120.15 127.20 130.30
81 6440 207I 208A C N 1638 1640 58.12 -68.20 126.39 10.57 -62.50 -145.00 32.32
81 208A 208A N CA 1640 1641 141.13 145.30 -40.90
82 6442 209E 210I C N 1652 1654 -14.65 -97.30 82.83 3.42 -120.60 105.98 7.43
82 210I 210I N CA 1654 1655 132.62 127.20 130.30
83 6443 210I 211E C N 1660 1662 86.79 -117.80 158.73 6.64 -63.60 -151.23 35.47
83 211E 211E N CA 1662 1663 104.51 136.80 -40.30
84 6446 213E 214F C N 1683 1685 -76.17 -124.20 74.67 2.11 -63.20 131.08 17.34
84 214F 214F N CA 1685 1686 86.13 143.30 -44.30
85 6451 218I 219D C N 1726 1728 46.81 -70.90 128.27 10.74 -70.90 128.27 10.74
85 219D 219D N CA 1728 1729 -158.73 150.30 150.30
86 6452 219D 220M C N 1734 1736 -106.48 -125.60 89.92 3.86 56.30 163.75 28.08
86 220M 220M N CA 1736 1737 52.64 140.50 34.80
87 6454 221A 222S C N 1747 1749 161.31 -136.60 100.36 3.46 -64.10 164.71 21.33
87 222S 222S N CA 1749 1750 -129.96 151.20 -35.00
88 6455 222S 223G C N 1753 1755 -159.46 -167.20 73.32 2.77 82.20 150.62 11.73
88 223G 223G N CA 1755 1756 101.69 174.60 8.50
89 6456 223G 224E C N 1757 1759 159.97 -117.80 83.96 2.70 -63.60 -145.19 35.86
89 224E 224E N CA 1759 1760 153.78 136.80 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 20 37 156 159 221 197 223 262 273 253
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_BPPHV.B99990001.pdb 2544.92261
LYS_BPPHV.B99990002.pdb 1916.66528
Используя известную структуру лизоцима форели как образец, была построена модель белка LYS_BPPHV.
In [11]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('LYS_BPPHV.B99990001.pdb')
w1
In [12]:
stroka=""
for i in alignm[0].residues:
stroka=stroka+i.code
stroka=stroka+"..."
out=open("With.fasta","w")
out.write(">WithLigand\n"+stroka)
out.close()
In [13]:
alignm.append(file='With.fasta', align_codes='all',alignment_format='FASTA')
Out[13]:
1
In [14]:
alignm.salign()
alignm.write(file='all_in_one(2).ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [15]:
s = alignm[2]
pdb = alignm[1]
print s.code, pdb.code
WithLigand 1lmp
In [16]:
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one(2).ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied 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: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
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: 16102 14513
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.
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 : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3698
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 : 2271.3462
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 : 1824 0 2 0.008 0.008 32.445 1.000
2 Bond angle potential : 2468 5 17 2.880 2.880 314.74 1.000
3 Stereochemical cosine torsion poten: 1168 0 64 52.386 52.386 505.46 1.000
4 Stereochemical improper torsion pot: 773 0 2 1.533 1.533 36.309 1.000
5 Soft-sphere overlap restraints : 3698 2 6 0.011 0.011 49.667 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) : 2407 6 27 0.515 0.515 272.70 1.000
10 Distance restraints 2 (N-O) : 2568 8 42 0.649 0.649 381.00 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: 225 4 9 5.957 5.957 94.167 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 2 89.195 89.195 70.331 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 0 80.340 80.340 69.084 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 100.666 100.666 47.088 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 96.370 96.370 15.967 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) : 905 0 0 0.539 0.539 22.064 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: 224 93 36 33.784 114.393 208.03 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 2 1.332 1.332 24.705 1.000
27 Distance restraints 5 (X-Y) : 1401 1 19 0.110 0.110 127.59 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: WithLigand.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: 38271.3008
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 2973 105A 105A N CA 818 819 130.31 107.00 23.31 6.70 107.00 23.31 6.70
-------------------------------------------------------------------------------------------------
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 8944 95V 111I CA CA 742 861 6.35 4.98 1.38 4.54 4.98 1.38 4.54
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11130 108A 105A N O 841 822 6.29 3.15 3.14 5.99 3.15 3.14 5.99
2 11148 109S 105A N O 846 822 8.11 5.07 3.03 5.30 5.07 3.03 5.30
-------------------------------------------------------------------------------------------------
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 6561 104H 104H CA C 809 816 -152.71 -180.00 27.29 5.46 -180.00 27.29 5.46
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6251 18R 19L C N 141 143 65.51 60.20 9.64 0.37 -63.50 143.47 26.45
1 19L 19L N CA 143 144 21.56 29.60 -41.20
2 6253 20T 21A C N 156 158 54.33 55.40 2.02 0.21 -62.50 140.13 28.46
2 21A 21A N CA 158 159 36.49 38.20 -40.90
3 6254 21A 22Y C N 161 163 63.78 55.90 11.01 0.67 -63.50 147.85 27.93
3 22Y 22Y N CA 163 164 31.82 39.50 -43.40
4 6270 37H 38Y C N 302 304 64.88 55.90 15.19 0.78 -63.50 146.54 27.63
4 38Y 38Y N CA 304 305 27.25 39.50 -43.40
5 6281 48Q 49A C N 385 387 82.56 55.40 35.45 2.12 -62.50 155.60 31.52
5 49A 49A N CA 387 388 15.41 38.20 -40.90
6 6295 62K 63Y C N 493 495 -61.90 -98.40 37.43 1.75 -63.50 163.50 26.02
6 63Y 63Y N CA 495 496 120.10 128.40 -43.40
7 6296 63Y 64A C N 505 507 -123.57 -134.00 18.24 1.11 -62.50 168.59 30.90
7 64A 64A N CA 507 508 161.97 147.00 -40.90
8 6298 65P 66M C N 517 519 -113.69 -125.60 25.26 0.91 -63.40 166.51 21.52
8 66M 66M N CA 519 520 118.23 140.50 -40.50
9 6300 67V 68D C N 532 534 -147.79 -96.50 51.46 2.10 -63.30 172.28 18.28
9 68D 68D N CA 534 535 110.14 114.20 -40.00
10 6301 68D 69A C N 540 542 -145.67 -134.00 14.91 0.84 -62.50 -162.96 29.58
10 69A 69A N CA 542 543 137.73 147.00 -40.90
11 6302 69A 70Y C N 545 547 -133.35 -124.30 9.24 0.74 -63.50 -169.75 27.07
11 70Y 70Y N CA 547 548 133.57 135.40 -43.40
12 6304 71V 72K C N 564 566 -152.61 -118.00 37.10 1.24 -62.90 -170.68 29.94
12 72K 72K N CA 566 567 152.48 139.10 -40.80
13 6305 72K 73G C N 573 575 170.36 -167.20 31.31 1.17 82.20 169.06 12.10
13 73G 73G N CA 575 576 152.76 174.60 8.50
14 6306 73G 74K C N 577 579 -131.44 -118.00 17.17 0.58 -62.90 -177.26 27.83
14 74K 74K N CA 579 580 149.80 139.10 -40.80
15 6307 74K 75A C N 586 588 -115.72 -134.00 23.73 0.64 -62.50 -179.23 27.55
15 75A 75A N CA 588 589 131.87 147.00 -40.90
16 6308 75A 76N C N 591 593 -139.28 -119.90 21.76 0.67 -63.20 -171.91 27.82
16 76N 76N N CA 593 594 146.89 137.00 -41.10
17 6309 76N 77Q C N 599 601 -73.55 -73.00 14.94 0.99 -63.80 166.36 23.96
17 77Q 77Q N CA 601 602 125.77 140.70 -40.30
18 6310 77Q 78N C N 608 610 -139.58 -119.90 32.55 1.00 -63.20 173.68 26.02
18 78N 78N N CA 610 611 162.92 137.00 -41.10
19 6312 79E 80F C N 625 627 -108.85 -124.20 18.54 0.48 -63.20 -177.01 22.56
19 80F 80F N CA 627 628 132.91 143.30 -44.30
20 6313 80F 81D C N 636 638 -99.85 -96.50 7.62 0.32 -63.30 151.82 16.86
20 81D 81D N CA 638 639 107.35 114.20 -40.00
21 6314 81D 82A C N 644 646 -129.42 -134.00 9.02 0.36 -62.50 -168.08 35.03
21 82A 82A N CA 646 647 139.22 147.00 -40.90
22 6315 82A 83L C N 649 651 -115.84 -108.50 8.63 0.47 -63.50 177.09 22.20
22 83L 83L N CA 651 652 127.97 132.50 -41.20
23 6317 84V 85S C N 664 666 -145.19 -136.60 8.59 0.34 -64.10 -168.19 19.69
23 85S 85S N CA 666 667 151.17 151.20 -35.00
24 6318 85S 86L C N 670 672 -124.50 -108.50 17.54 0.93 -63.50 177.32 22.00
24 86L 86L N CA 672 673 125.30 132.50 -41.20
25 6319 86L 87A C N 678 680 -157.86 -134.00 24.33 0.64 -62.50 -167.38 36.66
25 87A 87A N CA 680 681 151.75 147.00 -40.90
26 6320 87A 88Y C N 683 685 -136.71 -124.30 19.39 0.81 -63.50 -178.30 32.46
26 88Y 88Y N CA 685 686 150.30 135.40 -43.40
27 6321 88Y 89N C N 695 697 -116.32 -119.90 7.21 0.24 -63.20 179.87 20.04
27 89N 89N N CA 697 698 130.75 137.00 -41.10
28 6323 90C 91G C N 709 711 97.94 78.70 45.51 0.68 82.20 145.01 7.82
28 91G 91G N CA 711 712 152.66 -166.10 8.50
29 6324 91G 92N C N 713 715 -122.99 -119.90 56.09 2.48 -63.20 139.38 20.80
29 92N 92N N CA 715 716 -167.00 137.00 -41.10
30 6326 93V 94F C N 728 730 -146.35 -124.20 24.10 1.20 -63.20 -163.43 22.70
30 94F 94F N CA 730 731 133.81 143.30 -44.30
31 6333 100A 101P C N 782 784 -46.17 -58.70 48.93 3.15 -64.50 136.24 11.16
31 101P 101P N CA 784 785 -77.80 -30.50 147.20
32 6334 101P 102F C N 789 791 -92.85 -71.40 36.69 3.26 58.10 169.93 16.75
32 102F 102F N CA 791 792 110.94 140.70 32.90
33 6336 103S 104H C N 806 808 -152.06 -125.60 45.17 2.05 -63.20 169.63 18.06
33 104H 104H N CA 808 809 102.20 138.80 -42.30
34 6337 104H 105A C N 816 818 -81.49 -62.50 81.87 14.42 -62.50 81.87 14.42
34 105A 105A N CA 818 819 -120.53 -40.90 -40.90
35 6338 105A 106Y C N 821 823 -124.07 -124.30 40.63 2.14 -63.50 150.86 21.30
35 106Y 106Y N CA 823 824 94.77 135.40 -43.40
36 6339 106Y 107C C N 833 835 116.25 -117.90 -177.62 8.07 -63.00 -173.85 32.88
36 107C 107C N CA 835 836 9.10 141.10 -41.10
37 6340 107C 108A C N 839 841 61.91 55.40 12.85 0.48 -62.50 141.78 28.84
37 108A 108A N CA 841 842 27.12 38.20 -40.90
38 6368 135L 136F C N 1058 1060 65.98 -63.20 129.88 21.68 -63.20 129.88 21.68
38 136F 136F N CA 1060 1061 -30.85 -44.30 -44.30
39 6382 149Q 150T C N 1168 1170 -161.18 -124.80 62.49 1.94 -63.20 157.73 26.24
39 150T 150T N CA 1170 1171 -165.70 143.50 -42.10
40 6383 150T 151G C N 1175 1177 -118.83 -80.20 39.02 2.74 82.20 -134.41 17.29
40 151G 151G N CA 1177 1178 168.57 174.10 8.50
41 6385 152G 153M C N 1183 1185 -71.23 -73.00 1.79 0.14 -63.40 176.42 26.95
41 153M 153M N CA 1185 1186 143.25 143.00 -40.50
42 6387 154I 155K C N 1199 1201 -142.13 -118.00 46.60 2.41 -62.90 160.90 18.50
42 155K 155K N CA 1201 1202 99.24 139.10 -40.80
43 6388 155K 156M C N 1208 1210 -177.19 -125.60 65.50 1.94 -63.40 179.36 35.20
43 156M 156M N CA 1210 1211 -179.14 140.50 -40.50
44 6389 156M 157Y C N 1216 1218 -86.58 -98.40 12.40 0.64 -63.50 169.62 25.76
44 157Y 157Y N CA 1218 1219 124.64 128.40 -43.40
45 6390 157Y 158L C N 1228 1230 -114.41 -108.50 8.47 0.48 -63.50 175.19 21.99
45 158L 158L N CA 1230 1231 126.43 132.50 -41.20
46 6393 160I 161G C N 1252 1254 -152.55 -167.20 26.62 0.74 82.20 -169.24 14.41
46 161G 161G N CA 1254 1255 152.38 174.60 8.50
47 6394 161G 162L C N 1256 1258 -99.98 -108.50 9.82 0.43 -63.50 172.72 22.17
47 162L 162L N CA 1258 1259 127.62 132.50 -41.20
48 6395 162L 163D C N 1264 1266 -101.98 -96.50 33.09 1.38 -63.30 127.57 13.89
48 163D 163D N CA 1266 1267 81.57 114.20 -40.00
49 6396 163D 164N C N 1272 1274 -112.15 -119.90 19.14 0.67 -63.20 167.90 18.73
49 164N 164N N CA 1274 1275 119.50 137.00 -41.10
50 6397 164N 165S C N 1280 1282 -145.65 -136.60 12.08 0.38 -64.10 -175.23 19.23
50 165S 165S N CA 1282 1283 159.20 151.20 -35.00
51 6398 165S 166G C N 1286 1288 146.83 -167.20 52.29 1.66 82.20 155.25 10.51
51 166G 166G N CA 1288 1289 149.66 174.60 8.50
52 6399 166G 167K C N 1290 1292 -130.92 -118.00 12.95 0.50 -62.90 -168.50 22.19
52 167K 167K N CA 1292 1293 138.21 139.10 -40.80
53 6400 167K 168A C N 1299 1301 -120.51 -134.00 19.69 0.61 -62.50 -177.01 27.79
53 168A 168A N CA 1301 1302 132.66 147.00 -40.90
54 6401 168A 169K C N 1304 1306 -127.12 -118.00 17.60 0.91 -62.90 176.92 20.47
54 169K 169K N CA 1306 1307 124.05 139.10 -40.80
55 6402 169K 170H C N 1313 1315 -112.54 -125.60 70.46 2.42 -63.20 122.26 13.09
55 170H 170H N CA 1315 1316 69.56 138.80 -42.30
56 6403 170H 171W C N 1323 1325 -123.71 -124.90 29.75 1.42 -63.00 169.14 18.66
56 171W 171W N CA 1325 1326 113.68 143.40 -44.20
57 6404 171W 172Y C N 1337 1339 -131.79 -124.30 8.01 0.66 -63.50 -171.24 26.89
57 172Y 172Y N CA 1339 1340 132.57 135.40 -43.40
58 6406 173V 174S C N 1356 1358 -130.02 -136.60 22.48 0.98 -64.10 177.40 10.98
58 174S 174S N CA 1358 1359 129.70 151.20 -35.00
59 6407 174S 175D C N 1362 1364 -129.76 -96.50 33.53 1.37 -63.30 171.81 18.35
59 175D 175D N CA 1364 1365 118.43 114.20 -40.00
60 6408 175D 176G C N 1370 1372 162.43 -167.20 40.14 1.45 82.20 161.23 11.41
60 176G 176G N CA 1372 1373 148.35 174.60 8.50
61 6410 177V 178S C N 1381 1383 -109.51 -136.60 38.13 1.23 -64.10 165.71 10.25
61 178S 178S N CA 1383 1384 124.36 151.20 -35.00
62 6412 179V 180R C N 1394 1396 -134.04 -125.20 8.95 0.32 -63.00 -169.39 30.63
62 180R 180R N CA 1396 1397 142.03 140.60 -41.10
63 6413 180R 181H C N 1405 1407 -119.33 -125.60 18.88 0.59 -63.20 172.67 18.82
63 181H 181H N CA 1407 1408 120.99 138.80 -42.30
64 6415 182V 183R C N 1422 1424 -110.49 -125.20 23.27 0.74 -63.00 170.42 20.27
64 183R 183R N CA 1424 1425 122.57 140.60 -41.10
65 6416 183R 184T C N 1433 1435 -141.28 -124.80 32.54 1.02 -63.20 165.87 26.32
65 184T 184T N CA 1435 1436 171.56 143.50 -42.10
66 6418 185I 186R C N 1448 1450 -157.81 -125.20 33.06 1.47 -63.00 -159.86 22.69
66 186R 186R N CA 1450 1451 135.16 140.60 -41.10
67 6420 187M 188L C N 1467 1469 -71.77 -70.70 3.67 0.32 -63.50 179.49 24.46
67 188L 188L N CA 1469 1470 138.10 141.60 -41.20
68 6421 188L 189E C N 1475 1477 -138.56 -117.80 24.10 0.71 -63.60 -173.60 29.06
68 189E 189E N CA 1477 1478 149.04 136.80 -40.30
69 6422 189E 190N C N 1484 1486 -100.82 -119.90 48.60 1.73 -63.20 138.60 15.56
69 190N 190N N CA 1486 1487 92.30 137.00 -41.10
70 6423 190N 191Y C N 1492 1494 -120.63 -124.30 34.70 1.68 -63.50 155.20 22.08
70 191Y 191Y N CA 1494 1495 100.90 135.40 -43.40
71 6424 191Y 192Q C N 1504 1506 -170.19 -121.10 53.89 2.50 -63.80 -169.70 24.39
71 192Q 192Q N CA 1506 1507 117.48 139.70 -40.30
72 6425 192Q 193N C N 1513 1515 -151.73 -119.90 37.47 1.97 -63.20 -178.61 19.50
72 193N 193N N CA 1515 1516 117.22 137.00 -41.10
73 6426 193N 194K C N 1521 1523 -149.65 -118.00 44.09 2.21 -62.90 172.59 19.85
73 194K 194K N CA 1523 1524 108.40 139.10 -40.80
74 6427 194K 195W C N 1530 1532 -153.32 -124.90 28.62 1.35 -63.00 -162.34 30.79
74 195W 195W N CA 1532 1533 139.98 143.40 -44.20
75 6428 195W 196A C N 1544 1546 -158.99 -134.00 25.00 0.84 -62.50 -162.50 37.52
75 196A 196A N CA 1546 1547 146.78 147.00 -40.90
76 6429 196A 197K C N 1549 1551 -141.74 -118.00 29.00 1.40 -62.90 -178.71 20.83
76 197K 197K N CA 1551 1552 122.44 139.10 -40.80
77 6430 197K 198L C N 1558 1560 -127.19 -108.50 26.25 1.47 -63.50 167.83 20.70
77 198L 198L N CA 1560 1561 114.07 132.50 -41.20
78 6431 198L 199N C N 1566 1568 -138.03 -119.90 23.22 0.67 -63.20 -176.63 27.16
78 199N 199N N CA 1568 1569 151.50 137.00 -41.10
79 6432 199N 200L C N 1574 1576 -109.20 -108.50 6.52 0.36 -63.50 173.35 21.91
79 200L 200L N CA 1576 1577 126.02 132.50 -41.20
80 6435 202V 203D C N 1596 1598 -136.66 -96.50 41.39 1.70 -63.30 179.86 19.16
80 203D 203D N CA 1598 1599 124.23 114.20 -40.00
81 6436 203D 204T C N 1604 1606 -119.27 -124.80 7.09 0.43 -63.20 178.97 26.67
81 204T 204T N CA 1606 1607 147.94 143.50 -42.10
82 6437 204T 205M C N 1611 1613 -129.74 -125.60 42.74 2.13 -63.40 153.54 19.12
82 205M 205M N CA 1613 1614 97.96 140.50 -40.50
83 6438 205M 206F C N 1619 1621 -96.87 -71.40 38.44 3.40 -63.20 159.80 20.05
83 206F 206F N CA 1621 1622 111.91 140.70 -44.30
84 6439 206F 207I C N 1630 1632 -63.76 -63.40 4.56 0.76 -120.60 -172.71 8.63
84 207I 207I N CA 1632 1633 -48.15 -43.60 130.30
85 6440 207I 208A C N 1638 1640 123.13 -134.00 102.96 3.25 -62.50 -117.98 48.46
85 208A 208A N CA 1640 1641 151.27 147.00 -40.90
86 6441 208A 209E C N 1643 1645 178.79 -117.80 70.33 3.35 -63.60 -172.00 21.92
86 209E 209E N CA 1645 1646 106.37 136.80 -40.30
87 6442 209E 210I C N 1652 1654 -65.87 -63.40 3.50 0.66 -120.60 -175.31 8.55
87 210I 210I N CA 1654 1655 -46.09 -43.60 130.30
88 6443 210I 211E C N 1660 1662 -165.08 -117.80 51.52 1.52 -63.60 -168.47 31.10
88 211E 211E N CA 1662 1663 157.27 136.80 -40.30
89 6444 211E 212A C N 1669 1671 -85.61 -68.20 28.22 2.76 -62.50 165.61 26.10
89 212A 212A N CA 1671 1672 123.09 145.30 -40.90
90 6446 213E 214F C N 1683 1685 -76.71 -63.20 91.35 11.80 -63.20 91.35 11.80
90 214F 214F N CA 1685 1686 46.05 -44.30 -44.30
91 6454 221A 222S C N 1747 1749 63.49 56.90 7.02 0.67 -64.10 145.05 19.19
91 222S 222S N CA 1749 1750 33.99 36.40 -35.00
92 6455 222S 223G C N 1753 1755 -109.90 -80.20 50.41 3.36 82.20 -150.76 16.32
92 223G 223G N CA 1755 1756 133.37 174.10 8.50
93 6456 223G 224E C N 1757 1759 -65.85 -69.30 4.08 0.24 -63.60 179.38 24.04
93 224E 224E N CA 1759 1760 140.33 142.50 -40.30
-------------------------------------------------------------------------------------------------
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 13422 94F 229. CA O4 731 1823 10.33 9.21 1.12 5.59 9.21 1.12 5.59
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 21 38 146 143 196 199 189 232 268 286
<< 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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3853
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 : 2429.6609
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 : 1824 1 3 0.009 0.009 39.758 1.000
2 Bond angle potential : 2468 6 34 3.323 3.323 345.46 1.000
3 Stereochemical cosine torsion poten: 1168 0 58 51.032 51.032 479.46 1.000
4 Stereochemical improper torsion pot: 773 1 1 1.463 1.463 34.779 1.000
5 Soft-sphere overlap restraints : 3853 1 4 0.010 0.010 46.156 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) : 2407 5 34 0.540 0.540 304.93 1.000
10 Distance restraints 2 (N-O) : 2568 9 58 0.706 0.706 496.56 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: 225 1 5 5.112 5.112 69.338 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 3 85.709 85.709 66.185 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 4 82.563 82.563 79.080 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 90.488 90.488 41.515 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 98.805 98.805 15.277 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) : 905 0 0 0.482 0.482 15.341 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: 224 101 37 37.871 115.537 267.29 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 0 1.234 1.234 17.126 1.000
27 Distance restraints 5 (X-Y) : 1401 1 16 0.103 0.103 111.40 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: WithLigand.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: 39147.6719
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
1 758 94F 94F C CA 739 731 1.67 1.49 0.18 5.11 1.49 0.18 5.11
-------------------------------------------------------------------------------------------------
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 2995 106Y 107C C N 833 835 140.04 120.00 20.04 4.55 120.00 20.04 4.55
-------------------------------------------------------------------------------------------------
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 8944 95V 111I CA CA 742 861 6.58 4.98 1.60 5.27 4.98 1.60 5.27
-------------------------------------------------------------------------------------------------
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 9677 10L 6N N O 68 47 5.23 2.86 2.38 4.71 2.86 2.38 4.71
2 11259 114Y 110M N O 884 859 6.95 4.31 2.65 4.52 4.31 2.65 4.52
-------------------------------------------------------------------------------------------------
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 6513 56E 56E CA C 438 444 -139.13 -180.00 40.87 8.17 -180.00 40.87 8.17
-------------------------------------------------------------------------------------------------
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 6238 5Q 6N C N 38 40 -79.50 -119.90 52.17 2.80 -63.20 149.79 19.64
1 6N 6N N CA 40 41 170.00 137.00 -41.10
2 6239 6N 7G C N 46 48 88.72 82.20 64.88 2.82 -62.40 151.84 26.48
2 7G 7G N CA 48 49 -56.05 8.50 -41.20
3 6251 18R 19L C N 141 143 74.16 60.20 28.91 1.03 -63.50 144.98 26.51
3 19L 19L N CA 143 144 4.28 29.60 -41.20
4 6253 20T 21A C N 156 158 55.21 55.40 3.28 0.21 -62.50 140.01 28.45
4 21A 21A N CA 158 159 34.92 38.20 -40.90
5 6254 21A 22Y C N 161 163 65.46 55.90 14.52 0.81 -63.50 147.69 27.85
5 22Y 22Y N CA 163 164 28.57 39.50 -43.40
6 6265 32T 33I C N 262 264 -94.44 -120.60 62.95 2.71 -63.40 120.71 18.83
6 33I 33I N CA 264 265 73.05 130.30 -43.60
7 6266 33I 34G C N 270 272 176.34 82.20 109.59 4.63 -62.40 121.43 21.94
7 34G 34G N CA 272 273 -47.61 8.50 -41.20
8 6270 37H 38Y C N 302 304 61.97 55.90 12.84 0.61 -63.50 144.46 27.26
8 38Y 38Y N CA 304 305 28.19 39.50 -43.40
9 6281 48Q 49A C N 385 387 85.85 55.40 41.12 2.32 -62.50 157.01 31.72
9 49A 49A N CA 387 388 10.56 38.20 -40.90
10 6289 56E 57I C N 444 446 -97.46 -63.40 90.53 13.90 -63.40 90.53 13.90
10 57I 57I N CA 446 447 40.28 -43.60 -43.60
11 6290 57I 58D C N 452 454 -16.26 54.50 78.15 6.90 54.50 78.15 6.90
11 58D 58D N CA 454 455 74.06 40.90 40.90
12 6295 62K 63Y C N 493 495 -156.67 -124.30 38.90 2.02 -63.50 -175.18 33.78
12 63Y 63Y N CA 495 496 156.98 135.40 -43.40
13 6296 63Y 64A C N 505 507 -150.87 -134.00 22.57 0.63 -62.50 -179.73 34.26
13 64A 64A N CA 507 508 161.98 147.00 -40.90
14 6298 65P 66M C N 517 519 -154.68 -125.60 34.70 1.03 -63.40 -175.75 34.58
14 66M 66M N CA 519 520 159.44 140.50 -40.50
15 6300 67V 68D C N 532 534 -99.48 -96.50 9.33 0.39 -63.30 149.80 16.63
15 68D 68D N CA 534 535 105.36 114.20 -40.00
16 6301 68D 69A C N 540 542 -123.37 -134.00 16.02 0.52 -62.50 -173.85 28.22
16 69A 69A N CA 542 543 135.02 147.00 -40.90
17 6302 69A 70Y C N 545 547 -132.31 -124.30 11.35 0.50 -63.50 -173.66 33.00
17 70Y 70Y N CA 547 548 143.43 135.40 -43.40
18 6304 71V 72K C N 564 566 -128.16 -118.00 19.29 0.75 -62.90 176.23 26.79
18 72K 72K N CA 566 567 155.50 139.10 -40.80
19 6305 72K 73G C N 573 575 170.80 -167.20 25.73 0.85 82.20 176.58 12.52
19 73G 73G N CA 575 576 161.25 174.60 8.50
20 6306 73G 74K C N 577 579 -119.75 -118.00 10.93 0.50 -62.90 178.60 26.58
20 74K 74K N CA 579 580 149.89 139.10 -40.80
21 6307 74K 75A C N 586 588 -113.07 -134.00 23.00 0.52 -62.50 -174.61 28.36
21 75A 75A N CA 588 589 137.47 147.00 -40.90
22 6308 75A 76N C N 591 593 -124.62 -119.90 9.88 0.33 -63.20 -176.21 26.47
22 76N 76N N CA 593 594 145.68 137.00 -41.10
23 6309 76N 77Q C N 599 601 -80.27 -73.00 18.24 1.34 -63.80 165.10 23.44
23 77Q 77Q N CA 601 602 123.97 140.70 -40.30
24 6310 77Q 78N C N 608 610 -132.00 -119.90 13.60 0.42 -63.20 -171.33 27.50
24 78N 78N N CA 610 611 143.22 137.00 -41.10
25 6312 79E 80F C N 625 627 -135.30 -124.20 27.59 0.98 -63.20 163.86 27.40
25 80F 80F N CA 627 628 168.56 143.30 -44.30
26 6313 80F 81D C N 636 638 56.94 54.50 7.93 0.42 -63.30 140.84 24.03
26 81D 81D N CA 638 639 33.35 40.90 -40.00
27 6314 81D 82A C N 644 646 -71.93 -68.20 5.96 0.58 -62.50 178.70 29.76
27 82A 82A N CA 646 647 140.65 145.30 -40.90
28 6315 82A 83L C N 649 651 -123.52 -108.50 17.77 0.97 -63.50 174.84 21.69
28 83L 83L N CA 651 652 123.01 132.50 -41.20
29 6317 84V 85S C N 664 666 -142.21 -136.60 15.51 0.87 -64.10 -171.33 11.83
29 85S 85S N CA 666 667 136.74 151.20 -35.00
30 6318 85S 86L C N 670 672 -131.25 -108.50 26.67 1.45 -63.50 173.56 21.38
30 86L 86L N CA 672 673 118.59 132.50 -41.20
31 6319 86L 87A C N 678 680 -148.48 -134.00 15.08 0.66 -62.50 -163.85 36.75
31 87A 87A N CA 680 681 142.80 147.00 -40.90
32 6320 87A 88Y C N 683 685 -138.30 -124.30 22.58 0.93 -63.50 179.78 32.22
32 88Y 88Y N CA 685 686 153.12 135.40 -43.40
33 6321 88Y 89N C N 695 697 -106.66 -119.90 13.59 0.49 -63.20 -179.66 20.45
33 89N 89N N CA 697 698 133.92 137.00 -41.10
34 6323 90C 91G C N 709 711 99.65 78.70 64.29 1.06 82.20 125.83 6.97
34 91G 91G N CA 711 712 133.12 -166.10 8.50
35 6324 91G 92N C N 713 715 -167.31 -119.90 68.43 2.01 -63.20 168.55 26.68
35 92N 92N N CA 715 716 -173.66 137.00 -41.10
36 6326 93V 94F C N 728 730 73.29 -124.20 163.68 6.96 -63.20 -143.50 38.17
36 94F 94F N CA 730 731 123.76 143.30 -44.30
37 6333 100A 101P C N 782 784 -62.38 -58.70 25.44 2.41 -64.50 157.15 11.84
37 101P 101P N CA 784 785 -55.67 -30.50 147.20
38 6334 101P 102F C N 789 791 -69.12 -63.20 16.65 1.97 58.10 141.37 21.73
38 102F 102F N CA 791 792 -28.74 -44.30 32.90
39 6336 103S 104H C N 806 808 -110.09 -63.20 59.68 7.06 -63.20 59.68 7.06
39 104H 104H N CA 808 809 -5.39 -42.30 -42.30
40 6337 104H 105A C N 816 818 87.39 55.40 114.02 9.50 -62.50 -132.26 34.76
40 105A 105A N CA 818 819 147.64 38.20 -40.90
41 6338 105A 106Y C N 821 823 -120.46 -124.30 32.26 1.55 -63.50 157.44 22.43
41 106Y 106Y N CA 823 824 103.37 135.40 -43.40
42 6339 106Y 107C C N 833 835 121.02 -63.00 -179.92 27.74 -63.00 -179.92 27.74
42 107C 107C N CA 835 836 -2.87 -41.10 -41.10
43 6340 107C 108A C N 839 841 62.89 55.40 14.67 0.55 -62.50 141.92 28.86
43 108A 108A N CA 841 842 25.58 38.20 -40.90
44 6342 109S 110M C N 850 852 -62.27 -63.40 2.31 0.43 -125.60 -170.14 7.56
44 110M 110M N CA 852 853 -38.49 -40.50 140.50
45 6343 110M 111I C N 858 860 117.18 -63.40 -179.02 33.04 -63.40 -179.02 33.04
45 111I 111I N CA 860 861 -67.30 -43.60 -43.60
46 6366 133L 134N C N 1042 1044 -88.82 -119.90 56.13 1.78 -63.20 133.83 15.45
46 134N 134N N CA 1044 1045 90.26 137.00 -41.10
47 6367 134N 135L C N 1050 1052 -53.55 -63.50 63.83 8.34 -108.50 134.94 7.67
47 135L 135L N CA 1052 1053 -104.25 -41.20 132.50
48 6381 148N 149Q C N 1159 1161 -72.26 -63.80 11.63 1.53 -121.10 178.83 7.57
48 149Q 149Q N CA 1161 1162 -32.33 -40.30 139.70
49 6382 149Q 150T C N 1168 1170 -96.22 -78.10 54.46 1.85 -63.20 121.33 17.76
49 150T 150T N CA 1170 1171 -158.85 149.80 -42.10
50 6383 150T 151G C N 1175 1177 -69.93 -80.20 19.87 0.47 82.20 -147.35 6.74
50 151G 151G N CA 1177 1178 157.08 174.10 8.50
51 6384 151G 152G C N 1179 1181 -85.91 -80.20 6.16 0.32 82.20 -122.39 7.44
51 152G 152G N CA 1181 1182 176.43 174.10 8.50
52 6385 152G 153M C N 1183 1185 -140.23 -125.60 42.30 1.67 -63.40 159.09 29.72
52 153M 153M N CA 1185 1186 -179.81 140.50 -40.50
53 6387 154I 155K C N 1199 1201 59.33 56.60 2.82 0.29 -62.90 145.37 25.34
53 155K 155K N CA 1201 1202 37.89 38.60 -40.80
54 6388 155K 156M C N 1208 1210 -70.69 -73.00 2.55 0.17 -63.40 177.73 27.11
54 156M 156M N CA 1210 1211 141.92 143.00 -40.50
55 6389 156M 157Y C N 1216 1218 -109.24 -98.40 26.71 2.58 -63.50 154.32 22.35
55 157Y 157Y N CA 1218 1219 103.98 128.40 -43.40
56 6390 157Y 158L C N 1228 1230 -131.64 -108.50 25.02 1.11 -63.50 -170.55 30.52
56 158L 158L N CA 1230 1231 142.03 132.50 -41.20
57 6393 160I 161G C N 1252 1254 -174.61 -167.20 34.79 1.42 82.20 167.63 12.49
57 161G 161G N CA 1254 1255 140.61 174.60 8.50
58 6394 161G 162L C N 1256 1258 -109.80 -108.50 7.57 0.39 -63.50 -175.27 28.49
58 162L 162L N CA 1258 1259 139.96 132.50 -41.20
59 6395 162L 163D C N 1264 1266 -94.29 -96.50 29.11 1.22 -63.30 128.96 14.32
59 163D 163D N CA 1266 1267 85.18 114.20 -40.00
60 6396 163D 164N C N 1272 1274 -114.76 -119.90 19.55 0.76 -63.20 167.38 18.58
60 164N 164N N CA 1274 1275 118.14 137.00 -41.10
61 6397 164N 165S C N 1280 1282 -151.53 -136.60 18.51 0.57 -64.10 -175.16 19.67
61 165S 165S N CA 1282 1283 162.14 151.20 -35.00
62 6398 165S 166G C N 1286 1288 151.38 -167.20 48.59 1.60 82.20 156.77 10.77
62 166G 166G N CA 1288 1289 149.19 174.60 8.50
63 6399 166G 167K C N 1290 1292 -128.98 -118.00 16.27 0.83 -62.90 -179.57 20.87
63 167K 167K N CA 1292 1293 127.10 139.10 -40.80
64 6400 167K 168A C N 1299 1301 -144.13 -134.00 10.14 0.32 -62.50 -169.89 35.53
64 168A 168A N CA 1301 1302 147.41 147.00 -40.90
65 6401 168A 169K C N 1304 1306 -131.60 -118.00 13.61 0.52 -62.90 -167.90 22.25
65 169K 169K N CA 1306 1307 138.59 139.10 -40.80
66 6402 169K 170H C N 1313 1315 -109.43 -125.60 43.52 1.32 -63.20 148.10 16.20
66 170H 170H N CA 1315 1316 98.39 138.80 -42.30
67 6403 170H 171W C N 1323 1325 -128.37 -124.90 19.61 1.03 -63.00 -179.46 19.91
67 171W 171W N CA 1325 1326 124.10 143.40 -44.20
68 6404 171W 172Y C N 1337 1339 -127.45 -124.30 15.00 0.93 -63.50 176.16 25.09
68 172Y 172Y N CA 1339 1340 120.74 135.40 -43.40
69 6406 173V 174S C N 1356 1358 -86.23 -72.40 18.10 0.89 -64.10 162.43 13.21
69 174S 174S N CA 1358 1359 164.08 152.40 -35.00
70 6407 174S 175D C N 1362 1364 -101.79 -96.50 20.50 0.86 -63.30 139.79 15.34
70 175D 175D N CA 1364 1365 94.39 114.20 -40.00
71 6408 175D 176G C N 1370 1372 75.87 78.70 10.86 0.42 82.20 175.03 8.18
71 176G 176G N CA 1372 1373 -176.58 -166.10 8.50
72 6410 177V 178S C N 1381 1383 -113.49 -136.60 29.19 0.90 -64.10 175.47 10.84
72 178S 178S N CA 1383 1384 133.37 151.20 -35.00
73 6412 179V 180R C N 1394 1396 -123.77 -125.20 11.08 0.50 -63.00 -178.80 21.14
73 180R 180R N CA 1396 1397 129.61 140.60 -41.10
74 6413 180R 181H C N 1405 1407 -130.26 -125.60 12.15 0.53 -63.20 -177.37 19.69
74 181H 181H N CA 1407 1408 127.57 138.80 -42.30
75 6415 182V 183R C N 1422 1424 -95.15 -72.10 60.77 5.11 -63.00 130.78 15.76
75 183R 183R N CA 1424 1425 85.67 141.90 -41.10
76 6416 183R 184T C N 1433 1435 -147.40 -124.80 24.70 1.02 -63.20 -175.26 29.15
76 184T 184T N CA 1435 1436 153.46 143.50 -42.10
77 6418 185I 186R C N 1448 1450 -145.63 -125.20 28.29 0.86 -63.00 178.95 29.77
77 186R 186R N CA 1450 1451 160.17 140.60 -41.10
78 6420 187M 188L C N 1467 1469 -99.95 -108.50 31.04 1.57 -63.50 148.41 18.85
78 188L 188L N CA 1469 1470 102.66 132.50 -41.20
79 6422 189E 190N C N 1484 1486 -70.93 -71.20 12.35 0.80 -63.20 163.93 20.92
79 190N 190N N CA 1486 1487 155.15 142.80 -41.10
80 6423 190N 191Y C N 1492 1494 -115.23 -124.30 9.07 0.69 -63.50 -173.51 27.15
80 191Y 191Y N CA 1494 1495 135.77 135.40 -43.40
81 6424 191Y 192Q C N 1504 1506 -71.38 -73.00 9.54 0.59 -63.80 171.77 24.86
81 192Q 192Q N CA 1506 1507 131.30 140.70 -40.30
82 6425 192Q 193N C N 1513 1515 -146.38 -119.90 28.52 0.93 -63.20 -169.55 28.50
82 193N 193N N CA 1515 1516 147.58 137.00 -41.10
83 6426 193N 194K C N 1521 1523 -118.67 -118.00 5.92 0.28 -62.90 -177.07 27.07
83 194K 194K N CA 1523 1524 144.98 139.10 -40.80
84 6427 194K 195W C N 1530 1532 -137.69 -124.90 23.76 0.83 -63.00 169.70 26.24
84 195W 195W N CA 1532 1533 163.42 143.40 -44.20
85 6428 195W 196A C N 1544 1546 -112.71 -134.00 21.92 0.55 -62.50 -175.71 32.87
85 196A 196A N CA 1546 1547 141.78 147.00 -40.90
86 6429 196A 197K C N 1549 1551 -75.94 -70.20 6.67 0.41 -62.90 175.89 23.58
86 197K 197K N CA 1551 1552 143.79 140.40 -40.80
87 6430 197K 198L C N 1558 1560 -70.71 -70.70 0.03 0.00 -63.50 177.32 25.04
87 198L 198L N CA 1560 1561 141.63 141.60 -41.20
88 6431 198L 199N C N 1566 1568 -112.09 -119.90 17.12 0.91 -63.20 173.69 24.50
88 199N 199N N CA 1568 1569 152.24 137.00 -41.10
89 6432 199N 200L C N 1574 1576 -95.53 -108.50 14.01 0.62 -63.50 171.44 22.18
89 200L 200L N CA 1576 1577 127.22 132.50 -41.20
90 6435 202V 203D C N 1596 1598 -130.92 -96.50 50.96 2.09 -63.30 134.81 14.31
90 203D 203D N CA 1598 1599 76.62 114.20 -40.00
91 6437 204T 205M C N 1611 1613 -126.42 -125.60 7.36 0.33 -63.40 -177.12 32.31
91 205M 205M N CA 1613 1614 147.82 140.50 -40.50
92 6438 205M 206F C N 1619 1621 -121.59 -124.20 13.75 0.70 -63.20 169.29 27.36
92 206F 206F N CA 1621 1622 156.80 143.30 -44.30
93 6439 206F 207I C N 1630 1632 -64.79 -63.40 3.72 0.66 -120.60 -174.07 8.59
93 207I 207I N CA 1632 1633 -47.06 -43.60 130.30
94 6440 207I 208A C N 1638 1640 173.48 -134.00 57.99 1.32 -62.50 -167.28 38.02
94 208A 208A N CA 1640 1641 171.59 147.00 -40.90
95 6441 208A 209E C N 1643 1645 -86.77 -69.30 30.43 2.77 -63.60 159.58 20.09
95 209E 209E N CA 1645 1646 117.58 142.50 -40.30
96 6443 210I 211E C N 1660 1662 -106.56 -117.80 54.27 2.49 -63.60 131.24 15.58
96 211E 211E N CA 1662 1663 83.71 136.80 -40.30
97 6444 211E 212A C N 1669 1671 53.91 -68.20 124.14 11.23 -62.50 -168.99 28.89
97 212A 212A N CA 1671 1672 167.67 145.30 -40.90
98 6446 213E 214F C N 1683 1685 -91.50 -63.20 79.09 9.33 -63.20 79.09 9.33
98 214F 214F N CA 1685 1686 29.56 -44.30 -44.30
99 6454 221A 222S C N 1747 1749 65.38 56.90 19.87 0.81 -64.10 140.08 18.71
99 222S 222S N CA 1749 1750 18.43 36.40 -35.00
100 6455 222S 223G C N 1753 1755 -95.99 -80.20 15.79 1.04 82.20 -116.53 7.93
100 223G 223G N CA 1755 1756 174.41 174.10 8.50
101 6456 223G 224E C N 1757 1759 67.54 -69.30 136.84 10.36 -63.60 -139.52 25.58
101 224E 224E N CA 1759 1760 142.45 142.50 -40.30
-------------------------------------------------------------------------------------------------
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 13422 94F 229. CA O4 731 1823 10.25 9.21 1.04 5.22 9.21 1.04 5.22
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 25 39 138 156 238 195 210 226 260 298
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
WithLigand.B99990001.pdb 2271.34619
WithLigand.B99990002.pdb 2429.66089
Используя известную структуру лизоцима форели как образец, была построена модель белка LYS_BPPHV с лигандом.
In [17]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('WithLigand.B99990002.pdb')
w1
