Гомологичное моделирование комплекса белка с лигандом¶
Установка Modeller'а:
conda config --add channels salilab
conda install modeller
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, WinNT 10.0 build 19041, DESKTOP-E0GAFSS, SMP, unknown
Date and time of compilation : 2021/03/12 00:14:36
MODELLER executable type : x86_64-w64
Job starting time (YY/MM/DD HH:MM:SS): 2021/05/26 01:21:27
environ____W> The class 'environ' is deprecated; use 'Environ' instead
Вручную скачала модель 1lmp.pdb из PDB и последовательность LYS_LAMBD
In [3]:
# объект выравнивания
alignm=modeller.Alignment(env)
In [4]:
alignm.append(file='P03706.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.Model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'LYS_LAMBD'
alignm[1].code = '1lmp'
In [5]:
#Делаем выравнивание и сохраняем:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
Проверим файл 'all_in_one.ali':
In [6]:
# >P1;LYS_LAMBD
# sequence::: :: :::-1.00:-1.00
# MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD
# AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG
# GTVREIDV*
# >P1;1lmp
# structureX:1lmp.pdb:1:A:+129:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16
# KVYDRCELARALKASGMDGYAGNS-----------LPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWC
# DDGRTPGAKNVCGIRCSQLL--------------TDDLTVAIRCAKRVVLDPNGIG----AWVAWRLHCQNQDLR
# SYVAGCGV*
В нем не хватает лигандов. Чтобы они читались, добавим в обе последовательности "/" - конец последовательности, и "..." - три следующих лиганда. Еще изменим номер последнего остатка последовательности 1lmp с 129 на 132. Вот что получится:
In [21]:
# >P1;LYS_LAMBD
# sequence::: :: :::-1.00:-1.00
# MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD
# AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG
# GTVREIDV/...*
# >P1;1lmp
# structureX:1lmp.pdb:1:A:+132:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16
# KVYDRCELARALKASGMDGYAGNS-----------LPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWC
# DDGRTPGAKNVCGIRCSQLL--------------TDDLTVAIRCAKRVVLDPNGIG----AWVAWRLHCQNQDLR
# SYVAGCGV/...*
In [10]:
### Построим модель:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
LYS_LAMBD 1lmp
In [11]:
## Создаем объект automodel
a = modeller.automodel.AutoModel(env, alnfile='all_in_one.ali', knowns= pdb.code, sequence = s.code)
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
In [12]:
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
read_pd_459W> Residue type NDG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NAG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
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.)
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 45:A (type TYR)>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13524 12408
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_484W> Dihedral still outside +-90: -90.0028
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 : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12408 12408
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3354
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 : 1366.6874
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 : 1282 0 0 0.005 0.005 10.171 1.000
2 Bond angle potential : 1726 3 11 2.496 2.496 207.56 1.000
3 Stereochemical cosine torsion poten: 789 0 40 50.375 50.375 313.29 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.565 1.565 25.937 1.000
5 Soft-sphere overlap restraints : 3354 1 2 0.008 0.008 22.667 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 0 0 0.446 0.446 112.91 1.000
10 Distance restraints 2 (N-O) : 2568 0 9 0.523 0.523 195.32 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: 157 0 11 6.208 6.208 71.346 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 3 87.009 87.009 56.665 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 6 83.100 83.100 59.621 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 72.847 72.847 29.337 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 95.537 95.537 14.238 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) : 941 0 0 0.594 0.594 26.206 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: 156 44 38 40.500 88.706 176.64 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 2 1.197 1.197 21.711 1.000
27 Distance restraints 5 (X-Y) : 1401 0 1 0.044 0.044 23.066 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_LAMBD.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: 22848.2070
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 1672 35V 36I C N 285 287 139.95 120.00 19.95 4.53 120.00 19.95 4.53
2 1908 57P 57P N CA 454 455 134.74 108.20 26.54 6.03 108.20 26.54 6.03
3 2716 131G 131G N CA 1041 1042 123.87 107.00 16.87 4.85 107.00 16.87 4.85
-------------------------------------------------------------------------------------------------
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 4315 3E 4I C N 23 25 -68.61 -63.40 23.67 4.07 -120.60 171.10 11.73
1 4I 4I N CA 25 26 -66.69 -43.60 130.30
2 4316 4I 5N C N 31 33 -169.95 -63.20 111.21 17.95 -63.20 111.21 17.95
2 5N 5N N CA 33 34 -72.26 -41.10 -41.10
3 4327 15L 16A C N 124 126 77.83 55.40 25.78 1.93 -62.50 155.24 31.54
3 16A 16A N CA 126 127 25.49 38.20 -40.90
4 4329 17W 18S C N 143 145 -53.79 -64.10 19.07 1.30 -136.60 178.17 10.10
4 18S 18S N CA 145 146 -51.04 -35.00 151.20
5 4332 20G 21T C N 162 164 52.52 55.90 13.49 0.72 -124.80 -160.72 7.88
5 21T 21T N CA 164 165 52.56 39.50 143.50
6 4336 24G 25R C N 189 191 -158.81 -125.20 35.16 1.67 -63.00 -163.66 22.23
6 25R 25R N CA 191 192 130.27 140.60 -41.10
7 4337 25R 26Q C N 200 202 -109.36 -121.10 16.23 0.83 -63.80 174.84 28.14
7 26Q 26Q N CA 202 203 150.90 139.70 -40.30
8 4338 26Q 27K C N 209 211 -156.75 -118.00 38.76 1.45 -62.90 -157.40 31.92
8 27K 27K N CA 211 212 139.65 139.10 -40.80
9 4339 27K 28T C N 218 220 -150.24 -124.80 52.80 1.66 -63.20 154.89 25.33
9 28T 28T N CA 220 221 -170.23 143.50 -42.10
10 4340 28T 29R C N 225 227 -112.90 -125.20 21.08 0.70 -63.00 171.97 20.37
10 29R 29R N CA 227 228 123.48 140.60 -41.10
11 4341 29R 30N C N 236 238 -161.63 -119.90 58.31 1.70 -63.20 172.10 26.90
11 30N 30N N CA 238 239 177.72 137.00 -41.10
12 4342 30N 31H C N 244 246 -114.83 -125.60 31.74 1.38 -63.20 157.73 23.10
12 31H 31H N CA 246 247 168.66 138.80 -42.30
13 4344 32G 33Y C N 258 260 -119.14 -124.30 7.07 0.32 -63.50 -177.36 26.40
13 33Y 33Y N CA 260 261 130.56 135.40 -43.40
14 4345 33Y 34D C N 270 272 -141.79 -96.50 72.50 3.04 -63.30 168.58 25.86
14 34D 34D N CA 272 273 170.81 114.20 -40.00
15 4347 35V 36I C N 285 287 -96.72 -120.60 46.45 1.93 -63.40 138.14 21.60
15 36I 36I N CA 287 288 90.46 130.30 -43.60
16 4358 46S 47D C N 369 371 -140.26 -63.30 92.34 11.41 -63.30 92.34 11.41
16 47D 47D N CA 371 372 11.02 -40.00 -40.00
17 4368 56N 57P C N 452 454 -75.92 -58.70 41.56 2.44 -64.50 140.34 11.08
17 57P 57P N CA 454 455 7.33 -30.50 147.20
18 4369 57P 58K C N 459 461 81.18 -62.90 145.22 22.93 -62.90 145.22 22.93
18 58K 58K N CA 461 462 -58.96 -40.80 -40.80
19 4379 67Y 68Q C N 534 536 59.33 55.10 12.52 1.26 -121.10 -160.19 9.36
19 68Q 68Q N CA 536 537 52.08 40.30 139.70
20 4388 76A 77Y C N 617 619 -121.41 -63.50 91.87 12.68 -63.50 91.87 12.68
20 77Y 77Y N CA 619 620 27.92 -43.40 -43.40
21 4390 78R 79K C N 640 642 -147.41 -118.00 108.77 5.57 -62.90 113.11 14.04
21 79K 79K N CA 642 643 34.38 139.10 -40.80
22 4395 83L 84K C N 678 680 -133.39 -118.00 68.37 3.48 -62.90 133.44 15.39
22 84K 84K N CA 680 681 72.49 139.10 -40.80
23 4396 84K 85D C N 687 689 -59.00 -96.50 38.78 1.59 54.50 130.02 10.73
23 85D 85D N CA 689 690 104.31 114.20 40.90
24 4398 86F 87S C N 706 708 -98.21 -72.40 81.72 5.69 -64.10 115.04 7.09
24 87S 87S N CA 708 709 74.87 152.40 -35.00
25 4407 95A 96L C N 768 770 54.96 -70.70 137.99 10.37 -63.50 172.80 30.97
25 96L 96L N CA 770 771 84.60 141.60 -41.20
26 4408 96L 97Q C N 776 778 -156.08 -121.10 47.87 1.54 -63.80 173.83 30.25
26 97Q 97Q N CA 778 779 172.39 139.70 -40.30
27 4409 97Q 98Q C N 785 787 -78.15 -73.00 23.81 1.46 -63.80 156.41 23.76
27 98Q 98Q N CA 787 788 163.95 140.70 -40.30
28 4411 99I 100K C N 802 804 -54.70 -70.20 16.30 1.07 -62.90 176.34 23.36
28 100K 100K N CA 804 805 135.35 140.40 -40.80
29 4412 100K 101E C N 811 813 -151.66 -117.80 54.08 1.86 -63.60 166.01 26.96
29 101E 101E N CA 813 814 178.97 136.80 -40.30
30 4413 101E 102R C N 820 822 -74.09 -72.10 9.76 0.71 -63.00 167.81 23.42
30 102R 102R N CA 822 823 151.46 141.90 -41.10
31 4414 102R 103G C N 831 833 106.92 78.70 59.70 0.89 82.20 135.07 7.77
31 103G 103G N CA 833 834 141.29 -166.10 8.50
32 4417 105L 106P C N 848 850 -66.22 -58.70 10.47 0.75 -64.50 170.42 12.81
32 106P 106P N CA 850 851 -23.22 -30.50 147.20
33 4420 108I 109D C N 871 873 -124.84 -70.90 61.58 3.31 -63.30 152.93 22.85
33 109D 109D N CA 873 874 180.00 150.30 -40.00
34 4421 109D 110R C N 879 881 179.27 -125.20 97.72 3.28 -72.10 134.38 8.77
34 110R 110R N CA 881 882 -138.98 140.60 141.90
35 4422 110R 111G C N 890 892 97.09 78.70 27.49 0.56 -62.40 -144.23 30.79
35 111G 111G N CA 892 893 173.47 -166.10 -41.20
36 4442 130A 131G C N 1039 1041 61.26 82.20 71.27 2.43 -62.40 170.81 31.75
36 131G 131G N CA 1041 1042 76.63 8.50 -41.20
37 4443 131G 132Y C N 1043 1045 -128.38 -98.40 79.97 7.83 -63.50 117.26 16.20
37 132Y 132Y N CA 1045 1046 54.27 128.40 -43.40
38 4444 132Y 133G C N 1055 1057 -65.96 -62.40 4.83 0.90 82.20 157.35 12.00
38 133G 133G N CA 1057 1058 -44.47 -41.20 8.50
39 4445 133G 134Q C N 1059 1061 -176.04 -121.10 80.90 4.17 -63.80 164.76 21.37
39 134Q 134Q N CA 1061 1062 80.31 139.70 -40.30
40 4446 134Q 135F C N 1068 1070 -147.12 -124.20 87.68 3.50 -63.20 121.43 21.66
40 135F 135F N CA 1070 1071 -132.07 143.30 -44.30
41 4457 145K 146F C N 1156 1158 60.86 58.10 6.90 0.36 -63.20 142.88 25.72
41 146F 146F N CA 1158 1159 26.57 32.90 -44.30
42 4461 149A 150G C N 1190 1192 32.28 78.70 81.01 1.35 -62.40 111.30 16.81
42 150G 150G N CA 1192 1193 -99.71 -166.10 -41.20
43 4465 153V 154R C N 1212 1214 48.97 -72.10 134.05 11.33 -72.10 134.05 11.33
43 154R 154R N CA 1214 1215 -160.56 141.90 141.90
44 4466 154R 155E C N 1223 1225 -75.88 -69.30 70.97 5.64 -63.60 112.81 14.40
44 155E 155E N CA 1225 1226 71.84 142.50 -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 20 26 145 132 212 167 210 222 210 259
<< 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 : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12408 12408
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3414
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 : 1374.7776
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 : 1282 0 0 0.006 0.006 14.025 1.000
2 Bond angle potential : 1726 1 6 2.419 2.419 191.68 1.000
3 Stereochemical cosine torsion poten: 789 0 47 51.257 51.257 327.69 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.581 1.581 25.868 1.000
5 Soft-sphere overlap restraints : 3414 2 2 0.008 0.008 23.602 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 0 1 0.406 0.406 107.95 1.000
10 Distance restraints 2 (N-O) : 2568 1 15 0.533 0.533 212.96 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 157 1 3 5.398 5.398 53.958 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 9 88.764 88.764 72.219 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 1 77.667 77.667 52.620 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 78.164 78.164 33.599 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 93.352 93.352 17.411 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) : 941 0 0 0.512 0.512 28.031 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: 156 41 36 38.106 86.902 180.95 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 0 0.944 0.944 14.186 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.037 0.037 18.039 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_LAMBD.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: 23209.0801
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 1908 57P 57P N CA 454 455 135.49 108.20 27.29 6.20 108.20 27.29 6.20
-------------------------------------------------------------------------------------------------
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 7483 9K 5N N O 69 40 5.37 2.96 2.41 5.39 2.96 2.41 5.39
-------------------------------------------------------------------------------------------------
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 4516 48H 48H CA C 380 387 -157.33 -180.00 22.67 4.53 -180.00 22.67 4.53
-------------------------------------------------------------------------------------------------
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 4316 4I 5N C N 31 33 -63.61 -119.90 61.98 3.14 -63.20 155.95 19.52
1 5N 5N N CA 33 34 162.96 137.00 -41.10
2 4317 5N 6N C N 39 41 74.26 55.90 82.88 4.56 -63.20 137.46 20.82
2 6N 6N N CA 41 42 -41.32 39.50 -41.10
3 4327 15L 16A C N 124 126 76.86 55.40 24.43 1.86 -62.50 154.81 31.47
3 16A 16A N CA 126 127 26.53 38.20 -40.90
4 4330 18S 19E C N 149 151 59.10 54.60 12.92 0.69 -63.60 141.56 24.35
4 19E 19E N CA 151 152 30.29 42.40 -40.30
5 4332 20G 21T C N 162 164 46.10 55.90 11.01 0.91 -124.80 -162.50 7.53
5 21T 21T N CA 164 165 44.50 39.50 143.50
6 4335 23N 24G C N 185 187 -73.75 -80.20 26.40 0.74 82.20 -150.43 6.98
6 24G 24G N CA 187 188 148.50 174.10 8.50
7 4336 24G 25R C N 189 191 -163.84 -125.20 55.87 1.72 -63.00 170.88 29.69
7 25R 25R N CA 191 192 -179.05 140.60 -41.10
8 4337 25R 26Q C N 200 202 -109.10 -121.10 46.46 2.37 -63.80 142.51 23.36
8 26Q 26Q N CA 202 203 -175.42 139.70 -40.30
9 4338 26Q 27K C N 209 211 -133.85 -118.00 22.31 0.79 -62.90 179.06 27.50
9 27K 27K N CA 211 212 154.80 139.10 -40.80
10 4339 27K 28T C N 218 220 -134.07 -124.80 27.55 0.93 -63.20 164.51 25.72
10 28T 28T N CA 220 221 169.44 143.50 -42.10
11 4340 28T 29R C N 225 227 -141.72 -63.00 79.79 13.92 -63.00 79.79 13.92
11 29R 29R N CA 227 228 -54.13 -41.10 -41.10
12 4341 29R 30N C N 236 238 -80.68 -71.20 41.69 2.42 -63.20 136.62 18.06
12 30N 30N N CA 238 239 -176.60 142.80 -41.10
13 4342 30N 31H C N 244 246 -80.65 -67.60 19.06 1.13 -63.20 164.73 21.71
13 31H 31H N CA 246 247 153.90 140.00 -42.30
14 4343 31H 32G C N 254 256 152.85 -167.20 42.19 0.61 82.20 -166.94 12.68
14 32G 32G N CA 256 257 -171.83 174.60 8.50
15 4345 33Y 34D C N 270 272 26.61 54.50 76.08 3.82 -63.30 176.33 27.52
15 34D 34D N CA 272 273 111.68 40.90 -40.00
16 4347 35V 36I C N 285 287 -92.50 -120.60 46.46 1.91 -63.40 139.97 22.01
16 36I 36I N CA 287 288 93.30 130.30 -43.60
17 4358 46S 47D C N 369 371 -145.86 -63.30 97.36 12.20 -63.30 97.36 12.20
17 47D 47D N CA 371 372 11.61 -40.00 -40.00
18 4368 56N 57P C N 452 454 -73.92 -58.70 40.31 2.39 -64.50 140.69 11.00
18 57P 57P N CA 454 455 6.83 -30.50 147.20
19 4369 57P 58K C N 459 461 81.49 -62.90 145.49 22.99 -62.90 145.49 22.99
19 58K 58K N CA 461 462 -58.68 -40.80 -40.80
20 4388 76A 77Y C N 617 619 -126.65 -63.50 87.90 12.25 -63.50 87.90 12.25
20 77Y 77Y N CA 619 620 17.75 -43.40 -43.40
21 4395 83L 84K C N 678 680 -137.05 -118.00 73.76 3.77 -62.90 131.54 15.25
21 84K 84K N CA 680 681 67.84 139.10 -40.80
22 4396 84K 85D C N 687 689 -36.87 -96.50 66.20 2.74 54.50 101.65 8.85
22 85D 85D N CA 689 690 85.43 114.20 40.90
23 4398 86F 87S C N 706 708 -102.29 -72.40 80.89 5.77 -64.10 118.55 7.30
23 87S 87S N CA 708 709 77.23 152.40 -35.00
24 4407 95A 96L C N 768 770 71.48 -70.70 142.38 12.69 -63.50 -138.77 38.85
24 96L 96L N CA 770 771 134.07 141.60 -41.20
25 4408 96L 97Q C N 776 778 177.15 -121.10 61.79 2.28 -63.80 -145.99 37.46
25 97Q 97Q N CA 778 779 141.86 139.70 -40.30
26 4411 99I 100K C N 802 804 -82.83 -70.20 26.33 2.16 -62.90 159.34 19.69
26 100K 100K N CA 804 805 117.29 140.40 -40.80
27 4412 100K 101E C N 811 813 -143.55 -117.80 38.28 1.26 -63.60 174.02 27.65
27 101E 101E N CA 813 814 165.13 136.80 -40.30
28 4413 101E 102R C N 820 822 -73.30 -72.10 3.59 0.30 -63.00 179.91 23.63
28 102R 102R N CA 822 823 138.52 141.90 -41.10
29 4414 102R 103G C N 831 833 85.57 78.70 28.56 0.54 82.20 157.71 7.83
29 103G 103G N CA 833 834 166.18 -166.10 8.50
30 4415 103G 104A C N 835 837 -116.30 -134.00 20.27 0.47 -62.50 -174.05 28.36
30 104A 104A N CA 837 838 137.10 147.00 -40.90
31 4416 104A 105L C N 840 842 -103.94 -108.50 20.66 1.16 -63.50 170.99 26.22
31 105L 105L N CA 842 843 152.66 132.50 -41.20
32 4418 106P 107M C N 855 857 -179.03 -125.60 64.76 1.91 -63.40 -176.56 35.96
32 107M 107M N CA 857 858 177.09 140.50 -40.50
33 4420 108I 109D C N 871 873 -114.34 -96.50 39.03 1.62 -63.30 129.93 13.87
33 109D 109D N CA 873 874 79.49 114.20 -40.00
34 4421 109D 110R C N 879 881 154.34 -125.20 119.97 3.74 -72.10 159.78 10.50
34 110R 110R N CA 881 882 -130.41 140.60 141.90
35 4422 110R 111G C N 890 892 55.18 78.70 67.97 1.09 -62.40 132.52 20.51
35 111G 111G N CA 892 893 -102.34 -166.10 -41.20
36 4442 130A 131G C N 1039 1041 147.25 82.20 66.09 3.96 -62.40 155.09 25.90
36 131G 131G N CA 1041 1042 -3.15 8.50 -41.20
37 4443 131G 132Y C N 1043 1045 -57.55 -98.40 40.96 1.57 -63.50 174.82 28.04
37 132Y 132Y N CA 1045 1046 131.32 128.40 -43.40
38 4446 134Q 135F C N 1068 1070 153.79 -124.20 83.59 3.73 -63.20 -136.74 25.33
38 135F 135F N CA 1070 1071 127.14 143.30 -44.30
39 4457 145K 146F C N 1156 1158 56.06 58.10 2.22 0.34 -63.20 141.59 25.54
39 146F 146F N CA 1158 1159 32.02 32.90 -44.30
40 4461 149A 150G C N 1190 1192 30.33 78.70 88.50 1.41 -62.40 105.73 16.25
40 150G 150G N CA 1192 1193 -92.00 -166.10 -41.20
41 4466 154R 155E C N 1223 1225 70.82 54.60 27.97 1.48 -63.60 147.16 25.21
41 155E 155E N CA 1225 1226 19.61 42.40 -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 19 27 142 130 196 178 212 239 241 239
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_LAMBD.B99990001.pdb 1366.68738
LYS_LAMBD.B99990002.pdb 1374.77759
In [14]:
! pip install nglview
Collecting nglview
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Building wheels for collected packages: nglview
Building wheel for nglview (PEP 517): started
Building wheel for nglview (PEP 517): finished with status 'done'
Created wheel for nglview: filename=nglview-3.0.1-py3-none-any.whl size=8057517 sha256=cb4ddef57d63ede3bd8226ffbe3663fd8ab506eeba64e9bc06bac44062cd57ee
Stored in directory: c:\users\anton\appdata\local\pip\cache\wheels\9d\b7\68\7773fbf391bd5b02efe6e36bb9f9e8403c301472955458ab47
Successfully built nglview
Installing collected packages: jupyterlab-widgets, nglview
Successfully installed jupyterlab-widgets-1.0.0 nglview-3.0.1
In [16]:
# import nglview
# import ipywidgets
# w1 = nglview.show_structure_file('LYS_LAMBD.B99990001.pdb')
Построидись две модели, далее картинки для них. Голубая структура - исходная (1lmp).
In [18]:
from IPython.display import Image
In [19]:
Image(filename='mod1.png')
Out[19]:
In [20]:
Image(filename='mod2.png')
Out[20]:
In [60]:
#Поместите лиганд в другое место, переназначив объект automodel
class mymodel(modeller.automodel.AutoModel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:50:A','CA:125:A')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.3))
In [61]:
from modeller import *
from modeller.automodel import *
a2 = mymodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
In [62]:
a2.name='mod'+s.code
a2.starting_model = 1
a2.ending_model = 2
a2.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
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.)
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 45:A (type TYR)>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13525 12409
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 : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12409 12409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3570
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 : 2335.6367
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 : 1282 0 1 0.008 0.008 26.184 1.000
2 Bond angle potential : 1726 0 10 2.526 2.526 214.91 1.000
3 Stereochemical cosine torsion poten: 789 0 37 50.771 50.771 310.04 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.572 1.572 26.251 1.000
5 Soft-sphere overlap restraints : 3570 2 3 0.008 0.008 29.936 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 0 2 0.443 0.443 160.87 1.000
10 Distance restraints 2 (N-O) : 2568 1 28 0.652 0.652 318.99 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: 157 1 6 5.655 5.655 59.212 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 5 91.066 91.066 74.367 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 1 78.845 78.845 55.430 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 96.887 96.887 33.826 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 94.394 94.394 16.347 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) : 941 0 0 0.470 0.470 21.810 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: 156 40 37 39.233 86.729 198.26 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 0 1.059 1.059 17.280 1.000
27 Distance restraints 5 (X-Y) : 1402 1 4 0.403 0.403 771.91 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_LAMBD.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: 24525.9688
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 8220 53V 50R N O 424 406 5.72 3.29 2.43 4.57 3.29 2.43 4.57
-------------------------------------------------------------------------------------------------
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 4621 153V 153V CA C 1208 1212 -154.81 -180.00 25.19 5.04 -180.00 25.19 5.04
-------------------------------------------------------------------------------------------------
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 4327 15L 16A C N 124 126 76.94 55.40 23.32 1.97 -62.50 156.10 31.74
1 16A 16A N CA 126 127 29.27 38.20 -40.90
2 4328 16A 17W C N 129 131 -97.64 -63.00 81.24 8.92 -63.00 81.24 8.92
2 17W 17W N CA 131 132 29.29 -44.20 -44.20
3 4329 17W 18S C N 143 145 -65.20 -64.10 14.43 1.11 -136.60 174.68 9.85
3 18S 18S N CA 145 146 -49.39 -35.00 151.20
4 4330 18S 19E C N 149 151 -120.18 -117.80 53.77 2.74 -63.60 135.74 15.81
4 19E 19E N CA 151 152 83.08 136.80 -40.30
5 4334 22D 23N C N 177 179 -64.54 -63.20 5.42 0.75 -119.90 -174.88 9.49
5 23N 23N N CA 179 180 -46.35 -41.10 137.00
6 4336 24G 25R C N 189 191 -143.90 -125.20 19.60 0.64 -63.00 -169.56 31.25
6 25R 25R N CA 191 192 146.50 140.60 -41.10
7 4337 25R 26Q C N 200 202 -156.73 -121.10 38.12 1.21 -63.80 -169.38 32.81
7 26Q 26Q N CA 202 203 153.26 139.70 -40.30
8 4338 26Q 27K C N 209 211 -158.73 -118.00 41.60 1.44 -62.90 -163.45 31.24
8 27K 27K N CA 211 212 147.59 139.10 -40.80
9 4339 27K 28T C N 218 220 120.17 -124.80 115.05 6.03 -63.20 -113.40 41.93
9 28T 28T N CA 220 221 145.81 143.50 -42.10
10 4340 28T 29R C N 225 227 -149.96 -125.20 45.02 1.53 -63.00 165.40 28.15
10 29R 29R N CA 227 228 178.20 140.60 -41.10
11 4342 30N 31H C N 244 246 -135.16 -125.60 35.17 1.14 -63.20 161.93 24.92
11 31H 31H N CA 246 247 172.64 138.80 -42.30
12 4345 33Y 34D C N 270 272 -66.34 -70.90 26.06 1.07 -63.30 164.67 20.14
12 34D 34D N CA 272 273 124.64 150.30 -40.00
13 4347 35V 36I C N 285 287 -148.57 -120.60 65.16 4.73 -63.40 143.15 21.78
13 36I 36I N CA 287 288 71.45 130.30 -43.60
14 4348 36I 37V C N 293 295 3.47 -125.40 135.23 4.08 -62.40 158.99 24.17
14 37V 37V N CA 295 296 102.30 143.30 -42.40
15 4349 37V 38G C N 300 302 103.82 82.20 66.29 2.17 -62.40 166.72 29.23
15 38G 38G N CA 302 303 -54.16 8.50 -41.20
16 4358 46S 47D C N 369 371 -143.95 -96.50 92.14 3.81 -63.30 110.29 12.63
16 47D 47D N CA 371 372 35.22 114.20 -40.00
17 4359 47D 48H C N 377 379 63.19 -67.60 144.22 12.44 56.30 160.11 14.75
17 48H 48H N CA 379 380 -159.24 140.00 40.80
18 4360 48H 49P C N 387 389 -83.76 -58.70 61.49 3.61 -64.50 123.07 10.23
18 49P 49P N CA 389 390 25.65 -30.50 147.20
19 4362 50R 51K C N 405 407 -125.43 -62.90 62.57 10.15 -62.90 62.57 10.15
19 51K 51K N CA 407 408 -38.57 -40.80 -40.80
20 4378 66R 67Y C N 522 524 -106.26 -63.50 74.15 10.23 -63.50 74.15 10.23
20 67Y 67Y N CA 524 525 17.18 -43.40 -43.40
21 4388 76A 77Y C N 617 619 -118.18 -63.50 90.81 12.52 -63.50 90.81 12.52
21 77Y 77Y N CA 619 620 29.10 -43.40 -43.40
22 4390 78R 79K C N 640 642 -136.35 -118.00 94.14 4.77 -62.90 114.30 13.53
22 79K 79K N CA 642 643 46.77 139.10 -40.80
23 4398 86F 87S C N 706 708 -99.62 -72.40 82.16 5.76 -64.10 115.48 7.12
23 87S 87S N CA 708 709 74.88 152.40 -35.00
24 4407 95A 96L C N 768 770 116.89 -108.50 136.05 6.26 -63.50 -115.06 44.37
24 96L 96L N CA 770 771 152.25 132.50 -41.20
25 4408 96L 97Q C N 776 778 -55.85 -73.00 17.39 1.29 -63.80 176.27 25.51
25 97Q 97Q N CA 778 779 143.61 140.70 -40.30
26 4409 97Q 98Q C N 785 787 -92.29 -73.00 19.31 1.40 -63.80 -177.76 28.32
26 98Q 98Q N CA 787 788 139.70 140.70 -40.30
27 4411 99I 100K C N 802 804 -91.96 -70.20 29.33 2.45 -62.90 164.13 19.90
27 100K 100K N CA 804 805 120.73 140.40 -40.80
28 4412 100K 101E C N 811 813 -165.09 -117.80 55.37 1.62 -63.60 -175.49 30.13
28 101E 101E N CA 813 814 165.61 136.80 -40.30
29 4413 101E 102R C N 820 822 -118.49 -125.20 66.03 3.04 -63.00 128.59 14.66
29 102R 102R N CA 822 823 74.91 140.60 -41.10
30 4415 103G 104A C N 835 837 -114.45 -134.00 26.93 0.79 -62.50 177.16 27.01
30 104A 104A N CA 837 838 128.48 147.00 -40.90
31 4418 106P 107M C N 855 857 -79.96 -73.00 16.83 1.05 -63.40 162.02 25.50
31 107M 107M N CA 857 858 158.33 143.00 -40.50
32 4422 110R 111G C N 890 892 131.85 82.20 68.28 2.21 -62.40 165.77 29.50
32 111G 111G N CA 892 893 -38.37 8.50 -41.20
33 4442 130A 131G C N 1039 1041 139.04 82.20 57.41 4.12 -62.40 168.78 27.29
33 131G 131G N CA 1041 1042 16.64 8.50 -41.20
34 4444 132Y 133G C N 1055 1057 -70.43 -80.20 32.78 1.78 82.20 -136.61 17.02
34 133G 133G N CA 1057 1058 -154.61 174.10 8.50
35 4446 134Q 135F C N 1068 1070 -160.94 -124.20 60.17 3.34 -63.20 170.71 19.26
35 135F 135F N CA 1070 1071 95.65 143.30 -44.30
36 4457 145K 146F C N 1156 1158 61.07 58.10 6.70 0.34 -63.20 143.21 25.78
36 146F 146F N CA 1158 1159 26.89 32.90 -44.30
37 4461 149A 150G C N 1190 1192 36.87 78.70 90.90 1.35 -62.40 108.66 17.17
37 150G 150G N CA 1192 1193 -85.40 -166.10 -41.20
38 4465 153V 154R C N 1212 1214 -52.67 -63.00 13.43 1.65 -72.10 169.54 13.45
38 154R 154R N CA 1214 1215 -49.67 -41.10 141.90
39 4467 155E 156I C N 1232 1234 -113.77 -120.60 27.12 1.30 -63.40 156.01 24.10
39 156I 156I N CA 1234 1235 104.06 130.30 -43.60
40 4468 156I 157D C N 1240 1242 -68.71 -70.90 26.18 1.18 54.50 148.74 11.25
40 157D 157D N CA 1242 1243 124.21 150.30 40.90
-------------------------------------------------------------------------------------------------
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 12409 50R 125A O CA 406 1007 17.94 3.00 14.94 49.79 3.00 14.94 49.79
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 21 44 143 151 202 190 216 229 256 228
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 161
Number of all, selected real atoms : 1300 1300
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12409 12409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3463
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 : 2196.6033
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 : 1282 0 1 0.008 0.008 22.904 1.000
2 Bond angle potential : 1726 0 9 2.333 2.333 183.21 1.000
3 Stereochemical cosine torsion poten: 789 0 43 50.774 50.774 311.15 1.000
4 Stereochemical improper torsion pot: 515 1 1 1.751 1.751 31.167 1.000
5 Soft-sphere overlap restraints : 3463 2 2 0.008 0.008 28.092 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 0 5 0.520 0.520 194.62 1.000
10 Distance restraints 2 (N-O) : 2568 1 19 0.644 0.644 302.65 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: 157 0 3 4.789 4.789 42.470 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 5 88.376 88.376 67.837 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 1 78.293 78.293 43.190 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 88.631 88.631 29.137 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 94.490 94.490 14.832 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) : 941 0 0 0.459 0.459 18.812 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: 156 45 33 37.239 89.793 159.49 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 1 1.049 1.049 16.104 1.000
27 Distance restraints 5 (X-Y) : 1402 1 2 0.392 0.392 730.93 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_LAMBD.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: 24240.1172
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 8220 53V 50R N O 424 406 5.93 3.29 2.64 4.98 3.29 2.64 4.98
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4327 15L 16A C N 124 126 81.06 55.40 29.85 2.18 -62.50 157.11 31.90
1 16A 16A N CA 126 127 22.95 38.20 -40.90
2 4329 17W 18S C N 143 145 -50.67 -64.10 27.51 1.80 -136.60 172.69 9.80
2 18S 18S N CA 145 146 -59.01 -35.00 151.20
3 4330 18S 19E C N 149 151 -114.73 -117.80 64.31 3.17 -63.60 123.91 14.44
3 19E 19E N CA 151 152 72.57 136.80 -40.30
4 4335 23N 24G C N 185 187 -75.48 -80.20 22.92 0.68 82.20 -147.02 7.04
4 24G 24G N CA 187 188 151.67 174.10 8.50
5 4336 24G 25R C N 189 191 -157.66 -125.20 32.72 1.21 -63.00 -161.79 33.17
5 25R 25R N CA 191 192 144.75 140.60 -41.10
6 4337 25R 26Q C N 200 202 -126.68 -121.10 9.41 0.33 -63.80 -176.48 30.32
6 26Q 26Q N CA 202 203 147.28 139.70 -40.30
7 4338 26Q 27K C N 209 211 -112.88 -118.00 27.61 1.26 -62.90 160.74 18.78
7 27K 27K N CA 211 212 111.97 139.10 -40.80
8 4339 27K 28T C N 218 220 -57.36 -78.10 38.67 2.33 -63.20 135.58 17.01
8 28T 28T N CA 220 221 -177.56 149.80 -42.10
9 4340 28T 29R C N 225 227 -172.63 -125.20 83.74 4.64 -63.00 157.21 18.50
9 29R 29R N CA 227 228 71.58 140.60 -41.10
10 4341 29R 30N C N 236 238 179.37 -119.90 78.57 2.28 -63.20 176.72 28.30
10 30N 30N N CA 238 239 -173.15 137.00 -41.10
11 4342 30N 31H C N 244 246 -80.76 -67.60 23.00 1.40 -63.20 159.80 21.10
11 31H 31H N CA 246 247 158.86 140.00 -42.30
12 4343 31H 32G C N 254 256 98.28 78.70 26.20 0.65 82.20 168.75 9.00
12 32G 32G N CA 256 257 176.49 -166.10 8.50
13 4344 32G 33Y C N 258 260 -63.71 -98.40 35.05 1.50 -63.50 166.79 26.45
13 33Y 33Y N CA 260 261 123.39 128.40 -43.40
14 4345 33Y 34D C N 270 272 -146.29 -96.50 53.52 2.21 -63.30 -167.37 20.47
14 34D 34D N CA 272 273 133.84 114.20 -40.00
15 4347 35V 36I C N 285 287 -86.24 -120.60 42.59 1.98 -63.40 150.49 23.91
15 36I 36I N CA 287 288 105.15 130.30 -43.60
16 4348 36I 37V C N 293 295 -32.26 -125.40 94.69 3.18 -62.40 171.34 23.51
16 37V 37V N CA 295 296 126.26 143.30 -42.40
17 4349 37V 38G C N 300 302 87.44 82.20 61.28 2.71 -62.40 150.27 26.36
17 38G 38G N CA 302 303 -52.55 8.50 -41.20
18 4358 46S 47D C N 369 371 -146.42 -96.50 93.88 3.88 -63.30 111.75 12.90
18 47D 47D N CA 371 372 34.70 114.20 -40.00
19 4359 47D 48H C N 377 379 63.34 -67.60 137.71 11.54 56.30 142.03 13.16
19 48H 48H N CA 379 380 -177.35 140.00 40.80
20 4362 50R 51K C N 405 407 -129.96 -62.90 67.67 10.65 -62.90 67.67 10.65
20 51K 51K N CA 407 408 -31.70 -40.80 -40.80
21 4379 67Y 68Q C N 534 536 62.18 55.10 12.85 1.50 -121.10 -162.28 9.30
21 68Q 68Q N CA 536 537 51.03 40.30 139.70
22 4388 76A 77Y C N 617 619 -119.77 -63.50 91.59 12.63 -63.50 91.59 12.63
22 77Y 77Y N CA 619 620 28.86 -43.40 -43.40
23 4390 78R 79K C N 640 642 -152.79 -118.00 102.79 5.30 -62.90 122.47 15.09
23 79K 79K N CA 642 643 42.38 139.10 -40.80
24 4398 86F 87S C N 706 708 -103.61 -136.60 85.47 3.52 -64.10 114.39 7.05
24 87S 87S N CA 708 709 72.35 151.20 -35.00
25 4407 95A 96L C N 768 770 42.89 -70.70 125.07 9.37 -63.50 168.34 29.75
25 96L 96L N CA 770 771 89.26 141.60 -41.20
26 4408 96L 97Q C N 776 778 -147.95 -121.10 40.55 1.35 -63.80 171.66 29.57
26 97Q 97Q N CA 778 779 170.08 139.70 -40.30
27 4409 97Q 98Q C N 785 787 -116.15 -121.10 25.89 1.30 -63.80 163.21 26.78
27 98Q 98Q N CA 787 788 165.11 139.70 -40.30
28 4411 99I 100K C N 802 804 -64.42 -70.20 7.46 0.45 -62.90 176.48 22.84
28 100K 100K N CA 804 805 135.68 140.40 -40.80
29 4412 100K 101E C N 811 813 -109.16 -117.80 14.96 0.82 -63.60 176.66 26.13
29 101E 101E N CA 813 814 149.01 136.80 -40.30
30 4413 101E 102R C N 820 822 -63.52 -72.10 8.60 0.65 -63.00 177.45 24.01
30 102R 102R N CA 822 823 141.45 141.90 -41.10
31 4414 102R 103G C N 831 833 122.29 78.70 43.68 2.14 82.20 -178.16 6.82
31 103G 103G N CA 833 834 -168.87 -166.10 8.50
32 4415 103G 104A C N 835 837 -67.92 -68.20 2.56 0.22 -62.50 171.34 28.35
32 104A 104A N CA 837 838 147.85 145.30 -40.90
33 4416 104A 105L C N 840 842 -78.56 -70.70 13.69 1.32 -63.50 172.26 23.10
33 105L 105L N CA 842 843 130.40 141.60 -41.20
34 4418 106P 107M C N 855 857 -102.95 -125.60 25.89 0.77 -63.40 173.03 23.06
34 107M 107M N CA 857 858 127.95 140.50 -40.50
35 4420 108I 109D C N 871 873 -72.12 -70.90 5.05 0.19 -63.30 165.04 20.91
35 109D 109D N CA 873 874 155.20 150.30 -40.00
36 4421 109D 110R C N 879 881 -104.61 -125.20 93.32 4.01 -72.10 97.87 8.16
36 110R 110R N CA 881 882 49.58 140.60 141.90
37 4422 110R 111G C N 890 892 89.97 78.70 33.63 0.55 -62.40 -141.52 30.71
37 111G 111G N CA 892 893 162.22 -166.10 -41.20
38 4442 130A 131G C N 1039 1041 133.49 78.70 80.27 1.70 -62.40 -119.04 33.70
38 131G 131G N CA 1041 1042 135.24 -166.10 -41.20
39 4443 131G 132Y C N 1043 1045 -141.29 -124.30 93.72 4.28 -63.50 118.22 22.18
39 132Y 132Y N CA 1045 1046 -132.43 135.40 -43.40
40 4444 132Y 133G C N 1055 1057 -57.18 -62.40 5.56 0.90 82.20 148.64 11.36
40 133G 133G N CA 1057 1058 -43.13 -41.20 8.50
41 4445 133G 134Q C N 1059 1061 -92.62 -73.00 23.81 1.86 -63.80 169.96 23.57
41 134Q 134Q N CA 1061 1062 127.20 140.70 -40.30
42 4446 134Q 135F C N 1068 1070 -95.45 -71.40 36.16 3.19 -63.20 161.26 20.33
42 135F 135F N CA 1070 1071 113.70 140.70 -44.30
43 4457 145K 146F C N 1156 1158 58.54 58.10 1.91 0.12 -63.20 143.17 25.81
43 146F 146F N CA 1158 1159 31.04 32.90 -44.30
44 4461 149A 150G C N 1190 1192 33.33 78.70 92.73 1.39 -62.40 105.37 16.58
44 150G 150G N CA 1192 1193 -85.23 -166.10 -41.20
45 4466 154R 155E C N 1223 1225 61.64 54.60 11.89 0.63 -63.60 145.03 24.95
45 155E 155E N CA 1225 1226 32.82 42.40 -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 12409 50R 125A O CA 406 1007 17.51 3.00 14.51 48.36 3.00 14.51 48.36
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 37 40 141 153 187 185 170 222 237 270
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
LYS_LAMBD.B99990001.pdb 2335.63672
LYS_LAMBD.B99990002.pdb 2196.60327