Задание 8. Гомологичное моделирование комплекса белка с лигандом¶
Загружаем модули и данные.
In [1]:
import sys
import modeller
import _modeller
import modeller.automodel
In [2]:
env = modeller.environ()
env.io.hetatm = True
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux LAPTOP-EFAVKRV4 4.4.0-18362-Microsoft x86_64
Date and time of compilation : 2020/04/06 19:06:24
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2020/04/16 21:58:42
Скачаем модель белка-заготовки 1LMP и последовательность моделируемого белка LYS_LAMBD (P03706)
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
! wget https://www.uniprot.org/uniprot/P03706.fasta
Will not apply HSTS. The HSTS database must be a regular and non-world-writable file. ERROR: could not open HSTS store at '/home/dmitry/.wget-hsts'. HSTS will be disabled. --2020-04-16 22:00:06-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-04-16 22:00:07-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: http://files.rcsb.org/view/1lmp.pdb [following] --2020-04-16 22:00:08-- http://files.rcsb.org/view/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 128.6.244.12 Connecting to files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb’ 1lmp.pdb [ <=> ] 127.35K 185KB/s in 0.7s 2020-04-16 22:00:09 (185 KB/s) - ‘1lmp.pdb’ saved [130410] Will not apply HSTS. The HSTS database must be a regular and non-world-writable file. ERROR: could not open HSTS store at '/home/dmitry/.wget-hsts'. HSTS will be disabled. --2020-04-16 22:00:09-- https://www.uniprot.org/uniprot/P03706.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected. HTTP request sent, awaiting response... 200 Length: 246 [text/plain] Saving to: ‘P03706.fasta’ P03706.fasta 100%[===================>] 246 --.-KB/s in 0s 2020-04-16 22:00:10 (3.40 MB/s) - ‘P03706.fasta’ saved [246/246]
Создание модели¶
In [5]:
# Создаём объект выравнивания.
alignm = modeller.alignment(env)
# Загружаем туда последовательность целевого белка.
alignm.append(file='P03706.fasta', align_codes='all', alignment_format='FASTA')
# Создаём модель заготовки.
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
# Добавляем её в выравнивание.
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
# Добавляем идентификаторы.
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
# Делаем выравнивание.
alignm.salign()
# Сохраняем в файл.
alignm.write(file='all_in_one.ali', alignment_format='PIR')
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.
rdpdb___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.
SALIGN_____> adding the next group to the alignment; iteration 1
In [6]:
! cat all_in_one.ali
>P1;seq sequence:: : : : :::-1.00:-1.00 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG GTVREIDV* >P1;pdb 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 DDGRTPGAKNVCGIRCSQLLTDDLT---------------VAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYV AGCGV...*
Видим в белке-заготовке гэпы. Это нормально, так как его длина 129 АК, а у целевого белка длина 158 АК. На первый взгляд очень сложно найти участи точно совпадающих АК, но, в целом, видны участки схожик АК.
In [7]:
# Выбираем объект для моделирования.
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq pdb
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
transfe_404W> At least one template is aligned with model residue 156:
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 157:
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.
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 45 (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.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12085 10969
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 : 158
Number of all, selected real atoms : 1257 1257
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10969 10969
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3175
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 : 1573.7255
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 0.007 0.007 19.514 1.000
2 Bond angle potential : 1726 0 8 2.244 2.244 170.17 1.000
3 Stereochemical cosine torsion poten: 789 0 42 50.294 50.294 314.28 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.342 1.342 19.703 1.000
5 Soft-sphere overlap restraints : 3175 0 0 0.005 0.005 8.7388 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) : 2406 6 22 0.729 0.729 246.08 1.000
10 Distance restraints 2 (N-O) : 2593 8 43 0.765 0.765 374.30 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 157 0 3 5.190 5.190 49.877 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 5 80.861 80.861 48.307 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 3 71.608 71.608 54.805 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 82.188 82.188 35.672 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 87.935 87.935 17.539 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) : 895 0 0 0.414 0.414 16.163 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 33 39.497 85.859 182.18 1.000
26 Distance restraints 4 (SDCH-SDCH) : 141 0 1 1.241 1.241 16.394 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 21936.3613
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 5121 6N 153V CA CA 42 1208 9.44 4.92 4.52 7.90 4.92 4.52 7.90
2 5151 7Q 153V CA CA 50 1208 11.89 7.94 3.94 4.52 7.94 3.94 4.52
-------------------------------------------------------------------------------------------------
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 7773 36I 17W N O 287 144 8.06 4.62 3.44 4.84 4.62 3.44 4.84
2 8300 56N 158V N O 446 1256 13.36 8.62 4.73 5.31 8.62 4.73 5.31
3 8314 57P 158V N O 454 1256 13.04 8.17 4.87 6.56 8.17 4.87 6.56
4 8322 58K 158V N O 461 1256 15.03 9.76 5.27 4.66 9.76 5.27 4.66
5 8360 61S 158V N O 487 1256 13.99 9.99 4.00 5.18 9.99 4.00 5.18
6 8384 62T 158V N O 493 1256 11.75 8.19 3.56 5.21 8.19 3.56 5.21
7 8410 63G 158V N O 500 1256 9.43 6.08 3.34 5.95 6.08 3.34 5.95
-------------------------------------------------------------------------------------------------
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 77.53 55.40 24.98 1.93 -62.50 155.45 31.59
1 16A 16A N CA 126 127 26.61 38.20 -40.90
2 4330 18S 19E C N 149 151 55.14 54.60 14.78 1.09 -63.60 136.80 23.54
2 19E 19E N CA 151 152 27.63 42.40 -40.30
3 4332 20G 21T C N 162 164 48.39 55.90 7.61 0.79 -124.80 -158.62 7.62
3 21T 21T N CA 164 165 40.74 39.50 143.50
4 4336 24G 25R C N 189 191 -171.61 -63.00 115.98 20.92 -63.00 115.98 20.92
4 25R 25R N CA 191 192 -81.77 -41.10 -41.10
5 4337 25R 26Q C N 200 202 -147.16 -121.10 42.86 1.48 -63.80 168.10 29.00
5 26Q 26Q N CA 202 203 173.73 139.70 -40.30
6 4338 26Q 27K C N 209 211 -179.76 -62.90 118.55 18.45 -62.90 118.55 18.45
6 27K 27K N CA 211 212 -20.88 -40.80 -40.80
7 4339 27K 28T C N 218 220 -68.91 -78.10 9.35 0.60 -63.20 166.44 21.72
7 28T 28T N CA 220 221 151.55 149.80 -42.10
8 4340 28T 29R C N 225 227 -61.59 -72.10 12.74 1.10 -63.00 169.81 22.85
8 29R 29R N CA 227 228 149.10 141.90 -41.10
9 4341 29R 30N C N 236 238 -154.72 -119.90 87.01 3.07 -63.20 137.16 21.98
9 30N 30N N CA 238 239 -143.26 137.00 -41.10
10 4343 31H 32G C N 254 256 -163.94 -167.20 10.06 0.41 82.20 -150.71 15.14
10 32G 32G N CA 256 257 -175.89 174.60 8.50
11 4344 32G 33Y C N 258 260 26.33 -98.40 127.00 5.71 -63.50 173.04 31.73
11 33Y 33Y N CA 260 261 104.50 128.40 -43.40
12 4345 33Y 34D C N 270 272 -158.38 -96.50 63.45 2.58 -63.30 169.39 18.12
12 34D 34D N CA 272 273 100.18 114.20 -40.00
13 4347 35V 36I C N 285 287 -55.30 -120.60 85.33 3.81 -63.40 119.25 19.83
13 36I 36I N CA 287 288 75.37 130.30 -43.60
14 4348 36I 37V C N 293 295 -56.14 -125.40 72.54 2.20 -62.40 164.24 21.15
14 37V 37V N CA 295 296 121.73 143.30 -42.40
15 4358 46S 47D C N 369 371 -139.11 -63.30 91.18 11.25 -63.30 91.18 11.25
15 47D 47D N CA 371 372 10.66 -40.00 -40.00
16 4388 76A 77Y C N 617 619 -124.65 -63.50 86.59 12.04 -63.50 86.59 12.04
16 77Y 77Y N CA 619 620 17.90 -43.40 -43.40
17 4390 78R 79K C N 640 642 -135.27 -62.90 91.23 11.65 -62.90 91.23 11.65
17 79K 79K N CA 642 643 14.74 -40.80 -40.80
18 4395 83L 84K C N 678 680 -134.54 -118.00 67.52 3.45 -62.90 135.01 15.57
18 84K 84K N CA 680 681 73.64 139.10 -40.80
19 4396 84K 85D C N 687 689 -43.79 -96.50 58.15 2.40 54.50 109.71 9.49
19 85D 85D N CA 689 690 89.64 114.20 40.90
20 4398 86F 87S C N 706 708 -100.85 -72.40 78.05 5.55 -64.10 120.46 7.42
20 87S 87S N CA 708 709 79.72 152.40 -35.00
21 4411 99I 100K C N 802 804 -119.11 -118.00 64.03 3.09 -62.90 128.97 20.11
21 100K 100K N CA 804 805 -156.87 139.10 -40.80
22 4412 100K 101E C N 811 813 -129.23 -117.80 11.94 0.53 -63.60 -174.36 21.89
22 101E 101E N CA 813 814 133.34 136.80 -40.30
23 4413 101E 102R C N 820 822 -79.48 -72.10 8.10 0.55 -63.00 174.43 24.69
23 102R 102R N CA 822 823 145.26 141.90 -41.10
24 4414 102R 103G C N 831 833 74.24 78.70 18.82 0.72 82.20 167.30 7.72
24 103G 103G N CA 833 834 175.61 -166.10 8.50
25 4415 103G 104A C N 835 837 -153.11 -134.00 20.28 0.47 -62.50 -171.49 35.73
25 104A 104A N CA 837 838 153.80 147.00 -40.90
26 4416 104A 105L C N 840 842 -66.85 -70.70 19.38 1.33 -63.50 163.84 22.56
26 105L 105L N CA 842 843 122.61 141.60 -41.20
27 4418 106P 107M C N 855 857 178.79 -125.60 60.72 1.87 -63.40 -165.61 37.84
27 107M 107M N CA 857 858 164.88 140.50 -40.50
28 4420 108I 109D C N 871 873 -113.99 -70.90 44.76 2.91 -63.30 165.53 23.71
28 109D 109D N CA 873 874 162.42 150.30 -40.00
29 4421 109D 110R C N 879 881 -73.52 -72.10 15.97 1.20 -63.00 161.43 22.52
29 110R 110R N CA 881 882 157.81 141.90 -41.10
30 4422 110R 111G C N 890 892 105.35 78.70 79.05 1.28 82.20 113.36 6.64
30 111G 111G N CA 892 893 119.47 -166.10 8.50
31 4425 113I 114R C N 910 912 -140.93 -125.20 26.27 1.46 -63.00 178.55 20.33
31 114R 114R N CA 912 913 119.55 140.60 -41.10
32 4426 114R 115Q C N 921 923 -132.56 -121.10 28.76 1.14 -63.80 168.31 28.35
32 115Q 115Q N CA 923 924 166.08 139.70 -40.30
33 4440 128P 129G C N 1030 1032 -101.05 -62.40 110.55 15.13 82.20 -175.22 13.94
33 129G 129G N CA 1032 1033 62.37 -41.20 8.50
34 4441 129G 130A C N 1034 1036 -63.16 -68.20 6.75 0.43 -62.50 178.30 29.25
34 130A 130A N CA 1036 1037 140.80 145.30 -40.90
35 4454 142L 143I C N 1134 1136 26.74 -97.30 128.51 6.59 -63.40 164.18 30.12
35 143I 143I N CA 1136 1137 93.62 127.20 -43.60
36 4455 143I 144A C N 1142 1144 -162.85 -134.00 33.49 0.78 -68.20 96.48 7.52
36 144A 144A N CA 1144 1145 163.99 147.00 145.30
37 4457 145K 146F C N 1156 1158 -113.64 -124.20 92.66 4.10 -63.20 108.04 12.34
37 146F 146F N CA 1158 1159 51.24 143.30 -44.30
38 4462 150G 151G C N 1194 1196 72.73 78.70 29.10 0.59 82.20 146.43 7.58
38 151G 151G N CA 1196 1197 -137.62 -166.10 8.50
39 4464 152T 153V C N 1205 1207 -119.95 -125.40 13.87 0.53 -62.40 -177.73 20.42
39 153V 153V N CA 1207 1208 130.55 143.30 -42.40
40 4466 154R 155E C N 1223 1225 -169.10 -117.80 65.30 1.98 -63.60 177.31 29.31
40 155E 155E N CA 1225 1226 177.19 136.80 -40.30
41 4468 156I 157D C N 1240 1242 -148.46 -70.90 92.01 4.65 -63.30 147.33 23.56
41 157D 157D N CA 1242 1243 -160.22 150.30 -40.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 32 17 126 111 166 168 195 206 254 249
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 158
Number of all, selected real atoms : 1257 1257
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10969 10969
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3368
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 : 1910.6378
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 6 0.010 0.010 36.525 1.000
2 Bond angle potential : 1726 0 9 2.363 2.363 184.84 1.000
3 Stereochemical cosine torsion poten: 789 0 54 52.295 52.295 333.32 1.000
4 Stereochemical improper torsion pot: 515 0 1 1.509 1.509 25.167 1.000
5 Soft-sphere overlap restraints : 3368 0 0 0.007 0.007 16.876 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) : 2406 6 36 0.841 0.841 363.51 1.000
10 Distance restraints 2 (N-O) : 2593 12 46 0.837 0.837 510.20 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 5 5.043 5.043 47.094 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 1 81.658 81.658 48.533 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 1 70.280 70.280 46.540 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 80.728 80.728 38.024 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 83.048 83.048 17.579 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) : 895 0 0 0.379 0.379 14.363 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 38 40.035 93.960 212.55 1.000
26 Distance restraints 4 (SDCH-SDCH) : 141 0 2 1.354 1.354 15.513 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 23815.6758
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 5121 6N 153V CA CA 42 1208 8.25 4.92 3.33 5.82 4.92 3.33 5.82
2 5436 17W 36I CA CA 132 288 10.61 6.28 4.33 5.78 6.28 4.33 5.78
3 5467 18S 36I CA CA 146 288 9.18 4.31 4.86 6.18 4.31 4.86 6.18
-------------------------------------------------------------------------------------------------
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 7685 19E 23N N O 151 186 7.14 2.87 4.27 5.08 2.87 4.27 5.08
2 7773 36I 17W N O 287 144 9.43 4.62 4.81 6.78 4.62 4.81 6.78
3 8284 55L 158V N O 438 1256 13.29 8.18 5.12 5.64 8.18 5.12 5.64
4 8300 56N 158V N O 446 1256 14.72 8.62 6.09 6.84 8.62 6.09 6.84
5 8314 57P 158V N O 454 1256 14.20 8.17 6.03 8.12 8.17 6.03 8.12
6 8322 58K 158V N O 461 1256 16.48 9.76 6.72 5.94 9.76 6.72 5.94
7 8331 59L 158V N O 470 1256 16.89 10.84 6.04 5.88 10.84 6.04 5.88
8 8360 61S 158V N O 487 1256 15.76 9.99 5.77 7.46 9.99 5.77 7.46
9 8384 62T 158V N O 493 1256 13.57 8.19 5.39 7.87 8.19 5.39 7.87
10 8410 63G 158V N O 500 1256 11.32 6.08 5.24 9.32 6.08 5.24 9.32
11 8666 71S 158V N O 561 1256 11.35 8.00 3.35 4.99 8.00 3.35 4.99
-------------------------------------------------------------------------------------------------
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 78.38 55.40 24.12 2.18 -62.50 158.11 32.15
1 16A 16A N CA 126 127 30.88 38.20 -40.90
2 4329 17W 18S C N 143 145 -58.03 -64.10 7.24 0.69 -136.60 -172.86 10.57
2 18S 18S N CA 145 146 -38.95 -35.00 151.20
3 4330 18S 19E C N 149 151 -130.35 -117.80 72.90 3.85 -63.60 124.67 14.40
3 19E 19E N CA 151 152 64.99 136.80 -40.30
4 4332 20G 21T C N 162 164 55.57 55.90 9.18 0.67 -124.80 -147.69 12.87
4 21T 21T N CA 164 165 30.32 39.50 143.50
5 4336 24G 25R C N 189 191 -173.29 -125.20 68.25 2.09 -63.00 170.38 30.08
5 25R 25R N CA 191 192 -170.97 140.60 -41.10
6 4337 25R 26Q C N 200 202 -160.63 -121.10 40.62 1.73 -63.80 -163.80 25.22
6 26Q 26Q N CA 202 203 130.34 139.70 -40.30
7 4338 26Q 27K C N 209 211 -165.12 -118.00 47.42 1.88 -62.90 -157.65 23.28
7 27K 27K N CA 211 212 133.83 139.10 -40.80
8 4339 27K 28T C N 218 220 -158.75 -124.80 75.20 2.39 -63.20 143.68 24.17
8 28T 28T N CA 220 221 -149.40 143.50 -42.10
9 4340 28T 29R C N 225 227 -143.20 -125.20 35.04 1.23 -63.00 168.54 28.19
9 29R 29R N CA 227 228 170.66 140.60 -41.10
10 4341 29R 30N C N 236 238 55.68 55.90 14.24 0.98 -63.20 152.07 24.88
10 30N 30N N CA 238 239 53.73 39.50 -41.10
11 4342 30N 31H C N 244 246 -126.56 -125.60 36.20 1.36 -63.20 156.15 23.66
11 31H 31H N CA 246 247 174.99 138.80 -42.30
12 4343 31H 32G C N 254 256 -78.37 -80.20 10.10 0.49 82.20 -122.11 7.11
12 32G 32G N CA 256 257 -175.97 174.10 8.50
13 4344 32G 33Y C N 258 260 -72.62 -98.40 34.42 2.73 -63.50 149.27 23.22
13 33Y 33Y N CA 260 261 105.59 128.40 -43.40
14 4345 33Y 34D C N 270 272 -173.73 -96.50 77.35 3.15 -63.30 -173.78 20.07
14 34D 34D N CA 272 273 109.94 114.20 -40.00
15 4347 35V 36I C N 285 287 -99.02 -120.60 72.79 4.97 -63.40 121.90 21.29
15 36I 36I N CA 287 288 -160.18 130.30 -43.60
16 4348 36I 37V C N 293 295 142.27 -125.40 95.86 4.52 -62.40 -137.06 25.57
16 37V 37V N CA 295 296 117.52 143.30 -42.40
17 4349 37V 38G C N 300 302 -64.74 -62.40 7.31 1.01 82.20 153.05 11.50
17 38G 38G N CA 302 303 -34.28 -41.20 8.50
18 4358 46S 47D C N 369 371 -137.97 -63.30 81.54 10.97 -63.30 81.54 10.97
18 47D 47D N CA 371 372 -7.23 -40.00 -40.00
19 4368 56N 57P C N 452 454 -75.69 -58.70 39.96 2.34 -64.50 141.97 11.19
19 57P 57P N CA 454 455 5.67 -30.50 147.20
20 4369 57P 58K C N 459 461 79.03 -62.90 141.96 23.38 -62.90 141.96 23.38
20 58K 58K N CA 461 462 -38.11 -40.80 -40.80
21 4379 67Y 68Q C N 534 536 60.23 55.10 12.91 1.36 -121.10 -161.04 9.33
21 68Q 68Q N CA 536 537 52.15 40.30 139.70
22 4388 76A 77Y C N 617 619 -124.44 -63.50 89.19 12.36 -63.50 89.19 12.36
22 77Y 77Y N CA 619 620 21.73 -43.40 -43.40
23 4390 78R 79K C N 640 642 -153.42 -62.90 105.92 14.16 -62.90 105.92 14.16
23 79K 79K N CA 642 643 14.20 -40.80 -40.80
24 4398 86F 87S C N 706 708 -95.20 -72.40 77.30 5.33 -64.10 117.73 7.30
24 87S 87S N CA 708 709 78.54 152.40 -35.00
25 4411 99I 100K C N 802 804 -74.22 -118.00 79.52 4.11 -62.90 114.27 15.48
25 100K 100K N CA 804 805 -154.51 139.10 -40.80
26 4412 100K 101E C N 811 813 -118.91 -117.80 32.74 1.63 -63.60 160.04 24.46
26 101E 101E N CA 813 814 169.52 136.80 -40.30
27 4413 101E 102R C N 820 822 -119.10 -125.20 16.08 0.88 -63.00 172.78 27.21
27 102R 102R N CA 822 823 155.48 140.60 -41.10
28 4414 102R 103G C N 831 833 -170.28 -167.20 37.67 1.51 82.20 167.58 12.60
28 103G 103G N CA 833 834 137.05 174.60 8.50
29 4415 103G 104A C N 835 837 -108.11 -134.00 44.93 1.64 -62.50 157.90 24.09
29 104A 104A N CA 837 838 110.27 147.00 -40.90
30 4416 104A 105L C N 840 842 -172.84 -108.50 75.47 3.33 -63.50 -176.91 32.03
30 105L 105L N CA 842 843 171.94 132.50 -41.20
31 4418 106P 107M C N 855 857 -133.30 -125.60 20.16 0.78 -63.40 174.94 31.64
31 107M 107M N CA 857 858 159.13 140.50 -40.50
32 4422 110R 111G C N 890 892 -144.00 -167.20 64.44 2.12 82.20 170.68 13.29
32 111G 111G N CA 892 893 114.48 174.60 8.50
33 4423 111G 112D C N 894 896 -104.06 -96.50 24.56 1.02 -63.30 137.04 14.94
33 112D 112D N CA 896 897 90.84 114.20 -40.00
34 4425 113I 114R C N 910 912 -140.83 -125.20 20.89 1.14 -63.00 -175.00 21.13
34 114R 114R N CA 912 913 126.74 140.60 -41.10
35 4426 114R 115Q C N 921 923 -154.82 -121.10 57.65 3.01 -63.80 161.37 20.68
35 115Q 115Q N CA 923 924 92.94 139.70 -40.30
36 4439 127L 128P C N 1023 1025 -66.38 -64.50 1.94 0.18 -58.70 178.34 14.12
36 128P 128P N CA 1025 1026 147.67 147.20 -30.50
37 4441 129G 130A C N 1034 1036 -53.53 -68.20 15.62 1.13 -62.50 179.39 28.97
37 130A 130A N CA 1036 1037 139.93 145.30 -40.90
38 4454 142L 143I C N 1134 1136 24.98 -97.30 126.51 6.45 -63.40 164.20 30.07
38 143I 143I N CA 1136 1137 94.79 127.20 -43.60
39 4455 143I 144A C N 1142 1144 -164.77 -134.00 33.79 0.77 -68.20 97.83 7.74
39 144A 144A N CA 1144 1145 160.96 147.00 145.30
40 4457 145K 146F C N 1156 1158 -105.10 -124.20 91.83 3.82 -63.20 106.38 12.39
40 146F 146F N CA 1158 1159 53.48 143.30 -44.30
41 4461 149A 150G C N 1190 1192 138.77 78.70 81.15 1.98 -62.40 -120.34 43.98
41 150G 150G N CA 1192 1193 139.33 -166.10 -41.20
42 4463 151G 152T C N 1198 1200 -45.98 -78.10 56.73 1.89 -63.20 146.16 19.89
42 152T 152T N CA 1200 1201 103.04 149.80 -42.10
43 4464 152T 153V C N 1205 1207 -125.10 -62.40 96.86 10.89 -62.40 96.86 10.89
43 153V 153V N CA 1207 1208 31.44 -42.40 -42.40
44 4466 154R 155E C N 1223 1225 -170.43 -117.80 67.33 2.04 -63.60 176.83 29.30
44 155E 155E N CA 1225 1226 178.79 136.80 -40.30
45 4468 156I 157D C N 1240 1242 175.92 -96.50 106.13 4.41 -63.30 -170.63 30.88
45 157D 157D N CA 1242 1243 174.15 114.20 -40.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 26 36 146 129 187 167 187 218 235 267
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 1573.72546
seq.B99990002.pdb 1910.63782
Modeller нам написал кучу сообщений о результатах работы, пока что разбирать не будем, а посмотрим на результат. nglview был капризным, да ещё и в другой среды конды, поэтому просто нарисуем в pymol.
In [9]:
from IPython.display import display, Image
In [13]:
def show_model(pdb_1, pdb_2):
command = f"load {pdb_1}, model_1; load {pdb_2}, model_2; " \
f"util.cbag model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 3; set antialias, 2; bg_color white; " \
f"png tmp.png"
! pymol -Qcd "$command"
display(Image('tmp.png'))
In [14]:
show_model('seq.B99990001.pdb', '1lmp.pdb')
In [15]:
show_model('seq.B99990001.pdb', '1lmp.pdb')
Видим, что в целом вторичные структуры соответствуют друг другу, но достаточно сильно смещены. Петли смоделированы близко к заготовке. Но у нас нет лиганда в целевом белке! Его надо добавить.
Как это сделать? Делаем химерную последовательность целевого белка: берём все остатки из последовательности целевого белка и добавляем последние 3 остатка (лиганды) и белка-заготовки.
In [16]:
seq_liganded = ''
for res in alignm[0].residues:
seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'seq_liganded'
del alignm[0]
In [17]:
# Делаем выравнивание.
alignm.salign()
# Сохраняем в файл.
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [18]:
# Смотрим на выравнивание.
! cat all_in_one2.ali
>P1;pdb 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...* >P1;seq_liganded sequence::1 : :+161 : :undefined:undefined:-1.00:-1.00 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWD AYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAG GTVREIDV...*
Теперь у обеих последовательностей видим 3 точки на конце, что говорит нам о том, что в обеих последовательностях есть лиганд.
In [19]:
# Выбираем объект для моделирования.
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_liganded pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 158
atom names : C +N
atom indices : 1255 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 158
atom names : C CA +N O
atom indices : 1255 1251 0 1256
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 (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.
>> 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): 3350
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 : 1368.4260
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 11.467 1.000
2 Bond angle potential : 1726 1 8 2.382 2.382 190.63 1.000
3 Stereochemical cosine torsion poten: 789 0 41 50.128 50.128 310.67 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.524 1.524 25.367 1.000
5 Soft-sphere overlap restraints : 3350 2 2 0.008 0.008 24.562 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 0.351 0.351 94.915 1.000
10 Distance restraints 2 (N-O) : 2568 0 15 0.529 0.529 227.03 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 157 0 8 5.982 5.982 66.259 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 8 85.246 85.246 66.401 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 2 88.924 88.924 59.794 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 74.659 74.659 28.508 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 47.242 47.242 12.495 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 0.447 0.447 20.705 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 46 35 39.962 89.085 192.30 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 1 1.038 1.038 18.747 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.039 0.039 18.578 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_liganded.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: 22795.1230
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 454 455 135.25 108.20 27.05 6.15 108.20 27.05 6.15
-------------------------------------------------------------------------------------------------
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 -70.31 -63.40 22.63 3.96 -120.60 172.06 11.72
1 4I 4I N CA 25 26 -65.15 -43.60 130.30
2 4316 4I 5N C N 31 33 179.50 -63.20 119.96 19.13 -63.20 119.96 19.13
2 5N 5N N CA 33 34 -66.19 -41.10 -41.10
3 4327 15L 16A C N 124 126 78.64 55.40 28.62 1.89 -62.50 154.32 31.33
3 16A 16A N CA 126 127 21.50 38.20 -40.90
4 4329 17W 18S C N 143 145 -52.91 -64.10 12.56 1.30 -136.60 -172.23 10.63
4 18S 18S N CA 145 146 -40.71 -35.00 151.20
5 4332 20G 21T C N 162 164 53.56 55.90 20.16 1.24 -124.80 -162.85 7.99
5 21T 21T N CA 164 165 59.52 39.50 143.50
6 4335 23N 24G C N 185 187 -85.56 -80.20 14.63 0.35 82.20 -114.52 7.42
6 24G 24G N CA 187 188 -172.29 174.10 8.50
7 4336 24G 25R C N 189 191 56.21 57.30 35.19 2.24 -63.00 165.13 29.65
7 25R 25R N CA 191 192 73.17 38.00 -41.10
8 4337 25R 26Q C N 200 202 -56.82 -73.00 17.66 1.36 -63.80 172.05 24.94
8 26Q 26Q N CA 202 203 147.79 140.70 -40.30
9 4338 26Q 27K C N 209 211 -136.44 -118.00 20.90 0.69 -62.90 -174.54 28.49
9 27K 27K N CA 211 212 148.94 139.10 -40.80
10 4339 27K 28T C N 218 220 -102.13 -78.10 45.64 1.50 -63.20 135.02 19.91
10 28T 28T N CA 220 221 -171.39 149.80 -42.10
11 4340 28T 29R C N 225 227 -110.03 -125.20 21.55 0.66 -63.00 172.91 20.62
11 29R 29R N CA 227 228 125.29 140.60 -41.10
12 4341 29R 30N C N 236 238 -158.95 -119.90 67.73 2.11 -63.20 158.70 25.02
12 30N 30N N CA 238 239 -167.66 137.00 -41.10
13 4342 30N 31H C N 244 246 -119.04 -125.60 35.79 1.47 -63.20 154.18 22.93
13 31H 31H N CA 246 247 173.99 138.80 -42.30
14 4344 32G 33Y C N 258 260 -120.69 -124.30 10.60 0.43 -63.50 178.26 25.65
14 33Y 33Y N CA 260 261 125.44 135.40 -43.40
15 4345 33Y 34D C N 270 272 -143.83 -96.50 65.00 2.72 -63.30 -179.76 27.44
15 34D 34D N CA 272 273 158.76 114.20 -40.00
16 4347 35V 36I C N 285 287 -98.02 -120.60 33.27 1.40 -63.40 153.43 24.06
16 36I 36I N CA 287 288 105.87 130.30 -43.60
17 4358 46S 47D C N 369 371 -139.32 -63.30 90.14 11.24 -63.30 90.14 11.24
17 47D 47D N CA 371 372 8.44 -40.00 -40.00
18 4368 56N 57P C N 452 454 -76.17 -58.70 41.21 2.41 -64.50 140.86 11.14
18 57P 57P N CA 454 455 6.82 -30.50 147.20
19 4369 57P 58K C N 459 461 80.64 -62.90 145.17 22.74 -62.90 145.17 22.74
19 58K 58K N CA 461 462 -62.52 -40.80 -40.80
20 4379 67Y 68Q C N 534 536 58.92 55.10 13.82 1.32 -121.10 -160.48 9.32
20 68Q 68Q N CA 536 537 53.58 40.30 139.70
21 4388 76A 77Y C N 617 619 -123.97 -63.50 93.28 12.88 -63.50 93.28 12.88
21 77Y 77Y N CA 619 620 27.62 -43.40 -43.40
22 4390 78R 79K C N 640 642 -147.22 -62.90 108.61 13.72 -62.90 108.61 13.72
22 79K 79K N CA 642 643 27.65 -40.80 -40.80
23 4395 83L 84K C N 678 680 -133.40 -118.00 48.92 2.52 -62.90 150.95 17.34
23 84K 84K N CA 680 681 92.67 139.10 -40.80
24 4396 84K 85D C N 687 689 -47.95 -63.30 15.42 2.51 54.50 129.59 16.58
24 85D 85D N CA 689 690 -38.45 -40.00 40.90
25 4397 85D 86F C N 695 697 76.37 -63.20 145.41 20.80 -63.20 145.41 20.80
25 86F 86F N CA 697 698 -85.09 -44.30 -44.30
26 4398 86F 87S C N 706 708 -91.43 -72.40 78.23 5.26 -64.10 114.83 7.17
26 87S 87S N CA 708 709 76.53 152.40 -35.00
27 4407 95A 96L C N 768 770 50.47 -70.70 123.54 10.37 -63.50 -164.64 34.04
27 96L 96L N CA 770 771 117.48 141.60 -41.20
28 4408 96L 97Q C N 776 778 -143.49 -121.10 36.86 1.28 -63.80 170.48 29.19
28 97Q 97Q N CA 778 779 168.98 139.70 -40.30
29 4409 97Q 98Q C N 785 787 -125.16 -121.10 36.11 1.65 -63.80 156.64 26.26
29 98Q 98Q N CA 787 788 175.58 139.70 -40.30
30 4411 99I 100K C N 802 804 -156.56 -118.00 64.05 2.40 -62.90 159.38 26.21
30 100K 100K N CA 804 805 -169.76 139.10 -40.80
31 4412 100K 101E C N 811 813 -66.55 -69.30 16.66 1.36 -63.60 160.80 21.60
31 101E 101E N CA 813 814 158.93 142.50 -40.30
32 4413 101E 102R C N 820 822 -58.60 -72.10 16.46 1.08 -63.00 173.63 23.75
32 102R 102R N CA 822 823 132.48 141.90 -41.10
33 4414 102R 103G C N 831 833 151.91 -167.20 63.63 2.46 82.20 136.49 9.72
33 103G 103G N CA 833 834 125.85 174.60 8.50
34 4417 105L 106P C N 848 850 -67.09 -58.70 14.06 0.87 -64.50 166.44 12.56
34 106P 106P N CA 850 851 -19.22 -30.50 147.20
35 4418 106P 107M C N 855 857 -76.43 -73.00 20.86 1.36 -63.40 156.47 24.39
35 107M 107M N CA 857 858 163.57 143.00 -40.50
36 4420 108I 109D C N 871 873 -74.89 -70.90 14.05 0.52 -63.30 156.66 20.06
36 109D 109D N CA 873 874 163.77 150.30 -40.00
37 4424 112D 113I C N 902 904 -107.06 -63.40 90.34 13.75 -63.40 90.34 13.75
37 113I 113I N CA 904 905 35.48 -43.60 -43.60
38 4442 130A 131G C N 1039 1041 51.96 78.70 30.88 1.73 -62.40 -178.96 24.99
38 131G 131G N CA 1041 1042 178.46 -166.10 -41.20
39 4443 131G 132Y C N 1043 1045 -153.66 -124.30 30.04 2.04 -63.50 -163.24 35.61
39 132Y 132Y N CA 1045 1046 141.71 135.40 -43.40
40 4444 132Y 133G C N 1055 1057 52.00 78.70 72.03 1.12 82.20 111.86 6.88
40 133G 133G N CA 1057 1058 -99.21 -166.10 8.50
41 4445 133G 134Q C N 1059 1061 -80.80 -63.80 74.95 10.21 -63.80 74.95 10.21
41 134Q 134Q N CA 1061 1062 32.70 -40.30 -40.30
42 4446 134Q 135F C N 1068 1070 -160.82 -124.20 54.23 1.49 -63.20 164.50 28.76
42 135F 135F N CA 1070 1071 -176.70 143.30 -44.30
43 4457 145K 146F C N 1156 1158 59.09 58.10 3.53 0.20 -63.20 142.84 25.74
43 146F 146F N CA 1158 1159 29.52 32.90 -44.30
44 4461 149A 150G C N 1190 1192 28.76 78.70 86.37 1.46 -62.40 106.17 16.11
44 150G 150G N CA 1192 1193 -95.63 -166.10 -41.20
45 4465 153V 154R C N 1212 1214 57.60 -72.10 139.67 11.68 -72.10 139.67 11.68
45 154R 154R N CA 1214 1215 -166.28 141.90 141.90
46 4466 154R 155E C N 1223 1225 -77.20 -69.30 65.60 5.28 -63.60 118.46 15.09
46 155E 155E N CA 1225 1226 77.38 142.50 -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 2 26 34 135 116 220 165 192 225 222 251
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 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): 3410
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 : 1416.4287
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 15.106 1.000
2 Bond angle potential : 1726 1 10 2.409 2.409 192.29 1.000
3 Stereochemical cosine torsion poten: 789 0 46 51.492 51.492 331.36 1.000
4 Stereochemical improper torsion pot: 515 0 0 1.548 1.548 25.438 1.000
5 Soft-sphere overlap restraints : 3410 2 2 0.008 0.008 28.387 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 0.463 0.463 130.89 1.000
10 Distance restraints 2 (N-O) : 2568 2 17 0.587 0.587 246.58 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 4 5.340 5.340 52.805 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 4 86.738 86.738 60.907 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 2 82.420 82.420 51.036 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 81.590 81.590 33.396 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 101.787 101.787 18.511 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 0.525 0.525 28.366 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 42 30 37.957 90.941 169.19 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 0 1.007 1.007 14.966 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.037 0.037 17.211 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_liganded.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: 23860.3945
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 454 455 135.41 108.20 27.21 6.18 108.20 27.21 6.18
-------------------------------------------------------------------------------------------------
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 5.21 2.96 2.25 5.04 2.96 2.25 5.04
2 7774 36I 17W N O 287 144 7.91 4.62 3.30 5.29 4.62 3.30 5.29
-------------------------------------------------------------------------------------------------
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 -62.07 -119.90 62.71 3.14 -63.20 157.66 19.65
1 5N 5N N CA 33 34 161.25 137.00 -41.10
2 4317 5N 6N C N 39 41 78.38 55.90 83.56 4.39 -63.20 141.58 21.46
2 6N 6N N CA 41 42 -40.98 39.50 -41.10
3 4327 15L 16A C N 124 126 77.11 55.40 23.14 2.02 -62.50 156.67 31.86
3 16A 16A N CA 126 127 30.19 38.20 -40.90
4 4330 18S 19E C N 149 151 66.60 54.60 31.42 1.65 -63.60 140.82 24.07
4 19E 19E N CA 151 152 13.36 42.40 -40.30
5 4332 20G 21T C N 162 164 45.81 55.90 13.81 0.86 -124.80 -164.93 7.54
5 21T 21T N CA 164 165 48.93 39.50 143.50
6 4335 23N 24G C N 185 187 -73.16 -80.20 28.50 0.79 82.20 -152.21 6.96
6 24G 24G N CA 187 188 146.49 174.10 8.50
7 4336 24G 25R C N 189 191 -157.54 -125.20 32.71 1.19 -63.00 -162.50 33.07
7 25R 25R N CA 191 192 145.50 140.60 -41.10
8 4337 25R 26Q C N 200 202 -154.11 -121.10 34.50 1.51 -63.80 -167.54 24.80
8 26Q 26Q N CA 202 203 129.65 139.70 -40.30
9 4338 26Q 27K C N 209 211 178.09 -118.00 65.24 2.70 -62.90 -155.07 23.84
9 27K 27K N CA 211 212 126.03 139.10 -40.80
10 4339 27K 28T C N 218 220 -111.25 -124.80 18.06 1.09 -63.20 169.42 24.92
10 28T 28T N CA 220 221 155.44 143.50 -42.10
11 4340 28T 29R C N 225 227 -72.79 -72.10 21.80 1.69 -63.00 161.51 21.18
11 29R 29R N CA 227 228 120.11 141.90 -41.10
12 4341 29R 30N C N 236 238 -159.44 -119.90 58.84 1.74 -63.20 168.52 26.33
12 30N 30N N CA 238 239 -179.43 137.00 -41.10
13 4342 30N 31H C N 244 246 -69.52 -67.60 5.25 0.35 -63.20 172.92 22.02
13 31H 31H N CA 246 247 144.89 140.00 -42.30
14 4343 31H 32G C N 254 256 101.13 78.70 51.13 0.76 82.20 140.73 7.77
14 32G 32G N CA 256 257 147.95 -166.10 8.50
15 4344 32G 33Y C N 258 260 -113.75 -98.40 32.25 3.00 -63.50 151.98 21.82
15 33Y 33Y N CA 260 261 100.03 128.40 -43.40
16 4345 33Y 34D C N 270 272 -148.09 -96.50 79.92 3.35 -63.30 167.77 26.14
16 34D 34D N CA 272 273 175.24 114.20 -40.00
17 4347 35V 36I C N 285 287 -86.16 -120.60 38.29 2.02 -63.40 158.82 25.28
17 36I 36I N CA 287 288 113.57 130.30 -43.60
18 4348 36I 37V C N 293 295 -53.81 -125.40 74.63 2.29 -62.40 164.85 21.37
18 37V 37V N CA 295 296 122.23 143.30 -42.40
19 4349 37V 38G C N 300 302 94.59 82.20 59.88 2.29 -62.40 157.24 27.72
19 38G 38G N CA 302 303 -50.08 8.50 -41.20
20 4358 46S 47D C N 369 371 -141.44 -63.30 92.22 11.54 -63.30 92.22 11.54
20 47D 47D N CA 371 372 8.98 -40.00 -40.00
21 4368 56N 57P C N 452 454 -76.88 -58.70 41.57 2.43 -64.50 140.85 11.18
21 57P 57P N CA 454 455 6.89 -30.50 147.20
22 4369 57P 58K C N 459 461 81.79 -62.90 145.21 23.23 -62.90 145.21 23.23
22 58K 58K N CA 461 462 -53.11 -40.80 -40.80
23 4388 76A 77Y C N 617 619 -119.31 -63.50 92.05 12.70 -63.50 92.05 12.70
23 77Y 77Y N CA 619 620 29.80 -43.40 -43.40
24 4390 78R 79K C N 640 642 -155.01 -62.90 100.78 14.24 -62.90 100.78 14.24
24 79K 79K N CA 642 643 0.11 -40.80 -40.80
25 4398 86F 87S C N 706 708 -99.92 -72.40 81.08 5.70 -64.10 116.77 7.19
25 87S 87S N CA 708 709 76.14 152.40 -35.00
26 4407 95A 96L C N 768 770 93.68 -108.50 163.02 7.36 -63.50 -145.85 27.93
26 96L 96L N CA 770 771 173.35 132.50 -41.20
27 4408 96L 97Q C N 776 778 -57.23 -73.00 16.02 1.09 -63.80 178.31 26.56
27 97Q 97Q N CA 778 779 137.89 140.70 -40.30
28 4409 97Q 98Q C N 785 787 -152.36 -121.10 31.28 1.15 -63.80 -160.57 33.93
28 98Q 98Q N CA 787 788 141.01 139.70 -40.30
29 4411 99I 100K C N 802 804 -109.26 -118.00 12.89 0.46 -62.90 176.62 20.87
29 100K 100K N CA 804 805 129.63 139.10 -40.80
30 4412 100K 101E C N 811 813 -126.57 -117.80 33.08 1.47 -63.60 163.61 25.36
30 101E 101E N CA 813 814 168.69 136.80 -40.30
31 4413 101E 102R C N 820 822 -71.03 -72.10 7.95 0.59 -63.00 175.30 23.15
31 102R 102R N CA 822 823 134.02 141.90 -41.10
32 4415 103G 104A C N 835 837 -136.99 -134.00 7.17 0.31 -62.50 -178.43 33.75
32 104A 104A N CA 837 838 153.51 147.00 -40.90
33 4416 104A 105L C N 840 842 -115.61 -108.50 7.48 0.33 -63.50 -176.44 23.07
33 105L 105L N CA 842 843 134.80 132.50 -41.20
34 4420 108I 109D C N 871 873 -132.57 -96.50 37.08 1.51 -63.30 161.25 17.14
34 109D 109D N CA 873 874 105.62 114.20 -40.00
35 4421 109D 110R C N 879 881 -152.79 -125.20 94.56 3.89 -72.10 120.24 7.80
35 110R 110R N CA 881 882 -128.95 140.60 141.90
36 4422 110R 111G C N 890 892 109.15 78.70 43.19 0.97 -62.40 -128.44 33.06
36 111G 111G N CA 892 893 163.27 -166.10 -41.20
37 4442 130A 131G C N 1039 1041 133.59 82.20 55.46 2.77 -62.40 166.52 28.44
37 131G 131G N CA 1041 1042 -12.35 8.50 -41.20
38 4443 131G 132Y C N 1043 1045 -61.93 -98.40 37.72 1.84 -63.50 162.17 25.81
38 132Y 132Y N CA 1045 1046 118.76 128.40 -43.40
39 4446 134Q 135F C N 1068 1070 139.80 -124.20 98.30 4.44 -63.20 -131.18 26.23
39 135F 135F N CA 1070 1071 122.17 143.30 -44.30
40 4457 145K 146F C N 1156 1158 59.75 58.10 4.68 0.25 -63.20 142.90 25.74
40 146F 146F N CA 1158 1159 28.52 32.90 -44.30
41 4461 149A 150G C N 1190 1192 34.67 78.70 90.36 1.35 -62.40 107.41 16.83
41 150G 150G N CA 1192 1193 -87.20 -166.10 -41.20
42 4466 154R 155E C N 1223 1225 72.44 54.60 36.01 1.83 -63.60 145.43 24.78
42 155E 155E N CA 1225 1226 11.12 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 26 30 145 117 202 176 202 215 222 252
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_liganded.B99990001.pdb 1368.42603
seq_liganded.B99990002.pdb 1416.42871
In [20]:
show_model('seq_liganded.B99990001.pdb', '1lmp.pdb')
In [21]:
show_model('seq_liganded.B99990002.pdb', '1lmp.pdb')
Вот это магия лиганда! Обе модели очень похожи на белок-заготовку (лучше, чем без лиганда), немного различаясь в петях и в концах цепи.
Смена положения лиганда¶
Визуально посмотрели и решили взять карман белка между остатками 92 и 47 (остатки лиганда: 159 и 161). Этот карман сильно далеко от исходного.
In [28]:
command = "load seq_liganded.B99990001.pdb, model_1; " \
"select resi 92 or resi 97; util.cbac sele; " \
"as sticks, sele; orient sele; zoom sele, 30; " \
"rotate z, -90; rotate y, 60; " \
"set antialias, 2; set ray_trace_mode, 3; " \
"png tmp.png"
!pymol -Qcd "$command"
display(Image('tmp.png'))
Наверняка modeller нам не разрешит туда совать лиганд, но его конформация должна измениться по сравнению с конформацией лиганда в белке-заготовке.
In [22]:
! rm seq_liganded.rsr
In [23]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:92','O6:159'), ('N:47', 'O6:161')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
In [29]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 158
atom names : C +N
atom indices : 1255 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 158
atom names : C CA +N O
atom indices : 1255 1251 0 1256
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 (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: 13526 12410
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 : 12410 12410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3779
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 : 3903.7749
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 3 8 0.015 0.015 78.337 1.000
2 Bond angle potential : 1726 11 35 3.306 3.306 367.25 1.000
3 Stereochemical cosine torsion poten: 789 0 41 50.578 50.578 317.58 1.000
4 Stereochemical improper torsion pot: 515 0 3 1.950 1.950 42.510 1.000
5 Soft-sphere overlap restraints : 3779 2 3 0.009 0.009 37.454 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 20 68 0.917 0.917 737.16 1.000
10 Distance restraints 2 (N-O) : 2568 13 87 0.940 0.940 757.77 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 2 14 7.944 7.944 116.85 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 4 83.999 83.999 60.082 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 2 78.963 78.963 48.556 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 1 92.660 92.660 38.712 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 105.697 105.697 16.430 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 0.544 0.544 27.547 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 47 43 43.061 95.103 252.88 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 0 1.129 1.129 20.879 1.000
27 Distance restraints 5 (X-Y) : 1403 6 18 0.197 0.197 983.79 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_liganded.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: 29108.2852
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
1 382 47D 47D N CA 371 372 1.60 1.43 0.17 5.74 1.43 0.17 5.74
2 767 92D 92D N CA 745 746 1.60 1.43 0.17 5.47 1.43 0.17 5.47
3 769 92D 92D C CA 751 746 1.76 1.49 0.27 7.74 1.49 0.27 7.74
-------------------------------------------------------------------------------------------------
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 1792 47D 47D N CA 371 372 129.86 107.00 22.86 6.57 107.00 22.86 6.57
2 2076 73W 73W N CA 578 579 122.76 107.00 15.76 4.53 107.00 15.76 4.53
3 2299 91Q 91Q N CA 736 737 124.44 107.00 17.44 5.02 107.00 17.44 5.02
4 2302 91Q 91Q CA C 737 743 135.79 116.50 19.29 5.55 116.50 19.29 5.55
5 2311 92D 92D N CA 745 746 124.15 107.00 17.15 4.93 107.00 17.15 4.93
6 2322 93A 93A N CA 753 754 128.73 107.00 21.73 6.25 107.00 21.73 6.25
7 2329 94V 94V N CA 758 759 122.73 107.00 15.74 4.52 107.00 15.74 4.52
-------------------------------------------------------------------------------------------------
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 6144 52L 92D CA CA 417 746 13.86 9.16 4.69 4.65 9.16 4.69 4.65
2 6822 77Y 91Q CA CA 620 737 7.74 5.25 2.49 7.36 5.25 2.49 7.36
3 6823 77Y 92D CA CA 620 746 10.91 7.27 3.64 5.35 7.27 3.64 5.35
-------------------------------------------------------------------------------------------------
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 9016 91Q 76A N O 736 618 5.25 2.97 2.28 5.49 2.97 2.28 5.49
2 9017 91Q 77Y N O 736 630 9.25 6.78 2.47 4.53 6.78 2.47 4.53
3 9039 92D 76A N O 745 618 9.07 5.14 3.93 5.57 5.14 3.93 5.57
4 9040 92D 77Y N O 745 630 12.82 7.51 5.31 6.59 7.51 5.31 6.59
-------------------------------------------------------------------------------------------------
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 4559 91Q 91Q CA C 737 743 -130.14 -180.00 49.86 9.97 -180.00 49.86 9.97
-------------------------------------------------------------------------------------------------
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 -67.42 -63.40 11.65 1.79 -120.60 171.43 7.87
1 4I 4I N CA 25 26 -32.67 -43.60 130.30
2 4316 4I 5N C N 31 33 80.71 55.90 60.94 2.93 -63.20 146.05 23.11
2 5N 5N N CA 33 34 -16.16 39.50 -41.10
3 4327 15L 16A C N 124 126 77.88 55.40 25.17 1.98 -62.50 155.89 31.68
3 16A 16A N CA 126 127 26.89 38.20 -40.90
4 4330 18S 19E C N 149 151 68.00 -69.30 154.69 13.79 -63.60 168.94 20.82
4 19E 19E N CA 151 152 -146.25 142.50 -40.30
5 4331 19E 20G C N 158 160 85.01 82.20 90.32 4.53 -80.20 -178.43 8.98
5 20G 20G N CA 160 161 98.78 8.50 174.10
6 4332 20G 21T C N 162 164 51.16 55.90 4.97 0.47 -124.80 -156.37 7.75
6 21T 21T N CA 164 165 41.02 39.50 143.50
7 4336 24G 25R C N 189 191 -130.03 -125.20 21.79 0.94 -63.00 170.76 27.66
7 25R 25R N CA 191 192 161.85 140.60 -41.10
8 4337 25R 26Q C N 200 202 -153.02 -121.10 58.94 2.13 -63.80 158.05 27.71
8 26Q 26Q N CA 202 203 -170.76 139.70 -40.30
9 4338 26Q 27K C N 209 211 -145.08 -118.00 29.03 1.29 -62.90 -171.69 21.64
9 27K 27K N CA 211 212 128.63 139.10 -40.80
10 4339 27K 28T C N 218 220 -149.14 -124.80 26.74 1.09 -63.20 -175.44 29.23
10 28T 28T N CA 220 221 154.57 143.50 -42.10
11 4340 28T 29R C N 225 227 -136.15 -125.20 16.11 0.50 -63.00 -178.15 29.57
11 29R 29R N CA 227 228 152.42 140.60 -41.10
12 4341 29R 30N C N 236 238 -113.02 -119.90 59.23 2.84 -63.20 132.78 19.43
12 30N 30N N CA 238 239 -164.17 137.00 -41.10
13 4343 31H 32G C N 254 256 -70.85 -80.20 23.11 0.54 82.20 -149.53 6.80
13 32G 32G N CA 256 257 152.97 174.10 8.50
14 4344 32G 33Y C N 258 260 -71.37 -98.40 27.41 1.20 -63.50 167.44 26.17
14 33Y 33Y N CA 260 261 123.85 128.40 -43.40
15 4345 33Y 34D C N 270 272 -133.51 -70.90 72.70 3.80 -63.30 150.18 23.05
15 34D 34D N CA 272 273 -172.76 150.30 -40.00
16 4347 35V 36I C N 285 287 -112.39 -120.60 30.17 2.03 -63.40 164.53 28.77
16 36I 36I N CA 287 288 159.33 130.30 -43.60
17 4348 36I 37V C N 293 295 53.26 -62.40 143.50 17.57 -62.40 143.50 17.57
17 37V 37V N CA 295 296 -127.34 -42.40 -42.40
18 4388 76A 77Y C N 617 619 -126.54 -63.50 82.46 11.61 -63.50 82.46 11.61
18 77Y 77Y N CA 619 620 9.75 -43.40 -43.40
19 4390 78R 79K C N 640 642 -152.33 -62.90 109.38 14.21 -62.90 109.38 14.21
19 79K 79K N CA 642 643 22.17 -40.80 -40.80
20 4392 80Q 81L C N 658 660 -59.31 -63.50 8.98 1.10 -70.70 169.64 13.29
20 81L 81L N CA 660 661 -49.15 -41.20 141.60
21 4393 81L 82G C N 666 668 -141.77 -62.40 146.94 20.01 82.20 154.83 12.06
21 82G 82G N CA 668 669 82.46 -41.20 8.50
22 4398 86F 87S C N 706 708 -108.12 -136.60 85.78 3.66 -64.10 114.12 7.09
22 87S 87S N CA 708 709 70.28 151.20 -35.00
23 4402 90S 91Q C N 734 736 -59.58 -121.10 66.25 2.09 -63.80 155.46 23.08
23 91Q 91Q N CA 736 737 115.10 139.70 -40.30
24 4403 91Q 92D C N 743 745 30.51 -96.50 128.23 5.22 -63.30 -164.22 30.19
24 92D 92D N CA 745 746 131.85 114.20 -40.00
25 4405 93A 94V C N 756 758 -52.38 -125.40 76.35 3.65 -62.40 152.33 18.72
25 94V 94V N CA 758 759 165.60 143.30 -42.40
26 4407 95A 96L C N 768 770 63.57 -70.70 136.53 13.11 -63.50 -161.51 24.92
26 96L 96L N CA 770 771 166.32 141.60 -41.20
27 4408 96L 97Q C N 776 778 -92.69 -73.00 19.76 1.38 -63.80 179.75 27.97
27 97Q 97Q N CA 778 779 142.28 140.70 -40.30
28 4409 97Q 98Q C N 785 787 -72.78 -73.00 10.33 0.67 -63.80 170.92 24.67
28 98Q 98Q N CA 787 788 130.38 140.70 -40.30
29 4411 99I 100K C N 802 804 53.80 56.60 8.53 0.83 -62.90 136.78 23.86
29 100K 100K N CA 804 805 30.55 38.60 -40.80
30 4413 101E 102R C N 820 822 69.79 57.30 18.39 1.14 -63.00 148.11 26.94
30 102R 102R N CA 822 823 24.50 38.00 -41.10
31 4414 102R 103G C N 831 833 -174.41 -167.20 52.15 2.11 82.20 154.22 11.70
31 103G 103G N CA 833 834 122.95 174.60 8.50
32 4415 103G 104A C N 835 837 -116.19 -134.00 26.83 0.87 -62.50 176.21 26.81
32 104A 104A N CA 837 838 126.93 147.00 -40.90
33 4416 104A 105L C N 840 842 -158.26 -108.50 54.43 2.41 -63.50 -170.40 32.16
33 105L 105L N CA 842 843 154.57 132.50 -41.20
34 4418 106P 107M C N 855 857 -159.15 -125.60 64.90 2.27 -63.40 156.23 30.47
34 107M 107M N CA 857 858 -163.95 140.50 -40.50
35 4419 107M 108I C N 863 865 -63.27 -63.40 11.53 1.89 -120.60 172.20 7.78
35 108I 108I N CA 865 866 -32.07 -43.60 130.30
36 4421 109D 110R C N 879 881 -59.77 -63.00 22.10 2.78 -72.10 155.63 12.24
36 110R 110R N CA 881 882 -62.96 -41.10 141.90
37 4422 110R 111G C N 890 892 24.82 78.70 66.14 1.93 -62.40 122.87 17.34
37 111G 111G N CA 892 893 -127.75 -166.10 -41.20
38 4439 127L 128P C N 1023 1025 -72.38 -64.50 15.85 1.60 -58.70 164.52 12.52
38 128P 128P N CA 1025 1026 133.45 147.20 -30.50
39 4440 128P 129G C N 1030 1032 -93.25 -80.20 73.78 2.27 78.70 179.88 7.51
39 129G 129G N CA 1032 1033 -113.29 174.10 -166.10
40 4442 130A 131G C N 1039 1041 86.54 78.70 51.50 1.15 -62.40 -129.59 31.92
40 131G 131G N CA 1041 1042 143.00 -166.10 -41.20
41 4443 131G 132Y C N 1043 1045 -126.90 -124.30 23.13 1.34 -63.50 168.22 23.88
41 132Y 132Y N CA 1045 1046 112.41 135.40 -43.40
42 4446 134Q 135F C N 1068 1070 -87.62 -71.40 62.12 4.51 -63.20 117.59 17.97
42 135F 135F N CA 1070 1071 -159.33 140.70 -44.30
43 4457 145K 146F C N 1156 1158 62.17 58.10 8.71 0.44 -63.20 143.35 25.78
43 146F 146F N CA 1158 1159 25.20 32.90 -44.30
44 4461 149A 150G C N 1190 1192 33.48 78.70 93.59 1.40 -62.40 105.07 16.58
44 150G 150G N CA 1192 1193 -84.17 -166.10 -41.20
45 4466 154R 155E C N 1223 1225 79.72 54.60 55.34 2.82 -63.60 147.15 24.62
45 155E 155E N CA 1225 1226 -6.91 42.40 -40.30
46 4467 155E 156I C N 1232 1234 -121.61 -120.60 47.20 2.74 -63.40 139.45 21.32
46 156I 156I N CA 1234 1235 83.11 130.30 -43.60
47 4468 156I 157D C N 1240 1242 -60.37 -70.90 30.43 1.07 54.50 140.47 10.42
47 157D 157D N CA 1242 1243 121.75 150.30 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 92D 159. N O6 745 1270 6.72 3.00 3.72 37.23 3.00 3.72 37.23
2 12410 47D 161. N O6 371 1297 6.32 3.00 3.32 33.17 3.00 3.32 33.17
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 27 40 177 146 226 177 206 264 277 273
<< 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 : 12410 12410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3552
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 : 3845.0586
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 3 8 0.015 0.015 86.999 1.000
2 Bond angle potential : 1726 11 26 3.183 3.183 336.89 1.000
3 Stereochemical cosine torsion poten: 789 0 43 50.486 50.486 310.00 1.000
4 Stereochemical improper torsion pot: 515 0 3 1.959 1.959 43.305 1.000
5 Soft-sphere overlap restraints : 3552 2 4 0.010 0.010 40.621 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2407 18 67 0.851 0.851 658.55 1.000
10 Distance restraints 2 (N-O) : 2568 16 92 0.909 0.909 757.06 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 2 8 7.649 7.649 108.31 1.000
14 Sidechain Chi_1 dihedral restraints: 130 0 3 84.323 84.323 57.005 1.000
15 Sidechain Chi_2 dihedral restraints: 107 0 4 70.859 70.859 48.408 1.000
16 Sidechain Chi_3 dihedral restraints: 48 0 0 92.913 92.913 37.422 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 72.326 72.326 14.486 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 29.821 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 48 42 42.387 94.275 211.24 1.000
26 Distance restraints 4 (SDCH-SDCH) : 157 0 2 1.252 1.252 27.145 1.000
27 Distance restraints 5 (X-Y) : 1403 7 20 0.206 0.206 1077.8 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_liganded.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: 27958.9492
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
1 382 47D 47D N CA 371 372 1.62 1.43 0.19 6.38 1.43 0.19 6.38
2 767 92D 92D N CA 745 746 1.61 1.43 0.18 6.08 1.43 0.18 6.08
3 769 92D 92D C CA 751 746 1.76 1.49 0.27 7.71 1.49 0.27 7.71
-------------------------------------------------------------------------------------------------
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 1792 47D 47D N CA 371 372 133.51 107.00 26.51 7.62 107.00 26.51 7.62
2 2039 69L 69L C CA 551 546 128.64 108.00 20.63 4.78 108.00 20.63 4.78
3 2076 73W 73W N CA 578 579 122.78 107.00 15.78 4.54 107.00 15.78 4.54
4 2299 91Q 91Q N CA 736 737 122.86 107.00 15.86 4.56 107.00 15.86 4.56
5 2302 91Q 91Q CA C 737 743 135.69 116.50 19.19 5.52 116.50 19.19 5.52
6 2311 92D 92D N CA 745 746 128.86 107.00 21.86 6.28 107.00 21.86 6.28
7 2322 93A 93A N CA 753 754 126.65 107.00 19.65 5.65 107.00 19.65 5.65
8 2329 94V 94V N CA 758 759 128.09 107.00 21.09 6.07 107.00 21.09 6.07
-------------------------------------------------------------------------------------------------
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 6822 77Y 91Q CA CA 620 737 7.51 5.25 2.25 6.67 5.25 2.25 6.67
2 6823 77Y 92D CA CA 620 746 10.66 7.27 3.39 4.98 7.27 3.39 4.98
-------------------------------------------------------------------------------------------------
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 9016 91Q 76A N O 736 618 5.37 2.97 2.40 5.78 2.97 2.40 5.78
2 9039 92D 76A N O 745 618 9.19 5.14 4.06 5.75 5.14 4.06 5.75
3 9040 92D 77Y N O 745 630 12.49 7.51 4.98 6.18 7.51 4.98 6.18
-------------------------------------------------------------------------------------------------
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 4555 87S 87S CA C 709 712 -148.96 -180.00 31.04 6.20 -180.00 31.04 6.20
2 4559 91Q 91Q CA C 737 743 -126.94 -180.00 53.06 10.61 -180.00 53.06 10.61
-------------------------------------------------------------------------------------------------
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 78.76 55.40 25.35 2.13 -62.50 157.32 31.98
1 16A 16A N CA 126 127 28.36 38.20 -40.90
2 4329 17W 18S C N 143 145 -52.68 -64.10 12.23 1.35 -136.60 -170.92 10.70
2 18S 18S N CA 145 146 -39.37 -35.00 151.20
3 4330 18S 19E C N 149 151 -140.12 -117.80 93.89 5.03 -63.60 115.04 13.54
3 19E 19E N CA 151 152 45.61 136.80 -40.30
4 4332 20G 21T C N 162 164 45.17 55.90 12.46 0.97 -124.80 -163.97 7.49
4 21T 21T N CA 164 165 45.84 39.50 143.50
5 4336 24G 25R C N 189 191 -165.50 -125.20 48.35 1.43 -63.00 -177.02 31.50
5 25R 25R N CA 191 192 167.32 140.60 -41.10
6 4337 25R 26Q C N 200 202 -141.73 -121.10 33.88 1.17 -63.80 171.82 29.31
6 26Q 26Q N CA 202 203 166.57 139.70 -40.30
7 4338 26Q 27K C N 209 211 -71.19 -70.20 12.72 0.94 -62.90 168.72 21.47
7 27K 27K N CA 211 212 127.71 140.40 -40.80
8 4339 27K 28T C N 218 220 -147.41 -124.80 30.07 1.01 -63.20 176.03 28.00
8 28T 28T N CA 220 221 163.32 143.50 -42.10
9 4340 28T 29R C N 225 227 -128.98 -125.20 35.66 1.64 -63.00 157.34 25.76
9 29R 29R N CA 227 228 176.06 140.60 -41.10
10 4341 29R 30N C N 236 238 -89.50 -71.20 19.71 1.57 -63.20 178.52 20.97
10 30N 30N N CA 238 239 135.47 142.80 -41.10
11 4342 30N 31H C N 244 246 -138.92 -63.20 86.67 14.89 -63.20 86.67 14.89
11 31H 31H N CA 246 247 -84.47 -42.30 -42.30
12 4343 31H 32G C N 254 256 -103.00 -80.20 67.55 1.68 82.20 -141.67 8.11
12 32G 32G N CA 256 257 -122.32 174.10 8.50
13 4345 33Y 34D C N 270 272 55.79 54.50 116.27 8.65 -63.30 -158.26 21.73
13 34D 34D N CA 272 273 157.16 40.90 -40.00
14 4347 35V 36I C N 285 287 -101.90 -120.60 20.79 1.10 -63.40 169.26 26.53
14 36I 36I N CA 287 288 121.22 130.30 -43.60
15 4348 36I 37V C N 293 295 -33.12 -125.40 93.18 3.24 -62.40 175.25 23.96
15 37V 37V N CA 295 296 130.39 143.30 -42.40
16 4349 37V 38G C N 300 302 98.91 82.20 65.82 2.37 -62.40 161.91 28.32
16 38G 38G N CA 302 303 -55.16 8.50 -41.20
17 4357 45Y 46S C N 363 365 -73.27 -72.40 72.68 4.25 -64.10 100.34 7.85
17 46S 46S N CA 365 366 -134.92 152.40 -35.00
18 4358 46S 47D C N 369 371 -66.70 -96.50 72.34 3.05 -63.30 88.35 10.70
18 47D 47D N CA 371 372 48.29 114.20 -40.00
19 4359 47D 48H C N 377 379 61.12 56.30 128.75 11.80 56.30 128.75 11.80
19 48H 48H N CA 379 380 169.46 40.80 40.80
20 4360 48H 49P C N 387 389 -73.68 -58.70 42.21 2.53 -64.50 138.53 10.83
20 49P 49P N CA 389 390 8.97 -30.50 147.20
21 4379 67Y 68Q C N 534 536 63.44 55.10 18.18 2.00 -121.10 -165.79 9.06
21 68Q 68Q N CA 536 537 56.46 40.30 139.70
22 4390 78R 79K C N 640 642 -154.36 -62.90 104.63 14.23 -62.90 104.63 14.23
22 79K 79K N CA 642 643 10.02 -40.80 -40.80
23 4395 83L 84K C N 678 680 -136.68 -118.00 79.02 4.03 -62.90 126.80 14.76
23 84K 84K N CA 680 681 62.32 139.10 -40.80
24 4396 84K 85D C N 687 689 -44.94 -96.50 56.70 2.34 54.50 111.17 9.59
24 85D 85D N CA 689 690 90.62 114.20 40.90
25 4402 90S 91Q C N 734 736 -60.64 -121.10 63.07 2.05 -63.80 162.10 24.00
25 91Q 91Q N CA 736 737 121.77 139.70 -40.30
26 4403 91Q 92D C N 743 745 24.33 -96.50 122.48 4.99 -63.30 -164.95 29.72
26 92D 92D N CA 745 746 134.26 114.20 -40.00
27 4407 95A 96L C N 768 770 160.60 -108.50 91.02 4.39 -63.50 -143.05 27.13
27 96L 96L N CA 770 771 127.91 132.50 -41.20
28 4408 96L 97Q C N 776 778 -137.84 -121.10 35.75 1.87 -63.80 165.86 21.44
28 97Q 97Q N CA 778 779 108.11 139.70 -40.30
29 4409 97Q 98Q C N 785 787 -166.96 -121.10 65.67 2.15 -63.80 168.32 29.82
29 98Q 98Q N CA 787 788 -173.30 139.70 -40.30
30 4411 99I 100K C N 802 804 -78.38 -70.20 35.83 2.78 -62.90 147.13 18.31
30 100K 100K N CA 804 805 105.51 140.40 -40.80
31 4412 100K 101E C N 811 813 -142.81 -117.80 29.27 0.86 -63.60 -174.53 29.16
31 101E 101E N CA 813 814 152.00 136.80 -40.30
32 4413 101E 102R C N 820 822 -77.12 -72.10 7.52 0.49 -63.00 171.98 24.20
32 102R 102R N CA 822 823 147.50 141.90 -41.10
33 4414 102R 103G C N 831 833 -173.04 -167.20 15.06 0.49 82.20 -151.76 14.77
33 103G 103G N CA 833 834 -171.52 174.60 8.50
34 4415 103G 104A C N 835 837 -71.85 -68.20 16.35 1.19 -62.50 158.14 26.38
34 104A 104A N CA 837 838 161.24 145.30 -40.90
35 4417 105L 106P C N 848 850 -66.64 -58.70 8.53 0.88 -64.50 174.61 13.14
35 106P 106P N CA 850 851 -27.40 -30.50 147.20
36 4421 109D 110R C N 879 881 -53.92 -63.00 13.58 1.58 -72.10 167.90 13.30
36 110R 110R N CA 881 882 -51.19 -41.10 141.90
37 4432 120C 121S C N 968 970 -70.12 -72.40 5.50 0.40 -64.10 167.70 12.52
37 121S 121S N CA 970 971 157.41 152.40 -35.00
38 4433 121S 122N C N 974 976 73.85 55.90 77.58 4.22 -63.20 137.14 21.00
38 122N 122N N CA 976 977 -35.97 39.50 -41.10
39 4442 130A 131G C N 1039 1041 143.37 82.20 89.45 2.70 -62.40 155.01 28.27
39 131G 131G N CA 1041 1042 -56.77 8.50 -41.20
40 4443 131G 132Y C N 1043 1045 61.71 -63.50 171.31 23.93 -63.50 171.31 23.93
40 132Y 132Y N CA 1045 1046 -160.33 -43.40 -43.40
41 4444 132Y 133G C N 1055 1057 -56.52 -62.40 7.22 1.36 82.20 146.00 11.07
41 133G 133G N CA 1057 1058 -37.01 -41.20 8.50
42 4445 133G 134Q C N 1059 1061 -64.46 -73.00 28.27 2.02 -63.80 152.05 22.39
42 134Q 134Q N CA 1061 1062 167.65 140.70 -40.30
43 4446 134Q 135F C N 1068 1070 -118.11 -124.20 55.70 2.47 -63.20 143.19 16.74
43 135F 135F N CA 1070 1071 87.94 143.30 -44.30
44 4457 145K 146F C N 1156 1158 57.36 58.10 4.16 0.27 -63.20 145.40 26.24
44 146F 146F N CA 1158 1159 36.99 32.90 -44.30
45 4461 149A 150G C N 1190 1192 33.03 78.70 91.17 1.38 -62.40 105.94 16.57
45 150G 150G N CA 1192 1193 -87.19 -166.10 -41.20
46 4466 154R 155E C N 1223 1225 54.21 54.60 14.61 1.09 -63.60 152.80 26.15
46 155E 155E N CA 1225 1226 57.00 42.40 -40.30
47 4467 155E 156I C N 1232 1234 -103.83 -120.60 19.32 1.54 -63.40 -178.93 31.16
47 156I 156I N CA 1234 1235 139.90 130.30 -43.60
48 4468 156I 157D C N 1240 1242 -84.33 -96.50 58.11 2.45 54.50 139.81 15.53
48 157D 157D N CA 1242 1243 57.38 114.20 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 92D 159. N O6 745 1270 7.10 3.00 4.10 40.99 3.00 4.10 40.99
2 12410 47D 161. N O6 371 1297 6.22 3.00 3.22 32.18 3.00 3.22 32.18
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 28 46 169 142 190 172 198 228 246 260
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_liganded.B99990001.pdb 3903.77490
seq_liganded.B99990002.pdb 3845.05859
In [30]:
show_model('seq_liganded.B99990001.pdb', '1lmp.pdb')
In [31]:
show_model('seq_liganded.B99990002.pdb', '1lmp.pdb')
Действительно, в то время как лиганд в целевом белке немного поменял своё положение (теперь он не идеально совпадает с лигандом в белке-заготовке), петли белков стали по-другому различаться (кажется, что петли рядом с лигандом сильнее изменили своё положение в ответ на ограничение для положения лиганда).
Аланиновый лизоцим¶
Заменим все АК в целевом белке на аланин и припишем 3 лиганда в конец.
In [33]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
seq_ala = 'A' * 158 + '...'
alignm.append_sequence(seq_ala)
alignm[0].code = 'pdb'
alignm[1].code = 'seq_ala'
In [34]:
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [35]:
! cat all_in_one3.ali
>P1;pdb structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------------- ----------------WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLR SYVAGCGV...* >P1;seq_ala sequence::1 : :+161 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAA...*
Неудивительно, что даже удалось выровнять последовательности.
In [36]:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_ala pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 158
atom names : C +N
atom indices : 789 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 158
atom names : C CA +N O
atom indices : 789 787 0 790
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10782 9999
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 161
Number of all, selected real atoms : 834 834
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9999 9999
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1471
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 : 1440.1965
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 : 790 1 2 0.011 0.011 26.882 1.000
2 Bond angle potential : 1105 4 16 2.797 2.797 177.53 1.000
3 Stereochemical cosine torsion poten: 320 0 46 77.803 77.803 322.93 1.000
4 Stereochemical improper torsion pot: 316 1 3 1.863 1.863 24.075 1.000
5 Soft-sphere overlap restraints : 1471 1 4 0.014 0.014 32.514 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 6 37 0.581 0.581 292.93 1.000
10 Distance restraints 2 (N-O) : 2564 5 35 0.612 0.612 323.38 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 157 2 9 6.112 6.112 69.160 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.328 0.328 9.7680 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 22 33.763 94.939 95.435 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.777 0.777 3.9262 1.000
27 Distance restraints 5 (X-Y) : 1401 0 8 0.075 0.075 61.656 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_ala.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20537.0566
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
1 459 92A 92A C CA 459 457 1.65 1.49 0.16 4.59 1.49 0.16 4.59
-------------------------------------------------------------------------------------------------
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 1219 62A 62A N CA 306 307 132.87 107.00 25.87 7.44 107.00 25.87 7.44
2 1432 92A 92A C CA 459 457 131.74 108.00 23.74 5.50 108.00 23.74 5.50
3 1506 103A 103A N CA 511 512 123.39 107.00 16.39 4.71 107.00 16.39 4.71
4 1520 105A 105A N CA 521 522 126.36 107.00 19.36 5.57 107.00 19.36 5.57
-------------------------------------------------------------------------------------------------
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 4789 103A 106A CA CA 512 527 8.36 5.15 3.20 5.71 5.15 3.20 5.71
-------------------------------------------------------------------------------------------------
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 6868 106A 103A N O 526 515 7.06 3.15 3.91 6.94 3.15 3.91 6.94
-------------------------------------------------------------------------------------------------
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 2748 61A 61A CA C 302 304 -151.62 -180.00 28.37 5.67 -180.00 28.37 5.67
2 2791 104A 104A CA C 517 519 -143.11 -180.00 36.89 7.38 -180.00 36.89 7.38
-------------------------------------------------------------------------------------------------
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 2546 15A 16A C N 74 76 78.20 55.40 26.75 1.92 -62.50 155.03 31.49
1 16A 16A N CA 76 77 24.20 38.20 -40.90
2 2549 18A 19A C N 89 91 65.55 55.40 22.68 0.82 -62.50 140.91 28.62
2 19A 19A N CA 91 92 17.92 38.20 -40.90
3 2551 20A 21A C N 99 101 54.05 55.40 5.21 0.43 -62.50 138.09 28.06
3 21A 21A N CA 101 102 33.16 38.20 -40.90
4 2552 21A 22A C N 104 106 61.67 55.40 7.64 0.51 -62.50 144.93 29.47
4 22A 22A N CA 106 107 33.84 38.20 -40.90
5 2567 36A 37A C N 179 181 66.63 55.40 14.72 0.87 -62.50 146.69 29.83
5 37A 37A N CA 181 182 28.69 38.20 -40.90
6 2568 37A 38A C N 184 186 61.88 55.40 10.16 0.47 -62.50 143.35 29.15
6 38A 38A N CA 186 187 30.37 38.20 -40.90
7 2579 48A 49A C N 239 241 84.48 55.40 40.32 2.19 -62.50 155.62 31.45
7 49A 49A N CA 241 242 10.27 38.20 -40.90
8 2584 53A 54A C N 264 266 95.75 -134.00 135.14 3.32 -62.50 -151.29 32.83
8 54A 54A N CA 266 267 -176.98 147.00 -40.90
9 2587 56A 57A C N 279 281 56.96 55.40 19.32 1.29 -62.50 154.74 31.23
9 57A 57A N CA 281 282 57.45 38.20 -40.90
10 2593 62A 63A C N 309 311 -164.33 -134.00 30.34 0.97 -62.50 -160.73 38.08
10 63A 63A N CA 311 312 147.82 147.00 -40.90
11 2594 63A 64A C N 314 316 -176.56 -134.00 43.07 1.19 -62.50 -159.00 38.97
11 64A 64A N CA 316 317 153.60 147.00 -40.90
12 2595 64A 65A C N 319 321 -179.46 -134.00 50.27 1.14 -62.50 -169.27 37.38
12 65A 65A N CA 321 322 168.45 147.00 -40.90
13 2596 65A 66A C N 324 326 -108.13 -134.00 32.47 0.84 -62.50 174.36 26.73
13 66A 66A N CA 326 327 127.38 147.00 -40.90
14 2597 66A 67A C N 329 331 164.10 -134.00 68.48 1.56 -62.50 -164.57 38.86
14 67A 67A N CA 331 332 176.28 147.00 -40.90
15 2598 67A 68A C N 334 336 -65.54 -68.20 7.79 0.54 -62.50 178.90 29.17
15 68A 68A N CA 336 337 137.98 145.30 -40.90
16 2599 68A 69A C N 339 341 -124.89 -134.00 9.36 0.24 -62.50 -174.91 33.67
16 69A 69A N CA 341 342 144.84 147.00 -40.90
17 2600 69A 70A C N 344 346 -74.54 -68.20 12.11 0.78 -62.50 163.92 27.47
17 70A 70A N CA 346 347 155.62 145.30 -40.90
18 2601 70A 71A C N 349 351 -63.58 -68.20 5.39 0.36 -62.50 176.60 28.99
18 71A 71A N CA 351 352 142.51 145.30 -40.90
19 2602 71A 72A C N 354 356 -125.88 -134.00 10.98 0.63 -62.50 176.48 32.31
19 72A 72A N CA 356 357 154.39 147.00 -40.90
20 2603 72A 73A C N 359 361 -162.05 -134.00 32.50 0.76 -62.50 -175.21 35.57
20 73A 73A N CA 361 362 163.42 147.00 -40.90
21 2604 73A 74A C N 364 366 -121.84 -134.00 13.43 0.31 -62.50 -172.53 33.89
21 74A 74A N CA 366 367 141.27 147.00 -40.90
22 2605 74A 75A C N 369 371 175.86 -134.00 54.64 1.24 -62.50 -166.59 38.04
22 75A 75A N CA 371 372 168.73 147.00 -40.90
23 2606 75A 76A C N 374 376 -112.23 -134.00 32.72 1.05 -62.50 170.87 26.06
23 76A 76A N CA 376 377 122.57 147.00 -40.90
24 2607 76A 77A C N 379 381 179.10 -134.00 47.24 1.36 -62.50 -155.75 39.72
24 77A 77A N CA 381 382 152.67 147.00 -40.90
25 2608 77A 78A C N 384 386 -117.93 -134.00 22.96 0.70 -62.50 -179.77 27.41
25 78A 78A N CA 386 387 130.59 147.00 -40.90
26 2610 79A 80A C N 394 396 -64.87 -68.20 22.60 1.94 -62.50 151.47 24.94
26 80A 80A N CA 396 397 167.65 145.30 -40.90
27 2611 80A 81A C N 399 401 -55.96 -68.20 17.08 1.68 -62.50 162.02 26.24
27 81A 81A N CA 401 402 157.22 145.30 -40.90
28 2612 81A 82A C N 404 406 -53.58 -68.20 23.49 1.48 -62.50 168.05 27.99
28 82A 82A N CA 406 407 126.92 145.30 -40.90
29 2613 82A 83A C N 409 411 178.75 -134.00 59.44 1.54 -62.50 -179.42 35.73
29 83A 83A N CA 411 412 -176.94 147.00 -40.90
30 2614 83A 84A C N 414 416 -67.62 -68.20 4.32 0.33 -62.50 178.16 29.45
30 84A 84A N CA 416 417 141.02 145.30 -40.90
31 2615 84A 85A C N 419 421 -165.74 -134.00 34.45 0.79 -62.50 -170.66 36.51
31 85A 85A N CA 421 422 160.38 147.00 -40.90
32 2616 85A 86A C N 424 426 -107.11 -134.00 29.21 0.67 -62.50 -177.96 28.00
32 86A 86A N CA 426 427 135.59 147.00 -40.90
33 2617 86A 87A C N 429 431 -65.93 -68.20 4.88 0.46 -62.50 169.51 27.95
33 87A 87A N CA 431 432 149.62 145.30 -40.90
34 2618 87A 88A C N 434 436 -75.07 -68.20 10.24 0.64 -62.50 166.68 27.95
34 88A 88A N CA 436 437 152.89 145.30 -40.90
35 2619 88A 89A C N 439 441 -159.03 -134.00 25.43 0.68 -62.50 -166.61 36.84
35 89A 89A N CA 441 442 151.53 147.00 -40.90
36 2620 89A 90A C N 444 446 -109.59 -134.00 32.98 0.94 -62.50 172.28 26.35
36 90A 90A N CA 446 447 124.82 147.00 -40.90
37 2621 90A 91A C N 449 451 70.55 -68.20 139.37 12.24 -62.50 -151.40 31.70
37 91A 91A N CA 451 452 158.44 145.30 -40.90
38 2626 95A 96A C N 474 476 75.77 55.40 46.03 1.67 -62.50 143.34 28.78
38 96A 96A N CA 476 477 -3.08 38.20 -40.90
39 2630 99A 100A C N 494 496 49.33 55.40 10.81 0.43 -62.50 142.32 28.77
39 100A 100A N CA 496 497 47.14 38.20 -40.90
40 2633 102A 103A C N 509 511 179.97 -134.00 87.19 3.39 -62.50 153.06 30.87
40 103A 103A N CA 511 512 -138.96 147.00 -40.90
41 2634 103A 104A C N 514 516 105.18 -134.00 127.95 5.87 -62.50 -137.81 44.73
41 104A 104A N CA 516 517 104.87 147.00 -40.90
42 2663 132A 133A C N 659 661 80.26 -134.00 160.24 3.64 -62.50 177.51 28.47
42 133A 133A N CA 661 662 -146.39 147.00 -40.90
43 2675 144A 145A C N 719 721 39.36 -68.20 121.68 11.80 -68.20 121.68 11.80
43 145A 145A N CA 721 722 -157.79 145.30 145.30
44 2685 154A 155A C N 769 771 71.58 55.40 38.82 1.40 -62.50 141.06 28.46
44 155A 155A N CA 771 772 2.91 38.20 -40.90
45 2687 156A 157A C N 779 781 64.98 55.40 15.51 0.68 -62.50 143.96 29.28
45 157A 157A N CA 781 782 25.99 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 10 58 60 86 78 87 128 115 102
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 161
Number of all, selected real atoms : 834 834
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9999 9999
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1544
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 : 1663.6802
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 : 790 0 1 0.010 0.010 22.802 1.000
2 Bond angle potential : 1105 3 14 2.682 2.682 156.06 1.000
3 Stereochemical cosine torsion poten: 320 0 41 76.750 76.750 312.55 1.000
4 Stereochemical improper torsion pot: 316 2 4 2.515 2.515 39.002 1.000
5 Soft-sphere overlap restraints : 1544 1 2 0.013 0.013 28.690 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 11 43 0.655 0.655 365.11 1.000
10 Distance restraints 2 (N-O) : 2564 6 51 0.665 0.665 388.78 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: 157 2 6 7.080 7.080 92.815 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.289 0.289 7.2525 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 48 26 33.538 92.857 147.79 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 1 0.850 0.850 5.5629 1.000
27 Distance restraints 5 (X-Y) : 1401 3 9 0.095 0.095 97.269 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: seq_ala.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20352.8242
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 1432 92A 92A C CA 459 457 131.68 108.00 23.68 5.49 108.00 23.68 5.49
2 1433 92A 93A C N 459 461 143.35 120.00 23.35 5.31 120.00 23.35 5.31
3 1436 93A 93A N CA 461 462 123.13 107.00 16.13 4.64 107.00 16.13 4.64
-------------------------------------------------------------------------------------------------
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 4685 93A 109A CA CA 462 542 7.07 4.98 2.09 5.86 4.98 2.09 5.86
-------------------------------------------------------------------------------------------------
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 6868 106A 103A N O 526 515 6.00 3.15 2.85 5.04 3.15 2.85 5.04
-------------------------------------------------------------------------------------------------
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 2791 104A 104A CA C 517 519 -129.47 -180.00 50.53 10.10 -180.00 50.53 10.10
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2546 15A 16A C N 74 76 77.26 55.40 24.50 1.92 -62.50 155.44 31.59
1 16A 16A N CA 76 77 27.14 38.20 -40.90
2 2548 17A 18A C N 84 86 -1.56 -62.50 98.39 14.90 -134.00 162.91 8.93
2 18A 18A N CA 86 87 -118.15 -40.90 147.00
3 2551 20A 21A C N 99 101 59.61 55.40 10.35 0.37 -62.50 140.56 28.59
3 21A 21A N CA 101 102 28.74 38.20 -40.90
4 2552 21A 22A C N 104 106 66.00 55.40 23.33 0.85 -62.50 141.11 28.66
4 22A 22A N CA 106 107 17.41 38.20 -40.90
5 2567 36A 37A C N 179 181 66.59 55.40 13.57 0.92 -62.50 147.52 30.00
5 37A 37A N CA 181 182 30.51 38.20 -40.90
6 2568 37A 38A C N 184 186 61.41 55.40 9.73 0.43 -62.50 143.02 29.09
6 38A 38A N CA 186 187 30.54 38.20 -40.90
7 2579 48A 49A C N 239 241 87.76 55.40 44.59 2.44 -62.50 157.86 31.84
7 49A 49A N CA 241 242 7.52 38.20 -40.90
8 2584 53A 54A C N 264 266 93.26 -134.00 138.10 3.36 -62.50 -154.53 32.32
8 54A 54A N CA 266 267 -174.91 147.00 -40.90
9 2587 56A 57A C N 279 281 59.22 55.40 15.33 1.24 -62.50 153.75 31.10
9 57A 57A N CA 281 282 53.04 38.20 -40.90
10 2591 60A 61A C N 299 301 -60.32 -62.50 53.79 8.71 -62.50 53.79 8.71
10 61A 61A N CA 301 302 -94.64 -40.90 -40.90
11 2592 61A 62A C N 304 306 -97.40 -62.50 38.73 7.87 -62.50 38.73 7.87
11 62A 62A N CA 306 307 -57.69 -40.90 -40.90
12 2593 62A 63A C N 309 311 35.95 -68.20 114.63 8.01 -62.50 169.79 33.02
12 63A 63A N CA 311 312 97.43 145.30 -40.90
13 2594 63A 64A C N 314 316 -156.92 -134.00 58.56 2.62 -62.50 151.29 29.72
13 64A 64A N CA 316 317 -159.11 147.00 -40.90
14 2595 64A 65A C N 319 321 -132.72 -134.00 3.65 0.17 -62.50 -170.95 34.74
14 65A 65A N CA 321 322 143.58 147.00 -40.90
15 2596 65A 66A C N 324 326 -71.59 -68.20 5.96 0.38 -62.50 169.15 28.18
15 66A 66A N CA 326 327 150.20 145.30 -40.90
16 2597 66A 67A C N 329 331 -153.25 -134.00 24.06 0.62 -62.50 -178.07 34.66
16 67A 67A N CA 331 332 161.42 147.00 -40.90
17 2598 67A 68A C N 334 336 -148.19 -134.00 14.70 0.36 -62.50 -171.19 35.53
17 68A 68A N CA 336 337 150.85 147.00 -40.90
18 2599 68A 69A C N 339 341 -73.92 -68.20 5.74 0.47 -62.50 173.66 29.03
18 69A 69A N CA 341 342 145.82 145.30 -40.90
19 2600 69A 70A C N 344 346 -77.04 -68.20 8.88 0.78 -62.50 175.21 29.45
19 70A 70A N CA 346 347 144.50 145.30 -40.90
20 2602 71A 72A C N 354 356 -77.64 -68.20 11.95 0.77 -62.50 167.16 28.16
20 72A 72A N CA 356 357 152.63 145.30 -40.90
21 2603 72A 73A C N 359 361 -147.21 -134.00 14.49 0.33 -62.50 -173.49 35.10
21 73A 73A N CA 361 362 152.94 147.00 -40.90
22 2604 73A 74A C N 364 366 -77.93 -68.20 10.56 0.75 -62.50 170.41 28.71
22 74A 74A N CA 366 367 149.39 145.30 -40.90
23 2605 74A 75A C N 369 371 -82.25 -68.20 20.15 1.99 -62.50 172.88 27.43
23 75A 75A N CA 371 372 130.85 145.30 -40.90
24 2606 75A 76A C N 374 376 161.72 -134.00 69.27 1.59 -62.50 -160.39 39.68
24 76A 76A N CA 376 377 172.80 147.00 -40.90
25 2607 76A 77A C N 379 381 -106.22 -134.00 41.48 1.33 -62.50 163.06 24.97
25 77A 77A N CA 381 382 116.19 147.00 -40.90
26 2608 77A 78A C N 384 386 160.23 -134.00 69.90 1.63 -62.50 -157.81 40.18
26 78A 78A N CA 386 387 170.66 147.00 -40.90
27 2609 78A 79A C N 389 391 -75.47 -68.20 11.26 0.71 -62.50 165.71 27.81
27 79A 79A N CA 391 392 153.90 145.30 -40.90
28 2610 79A 80A C N 394 396 -69.26 -68.20 1.61 0.10 -62.50 172.72 28.64
28 80A 80A N CA 396 397 146.51 145.30 -40.90
29 2611 80A 81A C N 399 401 -169.76 -134.00 42.16 1.00 -62.50 -175.77 35.84
29 81A 81A N CA 401 402 169.32 147.00 -40.90
30 2612 81A 82A C N 404 406 -61.93 -68.20 6.43 0.59 -62.50 172.37 28.22
30 82A 82A N CA 406 407 146.73 145.30 -40.90
31 2613 82A 83A C N 409 411 -60.82 -68.20 19.25 1.30 -62.50 168.43 27.68
31 83A 83A N CA 411 412 127.52 145.30 -40.90
32 2614 83A 84A C N 414 416 170.64 -134.00 56.02 1.55 -62.50 -153.01 40.56
32 84A 84A N CA 416 417 155.55 147.00 -40.90
33 2615 84A 85A C N 419 421 -95.52 -68.20 42.23 4.14 -62.50 157.49 24.41
33 85A 85A N CA 421 422 113.09 145.30 -40.90
34 2616 85A 86A C N 424 426 172.28 -134.00 57.16 1.33 -62.50 -162.63 38.86
34 86A 86A N CA 426 427 166.54 147.00 -40.90
35 2617 86A 87A C N 429 431 -119.63 -134.00 15.07 0.36 -62.50 -174.35 33.47
35 87A 87A N CA 431 432 142.46 147.00 -40.90
36 2618 87A 88A C N 434 436 -131.32 -134.00 3.48 0.20 -62.50 -176.70 33.72
36 88A 88A N CA 436 437 149.22 147.00 -40.90
37 2619 88A 89A C N 439 441 -71.84 -68.20 11.17 0.77 -62.50 163.50 27.26
37 89A 89A N CA 441 442 155.86 145.30 -40.90
38 2621 90A 91A C N 449 451 -85.04 -68.20 45.68 3.11 -62.50 133.26 23.01
38 91A 91A N CA 451 452 -172.23 145.30 -40.90
39 2626 95A 96A C N 474 476 79.92 55.40 53.15 1.93 -62.50 145.96 29.15
39 96A 96A N CA 476 477 -8.95 38.20 -40.90
40 2629 98A 99A C N 489 491 -67.46 -62.50 9.77 1.87 -68.20 165.38 13.36
40 99A 99A N CA 491 492 -49.32 -40.90 145.30
41 2631 100A 101A C N 499 501 15.91 -68.20 100.35 6.62 -68.20 100.35 6.62
41 101A 101A N CA 501 502 90.58 145.30 145.30
42 2633 102A 103A C N 509 511 67.66 55.40 17.14 1.94 -62.50 158.85 32.22
42 103A 103A N CA 511 512 50.17 38.20 -40.90
43 2634 103A 104A C N 514 516 -116.14 -134.00 27.80 1.66 -62.50 160.05 29.09
43 104A 104A N CA 516 517 168.31 147.00 -40.90
44 2635 104A 105A C N 519 521 -23.76 -62.50 49.84 10.07 -62.50 49.84 10.07
44 105A 105A N CA 521 522 -9.53 -40.90 -40.90
45 2663 132A 133A C N 659 661 80.28 -134.00 160.18 3.64 -62.50 177.60 28.48
45 133A 133A N CA 661 662 -146.52 147.00 -40.90
46 2676 145A 146A C N 724 726 51.40 55.40 9.19 0.33 -62.50 143.55 29.04
46 146A 146A N CA 726 727 46.47 38.20 -40.90
47 2685 154A 155A C N 769 771 71.32 55.40 37.92 1.37 -62.50 141.08 28.48
47 155A 155A N CA 771 772 3.78 38.20 -40.90
48 2687 156A 157A C N 779 781 61.17 55.40 6.12 0.54 -62.50 145.70 29.61
48 157A 157A N CA 781 782 36.14 38.20 -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 8906 92A 160. CA O6 457 818 10.53 9.55 0.98 4.91 9.55 0.98 4.91
2 8908 92A 161. CA O4 457 830 10.15 9.21 0.94 4.72 9.21 0.94 4.72
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 3 7 6 49 67 83 79 110 131 117 116
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 1440.19653
seq_ala.B99990002.pdb 1663.68018
In [37]:
show_model('seq_ala.B99990001.pdb', '1lmp.pdb')
In [38]:
show_model('seq_ala.B99990002.pdb', '1lmp.pdb')
Модели покорёжило, особенно вылетили петли, но в целом вторичные структуры совпадают. Посмотрим на скоры разных моделей.
| Модель | Без лиганда | Нормальный лиганд | Сдвинутый лиганд | Аланины |
|---|---|---|---|---|
| Первая | 1573.72546 | 1368.42603 | 3903.77490 | 1440.19653 |
| Вторая | 1910.63782 | 1416.42871 | 3845.05859 | 1663.68018 |
Мы видим, что аланиновые лизоцимы оказываются лучше нормальных целевых моделей без лиганда и чуть хуже целевых моделей с лигандом. Модель со сдвинутым лигандом имеет высокий скор потому, что у неё неудовлетворённое ограничение на расстояние между лигандом и далёкими АК. В целом, такие результаты говорят о том, что смоделировать и подогнать можно много чего, это не всегда будет отражением биологии.
На самом деле, мы немного жульничаем, когда отрисовываем только картонки, ведь в PDB указывается, какие отрезки цепи как рисовать. Но ход цепи такие рисунки отражают правильно, добавляя информацию о структуре (но не боковых радикалов, что может быть не очень нужно в нашей задаче).