Гомологичное моделирование комплекса белка с лигандом¶
In [ ]:
import sys
import modeller
import _modeller
import modeller.automodel
In [3]:
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, Darwin MacBook-Pro-Polina.local 19.0.0 x86_64
Date and time of compilation : 2020/04/06 12:04:46
MODELLER executable type : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2020/04/17 17:03:28
In [4]:
alignm=modeller.alignment(env)
In [5]:
#добавим последовательность для моделирования и структуру известного лизоцима форели
alignm.append(file='Q6QGP7.fasta', align_codes='all',alignment_format='FASTA')
#создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
#и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
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.
In [6]:
#поправим идентификаторы
alignm[0].code = 'ENLYS_BPT5' #этот белок был использован
alignm[1].code = '1lmp'
In [7]:
#делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [8]:
#посмотрим на получившееся выравнивание
! cat all_in_one.ali
>P1;ENLYS_BPT5 sequence:: : : : :::-1.00:-1.00 MSFKFGKNSEKQLATVKPELQKVARRALELSPYDFTIVQGIRTVAQSAQNIANGTSFLKDPSKSKHITGDAIDFA PYINGKIDWNDLEAFWAVKKAFEQAGKELGIKLRFGADWNASGDYHDEIKRGTYDGGHVELV* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGA KNVCGIRCSQLLTD--DLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
In [9]:
#построим модель и выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
ENLYS_BPT5 1lmp
In [10]:
#создаем объект automodel и проводим моделирование
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns = pdb.code, sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied 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 135:
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 136:
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.
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: 11086 10127
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 : 137
Number of all, selected real atoms : 1081 1081
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10127 10127
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2727
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 : 1626.2356
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 : 1105 0 9 0.012 0.012 47.198 1.000
2 Bond angle potential : 1489 0 12 2.486 2.486 175.23 1.000
3 Stereochemical cosine torsion poten: 698 0 35 49.725 49.725 256.64 1.000
4 Stereochemical improper torsion pot: 459 0 0 1.425 1.425 19.156 1.000
5 Soft-sphere overlap restraints : 2727 0 1 0.007 0.007 16.473 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 4 17 0.528 0.528 224.92 1.000
10 Distance restraints 2 (N-O) : 2591 14 54 0.738 0.738 574.90 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: 136 0 2 4.871 4.871 38.056 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 3 81.059 81.059 42.414 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 5 76.517 76.517 49.816 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 1 68.884 68.884 29.958 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 68.271 68.271 11.934 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) : 764 0 0 0.365 0.365 12.123 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: 135 30 21 36.764 80.867 116.91 1.000
26 Distance restraints 4 (SDCH-SDCH) : 87 0 0 1.076 1.076 10.508 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: ENLYS_BPT5.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: 19456.0762
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7627 47S 137V N O 368 1080 12.98 8.18 4.80 6.01 8.18 4.80 6.01
2 7643 48A 137V N O 374 1080 14.97 8.62 6.35 7.99 8.62 6.35 7.99
3 7657 49Q 137V N O 379 1080 15.58 8.17 7.41 10.79 8.17 7.41 10.79
4 7665 50N 137V N O 388 1080 17.49 9.76 7.73 7.85 9.76 7.73 7.85
5 7674 51I 137V N O 396 1080 18.91 10.84 8.07 8.84 10.84 8.07 8.84
6 7703 53N 137V N O 409 1080 17.02 9.99 7.03 9.57 9.99 7.03 9.57
7 7727 54G 137V N O 417 1080 14.13 8.19 5.95 8.89 8.19 5.95 8.89
8 7753 55T 137V N O 421 1080 11.45 6.08 5.36 9.44 6.08 5.36 9.44
9 8009 63K 137V N O 483 1080 11.82 8.00 3.82 5.83 8.00 3.82 5.83
10 8034 64S 137V N O 492 1080 13.84 9.46 4.38 5.07 9.46 4.38 5.07
11 8966 114W 137V N O 889 1080 8.31 5.60 2.71 4.56 5.60 2.71 4.56
-------------------------------------------------------------------------------------------------
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 3752 1M 2S C N 7 9 -69.31 -72.40 3.42 0.19 -64.10 174.14 12.93
1 2S 2S N CA 9 10 150.94 152.40 -35.00
2 3753 2S 3F C N 13 15 -142.80 -124.20 26.36 0.71 -63.20 173.11 29.13
2 3F 3F N CA 15 16 161.98 143.30 -44.30
3 3754 3F 4K C N 24 26 -100.47 -118.00 44.98 1.88 -62.90 143.49 16.96
3 4K 4K N CA 26 27 97.68 139.10 -40.80
4 3769 18P 19E C N 141 143 63.32 54.60 9.19 1.19 -63.60 153.08 26.33
4 19E 19E N CA 143 144 45.28 42.40 -40.30
5 3774 23V 24A C N 183 185 55.81 55.40 5.92 0.32 -62.50 139.12 28.28
5 24A 24A N CA 185 186 32.30 38.20 -40.90
6 3789 38V 39Q C N 306 308 -132.40 -63.80 84.20 11.44 -63.80 84.20 11.44
6 39Q 39Q N CA 308 309 8.52 -40.30 -40.30
7 3790 39Q 40G C N 315 317 64.66 78.70 36.72 0.56 82.20 141.76 7.75
7 40G 40G N CA 317 318 -132.17 -166.10 8.50
8 3791 40G 41I C N 319 321 -133.07 -120.60 78.53 4.97 -63.40 118.92 18.09
8 41I 41I N CA 321 322 52.76 130.30 -43.60
9 3794 43T 44V C N 345 347 -104.13 -125.40 81.39 3.45 -62.40 114.98 12.74
9 44V 44V N CA 347 348 64.74 143.30 -42.40
10 3801 50N 51I C N 394 396 -109.09 -120.60 64.70 3.26 -63.40 119.33 18.31
10 51I 51I N CA 396 397 66.64 130.30 -43.60
11 3802 51I 52A C N 402 404 58.00 55.40 21.10 1.06 -62.50 133.80 27.19
11 52A 52A N CA 404 405 17.26 38.20 -40.90
12 3819 68T 69G C N 530 532 -96.89 -80.20 39.13 0.91 82.20 -120.51 18.54
12 69G 69G N CA 532 533 -150.50 174.10 8.50
13 3820 69G 70D C N 534 536 -128.00 -63.30 72.14 9.50 54.50 -175.87 18.61
13 70D 70D N CA 536 537 -8.10 -40.00 40.90
14 3824 73D 74F C N 563 565 57.02 58.10 6.55 0.44 -63.20 146.46 26.43
14 74F 74F N CA 565 566 39.36 32.90 -44.30
15 3826 75A 76P C N 579 581 -94.53 -64.50 32.94 2.69 -58.70 172.53 17.22
15 76P 76P N CA 581 582 160.73 147.20 -30.50
16 3827 76P 77Y C N 586 588 -111.47 -98.40 27.49 2.56 -63.50 155.22 22.41
16 77Y 77Y N CA 588 589 104.22 128.40 -43.40
17 3840 89A 90F C N 695 697 -37.44 -71.40 34.68 2.13 -63.20 179.85 26.71
17 90F 90F N CA 697 698 133.70 140.70 -44.30
18 3843 92A 93V C N 725 727 -115.53 -125.40 95.81 4.51 -62.40 104.86 11.48
18 93V 93V N CA 727 728 48.00 143.30 -42.40
19 3854 103E 104L C N 811 813 -70.98 -70.70 13.36 1.00 -63.50 164.01 23.21
19 104L 104L N CA 813 814 154.96 141.60 -41.20
20 3855 104L 105G C N 819 821 109.51 82.20 46.06 1.28 -62.40 172.37 31.27
20 105G 105G N CA 821 822 -28.59 8.50 -41.20
21 3861 110F 111G C N 870 872 -58.29 -62.40 19.93 3.19 82.20 143.70 10.57
21 111G 111G N CA 872 873 -21.70 -41.20 8.50
22 3867 116A 117S C N 914 916 -66.59 -72.40 12.00 0.90 -64.10 162.11 11.89
22 117S 117S N CA 916 917 162.90 152.40 -35.00
23 3868 117S 118G C N 920 922 86.41 78.70 49.47 1.72 -62.40 167.11 25.93
23 118G 118G N CA 922 923 -117.24 -166.10 -41.20
24 3876 125K 126R C N 988 990 -55.05 -125.20 71.10 3.15 -63.00 166.94 22.03
24 126R 126R N CA 990 991 152.15 140.60 -41.10
25 3877 126R 127G C N 999 1001 94.34 82.20 40.02 1.35 -62.40 157.17 28.52
25 127G 127G N CA 1001 1002 -29.63 8.50 -41.20
26 3879 128T 129Y C N 1010 1012 -136.31 -124.30 76.07 4.55 -63.50 126.69 17.48
26 129Y 129Y N CA 1012 1013 60.28 135.40 -43.40
27 3882 131G 132G C N 1034 1036 153.35 78.70 104.88 2.39 -62.40 -143.51 30.15
27 132G 132G N CA 1036 1037 120.23 -166.10 -41.20
28 3883 132G 133H C N 1038 1040 -84.53 -67.60 19.90 1.75 56.30 166.46 19.13
28 133H 133H N CA 1040 1041 129.55 140.00 40.80
29 3885 134V 135E C N 1055 1057 -177.29 -117.80 59.50 2.16 -63.60 -148.95 24.38
29 135E 135E N CA 1057 1058 137.50 136.80 -40.30
30 3886 135E 136L C N 1064 1066 -163.51 -108.50 90.69 4.19 -63.50 151.79 27.02
30 136L 136L N CA 1066 1067 -155.39 132.50 -41.20
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 13 21 90 113 166 148 171 178 198 212
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1081 1081
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10127 10127
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2713
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 : 1340.9211
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 : 1105 0 7 0.010 0.010 34.070 1.000
2 Bond angle potential : 1489 0 9 2.317 2.317 155.64 1.000
3 Stereochemical cosine torsion poten: 698 0 35 50.251 50.251 259.49 1.000
4 Stereochemical improper torsion pot: 459 0 0 1.243 1.243 14.285 1.000
5 Soft-sphere overlap restraints : 2713 0 0 0.005 0.005 6.5627 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 4 16 0.509 0.509 198.52 1.000
10 Distance restraints 2 (N-O) : 2591 13 28 0.632 0.632 399.58 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: 136 0 1 4.934 4.934 39.049 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 2 85.565 85.565 45.043 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 1 91.151 91.151 39.828 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 66.078 66.078 21.793 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 82.156 82.156 12.224 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) : 764 0 0 0.399 0.399 11.625 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: 135 19 19 35.716 68.088 92.595 1.000
26 Distance restraints 4 (SDCH-SDCH) : 87 0 0 1.154 1.154 10.609 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: ENLYS_BPT5.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: 17304.1328
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7627 47S 137V N O 368 1080 12.25 8.18 4.08 5.10 8.18 4.08 5.10
2 7643 48A 137V N O 374 1080 14.46 8.62 5.83 7.34 8.62 5.83 7.34
3 7657 49Q 137V N O 379 1080 14.80 8.17 6.63 9.66 8.17 6.63 9.66
4 7665 50N 137V N O 388 1080 16.96 9.76 7.19 7.31 9.76 7.19 7.31
5 7674 51I 137V N O 396 1080 18.11 10.84 7.26 7.96 10.84 7.26 7.96
6 7703 53N 137V N O 409 1080 16.31 9.99 6.32 8.60 9.99 6.32 8.60
7 7727 54G 137V N O 417 1080 13.49 8.19 5.31 7.93 8.19 5.31 7.93
8 7753 55T 137V N O 421 1080 10.75 6.08 4.67 8.22 6.08 4.67 8.22
9 8009 63K 137V N O 483 1080 11.29 8.00 3.28 5.02 8.00 3.28 5.02
10 8966 114W 137V N O 889 1080 8.30 5.60 2.70 4.56 5.60 2.70 4.56
-------------------------------------------------------------------------------------------------
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 3752 1M 2S C N 7 9 -74.73 -72.40 8.83 0.44 -64.10 164.43 12.58
1 2S 2S N CA 9 10 160.92 152.40 -35.00
2 3753 2S 3F C N 13 15 -72.13 -71.40 1.58 0.10 -63.20 173.82 24.74
2 3F 3F N CA 15 16 142.10 140.70 -44.30
3 3754 3F 4K C N 24 26 -85.24 -70.20 42.25 3.38 -62.90 143.47 17.53
3 4K 4K N CA 26 27 100.92 140.40 -40.80
4 3769 18P 19E C N 141 143 69.22 54.60 15.97 1.43 -63.60 153.16 26.35
4 19E 19E N CA 143 144 35.97 42.40 -40.30
5 3774 23V 24A C N 183 185 52.99 55.40 2.52 0.23 -62.50 140.40 28.49
5 24A 24A N CA 185 186 38.94 38.20 -40.90
6 3789 38V 39Q C N 306 308 -139.65 -63.80 87.81 12.27 -63.80 87.81 12.27
6 39Q 39Q N CA 308 309 3.93 -40.30 -40.30
7 3791 40G 41I C N 319 321 32.84 -97.30 139.89 8.07 -63.40 153.44 28.49
7 41I 41I N CA 321 322 75.90 127.20 -43.60
8 3801 50N 51I C N 394 396 -101.20 -120.60 76.10 3.63 -63.40 107.20 16.50
8 51I 51I N CA 396 397 56.72 130.30 -43.60
9 3802 51I 52A C N 402 404 64.09 55.40 31.64 1.28 -62.50 135.63 27.47
9 52A 52A N CA 404 405 7.77 38.20 -40.90
10 3819 68T 69G C N 530 532 -100.67 -80.20 40.12 0.95 82.20 -121.38 7.92
10 69G 69G N CA 532 533 -151.40 174.10 8.50
11 3820 69G 70D C N 534 536 -126.74 -63.30 67.65 9.36 54.50 -172.25 18.41
11 70D 70D N CA 536 537 -16.49 -40.00 40.90
12 3827 76P 77Y C N 586 588 55.60 55.90 15.70 1.08 -63.50 154.62 29.28
12 77Y 77Y N CA 588 589 55.20 39.50 -43.40
13 3840 89A 90F C N 695 697 -45.46 -71.40 29.07 2.38 -63.20 162.83 21.44
13 90F 90F N CA 697 698 153.84 140.70 -44.30
14 3861 110F 111G C N 870 872 -56.83 -62.40 20.56 3.36 82.20 142.21 10.47
14 111G 111G N CA 872 873 -21.41 -41.20 8.50
15 3869 118G 119D C N 924 926 -124.40 -63.30 62.39 9.22 -63.30 62.39 9.22
15 119D 119D N CA 926 927 -27.39 -40.00 -40.00
16 3875 124I 125K C N 979 981 -105.11 -118.00 84.98 3.93 -62.90 104.79 12.07
16 125K 125K N CA 981 982 55.11 139.10 -40.80
17 3882 131G 132G C N 1034 1036 143.58 82.20 82.17 2.75 -62.40 154.09 27.72
17 132G 132G N CA 1036 1037 -46.12 8.50 -41.20
18 3885 134V 135E C N 1055 1057 165.54 -117.80 78.74 2.49 -63.60 -149.46 35.04
18 135E 135E N CA 1057 1058 154.77 136.80 -40.30
19 3886 135E 136L C N 1064 1066 -148.16 -108.50 48.46 2.14 -63.50 179.66 30.17
19 136L 136L N CA 1066 1067 160.34 132.50 -41.20
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 19 19 93 97 143 140 171 200 194 197
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5.B99990001.pdb 1626.23560
ENLYS_BPT5.B99990002.pdb 1340.92114
In [20]:
print('ENLYS_BPT5.B99990001.pdb is green')
display(Image('1.png', width=600))
print('ENLYS_BPT5.B99990002.pdb is yellow')
display(Image('2.png', width=600))
ENLYS_BPT5.B99990001.pdb is green
ENLYS_BPT5.B99990002.pdb is yellow
Но нет лиганда в последовательности ENLYS_BPT5! Добавим его¶
In [11]:
#добавляем лиганд
seq_lig = ''
for res in alignm[0].residues:
seq_lig += res.code
for lig in alignm[1].residues[-3:]:
seq_lig += lig.code
alignm.append_sequence(seq_lig)
alignm[2].code = 'ENLYS_BPT5_lig'
del alignm[0]
In [12]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [13]:
! cat all_in_one2.ali
>P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGA KNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCG-----V...* >P1;ENLYS_BPT5_lig sequence::1 : :+140 : :undefined:undefined:-1.00:-1.00 MSFKFGKNSEKQLATVKPELQKVARRALELSPYDFTIVQGIRTVAQSAQNIANGTSFLKDPSKSKHITGDAIDFA PYINGKIDWNDLEAFWAVKKAFEQAGKELGIKLRFGADWNASGDYHDEIKRGTYDGGHVELV...*
In [14]:
# выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
# 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()
ENLYS_BPT5_lig 1lmp
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: 18 137
atom names : C +N
atom indices : 1079 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 137
atom names : C CA +N O
atom indices : 1079 1075 0 1080
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: 12474 11515
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 : 140
Number of all, selected real atoms : 1124 1124
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11515 11515
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2731
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 : 926.2369
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 : 1105 0 0 0.006 0.006 9.4303 1.000
2 Bond angle potential : 1489 0 5 2.207 2.207 138.05 1.000
3 Stereochemical cosine torsion poten: 698 0 35 50.352 50.352 264.66 1.000
4 Stereochemical improper torsion pot: 459 0 0 1.324 1.324 16.722 1.000
5 Soft-sphere overlap restraints : 2731 2 2 0.008 0.008 21.174 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.202 0.202 46.433 1.000
10 Distance restraints 2 (N-O) : 2564 0 3 0.350 0.350 128.65 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.479 4.479 32.171 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 2 84.316 84.316 57.115 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 1 75.422 75.422 47.875 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 75.124 75.124 23.952 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 87.033 87.033 12.758 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) : 758 0 0 0.363 0.363 9.7330 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: 135 24 22 35.599 73.404 100.54 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 0 0.681 0.681 4.5712 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.031 0.031 12.407 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: ENLYS_BPT5_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16356.3848
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3752 1M 2S C N 7 9 -133.57 -136.60 13.43 0.61 -64.10 -173.47 11.55
1 2S 2S N CA 9 10 138.12 151.20 -35.00
2 3753 2S 3F C N 13 15 -103.75 -124.20 24.60 0.64 -63.20 178.59 22.24
2 3F 3F N CA 15 16 129.63 143.30 -44.30
3 3754 3F 4K C N 24 26 -136.81 -118.00 24.18 1.19 -62.90 -179.48 20.78
3 4K 4K N CA 26 27 123.90 139.10 -40.80
4 3768 17K 18P C N 134 136 -77.60 -64.50 41.51 3.81 -58.70 139.60 10.08
4 18P 18P N CA 136 137 107.81 147.20 -30.50
5 3769 18P 19E C N 141 143 -50.07 -69.30 65.14 4.28 -63.60 121.32 16.93
5 19E 19E N CA 143 144 80.26 142.50 -40.30
6 3774 23V 24A C N 183 185 54.67 55.40 2.32 0.20 -62.50 140.15 28.46
6 24A 24A N CA 185 186 36.00 38.20 -40.90
7 3789 38V 39Q C N 306 308 -142.73 -63.80 94.90 13.01 -63.80 94.90 13.01
7 39Q 39Q N CA 308 309 12.38 -40.30 -40.30
8 3791 40G 41I C N 319 321 31.95 -97.30 139.73 8.18 -63.40 151.50 28.13
8 41I 41I N CA 321 322 74.12 127.20 -43.60
9 3794 43T 44V C N 345 347 -100.96 -125.40 97.62 4.17 -62.40 99.01 10.92
9 44V 44V N CA 347 348 48.79 143.30 -42.40
10 3801 50N 51I C N 394 396 -93.52 -120.60 90.02 4.16 -63.40 93.06 14.38
10 51I 51I N CA 396 397 44.45 130.30 -43.60
11 3802 51I 52A C N 402 404 54.31 55.40 5.50 0.42 -62.50 138.12 28.07
11 52A 52A N CA 404 405 32.81 38.20 -40.90
12 3819 68T 69G C N 530 532 -128.53 -62.40 76.17 11.63 82.20 149.74 9.59
12 69G 69G N CA 532 533 -3.42 -41.20 8.50
13 3824 73D 74F C N 563 565 58.77 58.10 8.18 0.75 -63.20 148.86 26.86
13 74F 74F N CA 565 566 41.05 32.90 -44.30
14 3827 76P 77Y C N 586 588 59.16 55.90 9.77 0.93 -63.50 153.39 29.06
14 77Y 77Y N CA 588 589 48.71 39.50 -43.40
15 3855 104L 105G C N 819 821 20.14 -62.40 88.95 14.23 82.20 103.52 7.66
15 105G 105G N CA 821 822 -74.35 -41.20 8.50
16 3867 116A 117S C N 914 916 -134.64 -136.60 8.30 0.38 -64.10 -168.40 11.86
16 117S 117S N CA 916 917 143.14 151.20 -35.00
17 3868 117S 118G C N 920 922 114.60 82.20 59.02 1.62 -62.40 177.00 31.64
17 118G 118G N CA 922 923 -40.83 8.50 -41.20
18 3870 119D 120Y C N 932 934 56.76 55.90 0.96 0.12 -63.50 146.30 27.71
18 120Y 120Y N CA 934 935 39.92 39.50 -43.40
19 3876 125K 126R C N 988 990 -82.78 -125.20 54.83 1.63 -63.00 148.29 18.77
19 126R 126R N CA 990 991 105.86 140.60 -41.10
20 3877 126R 127G C N 999 1001 116.61 82.20 37.90 1.80 -62.40 -177.82 33.70
20 127G 127G N CA 1001 1002 -7.38 8.50 -41.20
21 3879 128T 129Y C N 1010 1012 57.08 55.90 5.30 0.29 -124.30 -154.76 17.05
21 129Y 129Y N CA 1012 1013 34.33 39.50 135.40
22 3880 129Y 130D C N 1022 1024 -104.04 -96.50 36.17 1.51 -63.30 125.62 13.59
22 130D 130D N CA 1024 1025 78.83 114.20 -40.00
23 3881 130D 131G C N 1030 1032 -104.25 -80.20 58.36 1.37 82.20 -136.25 7.90
23 131G 131G N CA 1032 1033 -132.73 174.10 8.50
24 3886 135E 136L C N 1064 1066 -78.20 -70.70 11.33 0.71 -63.50 169.35 24.38
24 136L 136L N CA 1066 1067 150.09 141.60 -41.20
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 11 18 79 110 159 145 143 176 220 216
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1124 1124
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11515 11515
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2631
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 : 955.0385
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 : 1105 0 0 0.006 0.006 10.313 1.000
2 Bond angle potential : 1489 0 7 2.274 2.274 147.44 1.000
3 Stereochemical cosine torsion poten: 698 0 31 49.237 49.237 253.09 1.000
4 Stereochemical improper torsion pot: 459 1 1 1.874 1.874 30.385 1.000
5 Soft-sphere overlap restraints : 2631 1 2 0.008 0.008 20.538 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.219 0.219 49.279 1.000
10 Distance restraints 2 (N-O) : 2564 0 15 0.383 0.383 163.77 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: 136 0 4 4.690 4.690 35.280 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 6 87.565 87.565 56.054 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 1 81.096 81.096 43.068 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 72.873 72.873 22.520 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 84.722 84.722 11.577 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) : 758 0 0 0.331 0.331 10.793 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: 135 23 16 31.652 70.066 72.084 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 1 1.027 1.027 12.196 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.037 0.037 16.647 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: ENLYS_BPT5_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16298.3682
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3752 1M 2S C N 7 9 -68.00 -72.40 4.47 0.34 -64.10 171.88 12.69
1 2S 2S N CA 9 10 153.16 152.40 -35.00
2 3753 2S 3F C N 13 15 -99.57 -124.20 34.17 0.91 -63.20 167.90 21.00
2 3F 3F N CA 15 16 119.61 143.30 -44.30
3 3754 3F 4K C N 24 26 -134.42 -118.00 31.26 1.62 -62.90 169.17 19.45
3 4K 4K N CA 26 27 112.51 139.10 -40.80
4 3768 17K 18P C N 134 136 -77.44 -64.50 37.95 3.53 -58.70 143.25 10.39
4 18P 18P N CA 136 137 111.52 147.20 -30.50
5 3769 18P 19E C N 141 143 -50.64 -69.30 71.04 4.75 -63.60 114.99 16.06
5 19E 19E N CA 143 144 73.96 142.50 -40.30
6 3773 22K 23V C N 176 178 -58.27 -62.40 29.31 3.49 -125.40 160.04 9.10
6 23V 23V N CA 178 179 -71.42 -42.40 143.30
7 3774 23V 24A C N 183 185 -112.97 -134.00 76.58 3.76 -62.50 124.91 18.77
7 24A 24A N CA 185 186 73.36 147.00 -40.90
8 3789 38V 39Q C N 306 308 -151.37 -63.80 106.76 14.54 -63.80 106.76 14.54
8 39Q 39Q N CA 308 309 20.77 -40.30 -40.30
9 3790 39Q 40G C N 315 317 72.19 78.70 6.69 0.29 82.20 173.37 8.92
9 40G 40G N CA 317 318 -164.58 -166.10 8.50
10 3791 40G 41I C N 319 321 -110.34 -97.30 56.33 5.67 -63.40 125.14 19.21
10 41I 41I N CA 321 322 72.40 127.20 -43.60
11 3801 50N 51I C N 394 396 -91.27 -120.60 89.64 4.07 -63.40 93.46 14.49
11 51I 51I N CA 396 397 45.60 130.30 -43.60
12 3802 51I 52A C N 402 404 51.38 55.40 4.08 0.41 -62.50 139.04 28.20
12 52A 52A N CA 404 405 38.87 38.20 -40.90
13 3819 68T 69G C N 530 532 -132.00 -62.40 75.90 12.03 82.20 147.09 9.09
13 69G 69G N CA 532 533 -10.93 -41.20 8.50
14 3824 73D 74F C N 563 565 55.95 58.10 12.30 0.82 -63.20 148.91 26.86
14 74F 74F N CA 565 566 45.01 32.90 -44.30
15 3827 76P 77Y C N 586 588 59.11 55.90 11.46 1.04 -63.50 154.44 29.26
15 77Y 77Y N CA 588 589 50.50 39.50 -43.40
16 3855 104L 105G C N 819 821 -54.96 -62.40 7.48 1.30 82.20 146.16 11.17
16 105G 105G N CA 821 822 -41.97 -41.20 8.50
17 3867 116A 117S C N 914 916 -132.41 -136.60 11.38 0.47 -64.10 -171.56 11.65
17 117S 117S N CA 916 917 140.62 151.20 -35.00
18 3868 117S 118G C N 920 922 116.72 82.20 61.80 1.70 -62.40 179.13 31.94
18 118G 118G N CA 922 923 -42.76 8.50 -41.20
19 3870 119D 120Y C N 932 934 53.90 55.90 3.19 0.36 -63.50 142.30 26.95
19 120Y 120Y N CA 934 935 37.01 39.50 -43.40
20 3879 128T 129Y C N 1010 1012 58.89 55.90 6.56 0.31 -124.30 -156.01 16.95
20 129Y 129Y N CA 1012 1013 33.66 39.50 135.40
21 3881 130D 131G C N 1030 1032 57.76 78.70 42.27 0.64 82.20 140.03 8.00
21 131G 131G N CA 1032 1033 -129.38 -166.10 8.50
22 3882 131G 132G C N 1034 1036 86.10 78.70 15.46 0.23 82.20 171.86 8.54
22 132G 132G N CA 1036 1037 -179.68 -166.10 8.50
23 3886 135E 136L C N 1064 1066 -101.21 -108.50 7.58 0.34 -63.50 175.73 22.53
23 136L 136L N CA 1066 1067 130.43 132.50 -41.20
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 23 13 86 111 142 142 160 184 179 206
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5_lig.B99990001.pdb 926.23694
ENLYS_BPT5_lig.B99990002.pdb 955.03845
In [41]:
print('ENLYS_BPT5_lig.B99990001.pdb is red \nScore - 926.23694')
display(Image('1l.png', width=600))
print('ENLYS_BPT5_lig.B99990002.pdb is white \nScore - 955.03845')
display(Image('2l.png', width=600))
ENLYS_BPT5_lig.B99990001.pdb is red Score - 926.23694
ENLYS_BPT5_lig.B99990002.pdb is white Score - 955.03845
Получилось достаточно хорошо вырованять вторичные структуры, имеющиеся различия наблюдаются в петлях
Переместим лиганд в другое место¶
In [23]:
! rm ENLYS_BPT5_lig.rsr
In [30]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:123','CA:114')]:
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 [31]:
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: 18 137
atom names : C +N
atom indices : 1079 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 18 137
atom names : C CA +N O
atom indices : 1079 1075 0 1080
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: 12475 11516
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 : 140
Number of all, selected real atoms : 1124 1124
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11516 11516
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2821
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 : 1572.2550
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 : 1105 0 1 0.007 0.007 17.384 1.000
2 Bond angle potential : 1489 0 14 2.498 2.498 182.87 1.000
3 Stereochemical cosine torsion poten: 698 0 39 50.681 50.681 271.18 1.000
4 Stereochemical improper torsion pot: 459 0 2 1.751 1.751 29.527 1.000
5 Soft-sphere overlap restraints : 2821 1 2 0.009 0.009 27.200 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 15 0.494 0.494 221.84 1.000
10 Distance restraints 2 (N-O) : 2564 5 22 0.565 0.565 312.12 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: 136 0 3 5.056 5.056 41.007 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 5 92.593 92.593 74.891 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 2 79.838 79.838 50.667 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 61.305 61.305 21.677 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 78.578 78.578 12.174 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) : 758 0 0 0.417 0.417 16.084 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: 135 27 20 34.207 75.950 147.46 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 1 1.112 1.112 12.006 1.000
27 Distance restraints 5 (X-Y) : 1402 1 4 0.070 0.070 134.16 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: ENLYS_BPT5_lig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 18793.9395
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 6652 123E 126R CA CA 965 991 8.16 5.61 2.56 4.60 5.61 2.56 4.60
-------------------------------------------------------------------------------------------------
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 9161 126R 123E N O 990 972 6.76 2.93 3.83 8.51 2.93 3.83 8.51
2 9179 127G 123E N O 1001 972 7.67 4.11 3.55 6.37 4.11 3.55 6.37
-------------------------------------------------------------------------------------------------
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 3753 2S 3F C N 13 15 -71.76 -71.40 14.07 1.14 -63.20 171.15 23.19
1 3F 3F N CA 15 16 126.63 140.70 -44.30
2 3754 3F 4K C N 24 26 -137.75 -118.00 28.54 1.44 -62.90 176.00 20.24
2 4K 4K N CA 26 27 118.49 139.10 -40.80
3 3769 18P 19E C N 141 143 74.63 54.60 23.92 1.83 -63.60 154.78 26.59
3 19E 19E N CA 143 144 29.34 42.40 -40.30
4 3774 23V 24A C N 183 185 53.78 55.40 4.70 0.42 -62.50 138.20 28.08
4 24A 24A N CA 185 186 33.78 38.20 -40.90
5 3782 31S 32P C N 246 248 -65.32 -64.50 90.09 6.68 -58.70 92.46 8.18
5 32P 32P N CA 248 249 -122.72 147.20 -30.50
6 3783 32P 33Y C N 253 255 37.37 -63.50 104.16 16.65 -63.50 104.16 16.65
6 33Y 33Y N CA 255 256 -69.36 -43.40 -43.40
7 3789 38V 39Q C N 306 308 -131.01 -63.80 72.97 10.66 -63.80 72.97 10.66
7 39Q 39Q N CA 308 309 -11.90 -40.30 -40.30
8 3791 40G 41I C N 319 321 26.65 -97.30 135.91 8.23 -63.40 146.10 27.08
8 41I 41I N CA 321 322 71.45 127.20 -43.60
9 3794 43T 44V C N 345 347 -96.65 -62.40 88.93 9.81 -62.40 88.93 9.81
9 44V 44V N CA 347 348 39.67 -42.40 -42.40
10 3801 50N 51I C N 394 396 -90.64 -63.40 88.63 13.72 -63.40 88.63 13.72
10 51I 51I N CA 396 397 40.73 -43.60 -43.60
11 3802 51I 52A C N 402 404 64.25 55.40 29.87 1.18 -62.50 136.46 27.66
11 52A 52A N CA 404 405 9.67 38.20 -40.90
12 3819 68T 69G C N 530 532 -97.46 -80.20 43.35 1.03 82.20 -122.95 18.38
12 69G 69G N CA 532 533 -146.14 174.10 8.50
13 3820 69G 70D C N 534 536 -126.20 -63.30 65.95 9.33 54.50 -170.59 18.33
13 70D 70D N CA 536 537 -20.16 -40.00 40.90
14 3824 73D 74F C N 563 565 51.35 58.10 20.15 1.09 -63.20 149.57 26.93
14 74F 74F N CA 565 566 51.89 32.90 -44.30
15 3827 76P 77Y C N 586 588 58.55 55.90 12.27 1.06 -63.50 154.59 29.29
15 77Y 77Y N CA 588 589 51.48 39.50 -43.40
16 3855 104L 105G C N 819 821 -57.08 -62.40 5.94 0.93 82.20 148.79 11.38
16 105G 105G N CA 821 822 -43.83 -41.20 8.50
17 3856 105G 106I C N 823 825 -93.97 -120.60 60.92 2.60 -63.40 122.98 19.21
17 106I 106I N CA 825 826 75.51 130.30 -43.60
18 3857 106I 107K C N 831 833 -26.25 -62.90 87.93 10.11 -118.00 135.84 6.89
18 107K 107K N CA 833 834 -120.73 -40.80 139.10
19 3867 116A 117S C N 914 916 -120.33 -136.60 37.55 1.49 -64.10 162.40 10.02
19 117S 117S N CA 916 917 117.35 151.20 -35.00
20 3868 117S 118G C N 920 922 127.33 82.20 59.47 2.03 -62.40 170.62 30.01
20 118G 118G N CA 922 923 -30.23 8.50 -41.20
21 3870 119D 120Y C N 932 934 52.54 55.90 4.11 0.50 -63.50 141.25 26.75
21 120Y 120Y N CA 934 935 37.14 39.50 -43.40
22 3874 123E 124I C N 971 973 -158.75 -120.60 38.36 2.53 -63.40 -158.09 30.75
22 124I 124I N CA 973 974 134.37 130.30 -43.60
23 3879 128T 129Y C N 1010 1012 53.15 55.90 3.73 0.45 -124.30 -157.09 11.22
23 129Y 129Y N CA 1012 1013 36.97 39.50 135.40
24 3880 129Y 130D C N 1022 1024 -120.65 -96.50 33.62 1.38 -63.30 142.83 15.22
24 130D 130D N CA 1024 1025 90.81 114.20 -40.00
25 3882 131G 132G C N 1034 1036 -81.70 -80.20 7.15 0.21 82.20 -121.99 7.24
25 132G 132G N CA 1036 1037 -178.91 174.10 8.50
26 3883 132G 133H C N 1038 1040 -84.64 -67.60 52.85 4.51 -63.20 134.00 15.53
26 133H 133H N CA 1040 1041 89.97 140.00 -42.30
27 3886 135E 136L C N 1064 1066 -78.46 -70.70 21.02 1.34 -63.50 158.37 22.88
27 136L 136L N CA 1066 1067 161.13 141.60 -41.20
-------------------------------------------------------------------------------------------------
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 11516 123E 114W O CA 972 890 4.90 3.00 1.90 19.03 3.00 1.90 19.03
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 19 20 109 123 168 183 133 186 224 213
<< 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 : 140
Number of all, selected real atoms : 1124 1124
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11516 11516
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2808
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 : 1608.3838
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 : 1105 0 1 0.007 0.007 17.798 1.000
2 Bond angle potential : 1489 0 8 2.425 2.425 169.51 1.000
3 Stereochemical cosine torsion poten: 698 0 32 49.840 49.840 261.66 1.000
4 Stereochemical improper torsion pot: 459 0 1 1.574 1.574 23.233 1.000
5 Soft-sphere overlap restraints : 2808 2 2 0.010 0.010 32.087 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 5 19 0.497 0.497 235.31 1.000
10 Distance restraints 2 (N-O) : 2564 7 44 0.619 0.619 417.49 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: 136 0 1 5.061 5.061 41.078 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 2 85.724 85.724 50.985 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 2 75.982 75.982 41.447 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 77.235 77.235 25.397 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 86.248 86.248 12.914 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) : 758 0 0 0.367 0.367 13.778 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: 135 33 22 38.263 85.782 133.73 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 0 0.713 0.713 5.2619 1.000
27 Distance restraints 5 (X-Y) : 1402 1 4 0.070 0.070 126.71 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: ENLYS_BPT5_lig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 20273.0918
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 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 9161 126R 123E N O 990 972 6.61 2.93 3.68 8.18 2.93 3.68 8.18
2 9179 127G 123E N O 1001 972 8.88 4.11 4.77 8.54 4.11 4.77 8.54
3 9194 128T 123E N O 1005 972 10.19 5.93 4.26 4.74 5.93 4.26 4.74
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3752 1M 2S C N 7 9 -140.03 -136.60 15.52 0.71 -64.10 175.89 18.17
1 2S 2S N CA 9 10 166.34 151.20 -35.00
2 3753 2S 3F C N 13 15 -71.74 -71.40 4.67 0.39 -63.20 179.86 25.55
2 3F 3F N CA 15 16 136.05 140.70 -44.30
3 3754 3F 4K C N 24 26 -132.12 -118.00 14.77 0.64 -62.90 -171.29 21.82
3 4K 4K N CA 26 27 134.76 139.10 -40.80
4 3769 18P 19E C N 141 143 68.99 54.60 17.08 1.32 -63.60 151.60 26.07
4 19E 19E N CA 143 144 33.20 42.40 -40.30
5 3774 23V 24A C N 183 185 63.09 -68.20 143.94 13.82 -62.50 170.15 26.57
5 24A 24A N CA 185 186 -155.70 145.30 -40.90
6 3775 24A 25R C N 188 190 -76.06 -63.00 20.20 2.33 57.30 147.79 18.39
6 25R 25R N CA 190 191 -25.69 -41.10 38.00
7 3791 40G 41I C N 319 321 43.24 -63.40 153.12 28.67 -63.40 153.12 28.67
7 41I 41I N CA 321 322 66.29 -43.60 -43.60
8 3794 43T 44V C N 345 347 -101.07 -125.40 79.94 3.28 -62.40 116.18 12.96
8 44V 44V N CA 347 348 67.15 143.30 -42.40
9 3801 50N 51I C N 394 396 -93.52 -63.40 89.90 13.87 -63.40 89.90 13.87
9 51I 51I N CA 396 397 41.11 -43.60 -43.60
10 3802 51I 52A C N 402 404 59.17 55.40 21.82 1.02 -62.50 134.62 27.35
10 52A 52A N CA 404 405 16.71 38.20 -40.90
11 3815 64S 65K C N 496 498 -120.15 -62.90 64.70 8.88 -62.90 64.70 8.88
11 65K 65K N CA 498 499 -10.66 -40.80 -40.80
12 3816 65K 66H C N 505 507 -131.19 -63.20 79.60 9.98 -63.20 79.60 9.98
12 66H 66H N CA 507 508 -0.92 -42.30 -42.30
13 3819 68T 69G C N 530 532 -104.49 -80.20 25.39 1.85 82.20 -125.36 18.13
13 69G 69G N CA 532 533 166.68 174.10 8.50
14 3820 69G 70D C N 534 536 -76.38 -63.30 14.75 1.92 54.50 150.40 19.51
14 70D 70D N CA 536 537 -33.19 -40.00 40.90
15 3824 73D 74F C N 563 565 51.95 58.10 16.39 0.86 -63.20 147.64 26.61
15 74F 74F N CA 565 566 48.10 32.90 -44.30
16 3826 75A 76P C N 579 581 -89.21 -64.50 34.40 3.77 -58.70 156.77 10.68
16 76P 76P N CA 581 582 123.27 147.20 -30.50
17 3827 76P 77Y C N 586 588 -81.37 -98.40 20.10 1.38 -63.50 162.11 24.83
17 77Y 77Y N CA 588 589 117.72 128.40 -43.40
18 3828 77Y 78I C N 598 600 -107.68 -120.60 13.85 1.08 -63.40 -175.73 28.82
18 78I 78I N CA 600 601 135.27 130.30 -43.60
19 3829 78I 79N C N 606 608 102.85 55.90 65.12 3.97 -63.20 169.79 27.07
19 79N 79N N CA 608 609 -5.63 39.50 -41.10
20 3841 90F 91W C N 706 708 -110.55 -63.00 83.60 9.36 -63.00 83.60 9.36
20 91W 91W N CA 708 709 24.56 -44.20 -44.20
21 3855 104L 105G C N 819 821 -55.38 -62.40 7.60 1.43 82.20 145.32 11.04
21 105G 105G N CA 821 822 -38.29 -41.20 8.50
22 3867 116A 117S C N 914 916 -118.47 -136.60 30.82 1.09 -64.10 170.19 10.48
22 117S 117S N CA 916 917 126.27 151.20 -35.00
23 3868 117S 118G C N 920 922 123.23 82.20 58.19 1.81 -62.40 174.58 30.83
23 118G 118G N CA 922 923 -32.76 8.50 -41.20
24 3870 119D 120Y C N 932 934 53.12 55.90 4.16 0.48 -63.50 141.31 26.76
24 120Y 120Y N CA 934 935 36.41 39.50 -43.40
25 3874 123E 124I C N 971 973 -178.85 -120.60 65.59 3.40 -63.40 -165.98 35.85
25 124I 124I N CA 973 974 160.46 130.30 -43.60
26 3876 125K 126R C N 988 990 -55.65 -125.20 71.72 2.45 -63.00 164.33 22.70
26 126R 126R N CA 990 991 123.07 140.60 -41.10
27 3877 126R 127G C N 999 1001 119.46 82.20 51.49 1.65 -62.40 178.71 31.32
27 127G 127G N CA 1001 1002 -27.04 8.50 -41.20
28 3879 128T 129Y C N 1010 1012 57.75 55.90 5.82 0.29 -124.30 -155.17 17.02
28 129Y 129Y N CA 1012 1013 33.98 39.50 135.40
29 3881 130D 131G C N 1030 1032 -88.55 -80.20 54.63 1.74 82.20 -138.93 17.18
29 131G 131G N CA 1032 1033 -131.91 174.10 8.50
30 3883 132G 133H C N 1038 1040 -110.49 -125.60 49.23 2.12 -63.20 140.26 20.63
30 133H 133H N CA 1040 1041 -174.35 138.80 -42.30
31 3884 133H 134V C N 1048 1050 -62.18 -62.40 2.67 0.33 -125.40 -177.09 10.27
31 134V 134V N CA 1050 1051 -45.06 -42.40 143.30
32 3885 134V 135E C N 1055 1057 -102.12 -117.80 17.00 0.79 -63.60 -179.51 26.24
32 135E 135E N CA 1057 1058 143.37 136.80 -40.30
33 3886 135E 136L C N 1064 1066 -96.71 -108.50 21.63 1.23 -63.50 171.41 25.82
33 136L 136L N CA 1066 1067 150.63 132.50 -41.20
-------------------------------------------------------------------------------------------------
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 11516 123E 114W O CA 972 890 4.81 3.00 1.81 18.15 3.00 1.81 18.15
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 10 16 99 132 159 148 189 184 212 212
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5_lig.B99990001.pdb 1572.25500
ENLYS_BPT5_lig.B99990002.pdb 1608.38379
In [33]:
print('ENLYS_BPT5_lig.B99990001.pdb is purple')
display(Image('1lc.png', width=600))
print('ENLYS_BPT5_lig.B99990002.pdb is orange')
display(Image('2lc.png', width=600))
ENLYS_BPT5_lig.B99990001.pdb is purple
ENLYS_BPT5_lig.B99990002.pdb is orange
В целом все выглядит достаточно похоже, однако Score стал хуже 926.23694 и 955.03845 против 1572.25500 и 1608.38379
Заменим всех аминокислот на Ala¶
In [34]:
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')
ala_prot = 'A' * 120 + '...'
alignm.append_sequence(ala_prot)
alignm[0].code = 'pdb'
alignm[1].code = 'ala_changed'
In [35]:
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [36]:
! cat align_ala.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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;ala_changed sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [37]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ala_changed 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
----------------------------------------------
55 1 55 65 A A 16.730
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C +N
atom indices : 599 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C CA +N O
atom indices : 599 597 0 600
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: 8748 8155
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1129
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 : 1089.3650
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 : 600 0 1 0.008 0.008 11.707 1.000
2 Bond angle potential : 839 0 5 2.284 2.284 91.605 1.000
3 Stereochemical cosine torsion poten: 244 0 36 76.450 76.450 233.34 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.916 0.916 5.4183 1.000
5 Soft-sphere overlap restraints : 1129 1 2 0.011 0.011 15.809 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) : 1968 7 23 0.777 0.777 265.24 1.000
10 Distance restraints 2 (N-O) : 2093 7 33 0.773 0.773 343.90 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: 119 0 4 5.109 5.109 36.637 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) : 668 0 0 0.288 0.288 5.9758 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: 118 22 15 34.431 76.569 55.979 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.111 1.111 4.7122 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.043 0.043 19.048 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: ala_changed.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: 12038.6514
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 3583 56A 63A CA CA 277 312 12.79 7.04 5.75 5.43 7.04 5.75 5.43
2 3584 56A 64A CA CA 277 317 13.93 7.69 6.24 4.85 7.69 6.24 4.85
3 3585 56A 65A CA CA 277 322 11.20 5.45 5.75 6.61 5.45 5.75 6.61
4 3588 56A 68A CA CA 277 337 12.46 7.46 5.00 4.85 7.46 5.00 4.85
5 3589 56A 69A CA CA 277 342 9.99 6.07 3.92 5.50 6.07 3.92 5.50
6 3590 56A 70A CA CA 277 347 9.66 4.69 4.97 7.09 4.69 4.97 7.09
-------------------------------------------------------------------------------------------------
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 4905 38A 55A N O 186 275 8.35 5.51 2.85 4.85 5.51 2.85 4.85
2 5216 56A 63A N O 276 315 13.67 7.89 5.79 4.70 7.89 5.79 4.70
3 5217 56A 64A N O 276 320 13.36 7.21 6.15 4.67 7.21 6.15 4.67
4 5218 56A 65A N O 276 325 13.30 6.37 6.93 6.55 6.37 6.93 6.55
5 5221 56A 68A N O 276 340 12.97 7.02 5.95 5.55 7.02 5.95 5.55
6 5222 56A 69A N O 276 345 8.81 2.70 6.12 11.95 2.70 6.12 11.95
7 5389 71A 56A N O 351 280 5.86 2.97 2.89 6.10 2.97 2.89 6.10
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1938 15A 16A C N 74 76 78.84 55.40 27.25 1.99 -62.50 155.66 31.62
1 16A 16A N CA 76 77 24.31 38.20 -40.90
2 1941 18A 19A C N 89 91 65.66 55.40 23.81 0.86 -62.50 140.51 28.53
2 19A 19A N CA 91 92 16.71 38.20 -40.90
3 1943 20A 21A C N 99 101 53.99 55.40 3.98 0.35 -62.50 138.75 28.19
3 21A 21A N CA 101 102 34.48 38.20 -40.90
4 1944 21A 22A C N 104 106 64.18 55.40 15.29 0.63 -62.50 143.11 29.10
4 22A 22A N CA 106 107 25.69 38.20 -40.90
5 1959 36A 37A C N 179 181 66.01 55.40 13.69 0.83 -62.50 146.55 29.80
5 37A 37A N CA 181 182 29.54 38.20 -40.90
6 1960 37A 38A C N 184 186 62.34 55.40 10.94 0.50 -62.50 143.44 29.17
6 38A 38A N CA 186 187 29.74 38.20 -40.90
7 1971 48A 49A C N 239 241 77.02 55.40 21.65 2.40 -62.50 160.87 32.72
7 49A 49A N CA 241 242 39.19 38.20 -40.90
8 1974 51A 52A C N 254 256 -68.25 -62.50 9.67 1.46 -134.00 -168.49 11.78
8 52A 52A N CA 256 257 -33.13 -40.90 147.00
9 1975 52A 53A C N 259 261 49.83 55.40 47.74 2.43 -134.00 -173.44 8.56
9 53A 53A N CA 261 262 85.61 38.20 147.00
10 1976 53A 54A C N 264 266 61.76 -68.20 147.46 14.32 -62.50 162.12 25.58
10 54A 54A N CA 266 267 -145.03 145.30 -40.90
11 1979 56A 57A C N 279 281 -165.27 -134.00 31.46 1.17 -62.50 -156.62 38.81
11 57A 57A N CA 281 282 143.60 147.00 -40.90
12 1980 57A 58A C N 284 286 -56.73 -68.20 13.78 0.91 -62.50 178.65 29.56
12 58A 58A N CA 286 287 137.66 145.30 -40.90
13 1983 60A 61A C N 299 301 100.70 -134.00 137.12 3.12 -68.20 178.37 16.79
13 61A 61A N CA 301 302 -157.33 147.00 145.30
14 1986 63A 64A C N 314 316 -66.19 -68.20 2.10 0.16 -62.50 174.47 28.77
14 64A 64A N CA 316 317 144.67 145.30 -40.90
15 1987 64A 65A C N 319 321 -93.83 -68.20 51.06 4.89 -62.50 145.45 22.51
15 65A 65A N CA 321 322 101.14 145.30 -40.90
16 1988 65A 66A C N 324 326 -72.34 -68.20 8.84 0.58 -62.50 166.27 27.74
16 66A 66A N CA 326 327 153.12 145.30 -40.90
17 1989 66A 67A C N 329 331 94.27 -62.50 158.09 31.15 -62.50 158.09 31.15
17 67A 67A N CA 331 332 -20.47 -40.90 -40.90
18 1990 67A 68A C N 334 336 55.67 55.40 2.67 0.14 -62.50 140.73 28.59
18 68A 68A N CA 336 337 35.54 38.20 -40.90
19 2017 94A 95A C N 469 471 80.79 -134.00 159.99 3.63 -62.50 177.61 28.52
19 95A 95A N CA 471 472 -145.84 147.00 -40.90
20 2030 107A 108A C N 534 536 49.96 55.40 10.53 0.40 -62.50 142.87 28.89
20 108A 108A N CA 536 537 47.21 38.20 -40.90
21 2038 115A 116A C N 574 576 -54.82 -62.50 10.88 1.68 -68.20 166.63 13.91
21 116A 116A N CA 576 577 -48.60 -40.90 145.30
22 2041 118A 119A C N 589 591 73.95 55.40 129.21 9.32 -62.50 -154.97 31.35
22 119A 119A N CA 591 592 166.07 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 2 4 43 47 58 65 73 101 95 76
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1123
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 : 1067.8749
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 : 600 0 1 0.008 0.008 13.086 1.000
2 Bond angle potential : 839 0 7 2.261 2.261 88.638 1.000
3 Stereochemical cosine torsion poten: 244 0 35 75.688 75.688 232.20 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.910 0.910 4.8995 1.000
5 Soft-sphere overlap restraints : 1123 1 2 0.011 0.011 15.769 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) : 1968 7 23 0.775 0.775 272.79 1.000
10 Distance restraints 2 (N-O) : 2093 7 24 0.747 0.747 327.61 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: 119 0 3 4.977 4.977 34.755 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) : 668 0 0 0.315 0.315 7.3470 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: 118 23 16 34.412 73.903 42.820 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.114 1.114 4.8604 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.047 0.047 23.108 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: ala_changed.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: 12375.7383
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 3583 56A 63A CA CA 277 312 13.28 7.04 6.24 5.89 7.04 6.24 5.89
2 3584 56A 64A CA CA 277 317 14.05 7.69 6.36 4.95 7.69 6.36 4.95
3 3585 56A 65A CA CA 277 322 11.29 5.45 5.84 6.71 5.45 5.84 6.71
4 3588 56A 68A CA CA 277 337 12.66 7.46 5.20 5.05 7.46 5.20 5.05
5 3589 56A 69A CA CA 277 342 10.20 6.07 4.12 5.80 6.07 4.12 5.80
6 3590 56A 70A CA CA 277 347 9.61 4.69 4.92 7.02 4.69 4.92 7.02
-------------------------------------------------------------------------------------------------
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 4905 38A 55A N O 186 275 8.35 5.51 2.85 4.85 5.51 2.85 4.85
2 5216 56A 63A N O 276 315 14.04 7.89 6.15 4.99 7.89 6.15 4.99
3 5217 56A 64A N O 276 320 13.42 7.21 6.21 4.72 7.21 6.21 4.72
4 5218 56A 65A N O 276 325 13.33 6.37 6.97 6.59 6.37 6.97 6.59
5 5221 56A 68A N O 276 340 12.62 7.02 5.59 5.22 7.02 5.59 5.22
6 5222 56A 69A N O 276 345 8.96 2.70 6.27 12.24 2.70 6.27 12.24
7 5389 71A 56A N O 351 280 5.67 2.97 2.70 5.69 2.97 2.70 5.69
-------------------------------------------------------------------------------------------------
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 1938 15A 16A C N 74 76 77.81 55.40 25.79 1.92 -62.50 155.20 31.54
1 16A 16A N CA 76 77 25.45 38.20 -40.90
2 1941 18A 19A C N 89 91 65.82 55.40 22.88 0.83 -62.50 141.12 28.66
2 19A 19A N CA 91 92 17.83 38.20 -40.90
3 1943 20A 21A C N 99 101 56.04 55.40 8.05 0.43 -62.50 138.21 28.10
3 21A 21A N CA 101 102 30.17 38.20 -40.90
4 1944 21A 22A C N 104 106 64.47 55.40 13.90 0.66 -62.50 144.29 29.35
4 22A 22A N CA 106 107 27.66 38.20 -40.90
5 1959 36A 37A C N 179 181 65.31 55.40 12.78 0.78 -62.50 146.23 29.74
5 37A 37A N CA 181 182 30.14 38.20 -40.90
6 1960 37A 38A C N 184 186 60.16 55.40 6.82 0.35 -62.50 143.36 29.15
6 38A 38A N CA 186 187 33.31 38.20 -40.90
7 1971 48A 49A C N 239 241 165.02 -134.00 61.37 1.78 -62.50 -148.21 41.62
7 49A 49A N CA 241 242 153.87 147.00 -40.90
8 1972 49A 50A C N 244 246 87.42 -134.00 138.94 4.23 -68.20 156.06 13.61
8 50A 50A N CA 246 247 157.01 147.00 145.30
9 1976 53A 54A C N 264 266 58.81 -68.20 143.62 13.93 -62.50 161.59 25.35
9 54A 54A N CA 266 267 -147.65 145.30 -40.90
10 1979 56A 57A C N 279 281 -167.32 -134.00 33.48 1.23 -62.50 -155.74 39.06
10 57A 57A N CA 281 282 143.79 147.00 -40.90
11 1980 57A 58A C N 284 286 -67.13 -68.20 6.23 0.46 -62.50 180.00 29.73
11 58A 58A N CA 286 287 139.16 145.30 -40.90
12 1984 61A 62A C N 304 306 63.20 55.40 26.69 1.06 -62.50 136.64 27.73
12 62A 62A N CA 306 307 12.68 38.20 -40.90
13 1986 63A 64A C N 314 316 -72.31 -68.20 5.59 0.55 -62.50 177.86 29.64
13 64A 64A N CA 316 317 141.51 145.30 -40.90
14 1987 64A 65A C N 319 321 -91.19 -68.20 49.35 4.69 -62.50 145.39 22.60
14 65A 65A N CA 321 322 101.63 145.30 -40.90
15 1988 65A 66A C N 324 326 -63.49 -68.20 11.05 1.04 -62.50 163.81 26.89
15 66A 66A N CA 326 327 155.30 145.30 -40.90
16 1989 66A 67A C N 329 331 46.65 -68.20 127.71 8.85 -62.50 170.03 33.53
16 67A 67A N CA 331 332 89.47 145.30 -40.90
17 1990 67A 68A C N 334 336 -56.07 -68.20 39.02 2.72 -62.50 149.26 24.78
17 68A 68A N CA 336 337 108.22 145.30 -40.90
18 2017 94A 95A C N 469 471 81.86 -134.00 159.74 3.63 -62.50 177.48 28.59
18 95A 95A N CA 471 472 -144.15 147.00 -40.90
19 2030 107A 108A C N 534 536 74.86 -68.20 150.80 14.18 -62.50 -173.52 29.10
19 108A 108A N CA 536 537 -167.01 145.30 -40.90
20 2031 108A 109A C N 539 541 -159.22 -134.00 51.45 3.17 -68.20 100.73 9.71
20 109A 109A N CA 541 542 102.15 147.00 145.30
21 2032 109A 110A C N 544 546 -77.15 -62.50 30.95 4.64 -134.00 170.40 7.99
21 110A 110A N CA 546 547 -13.63 -40.90 147.00
22 2039 116A 117A C N 579 581 67.50 55.40 34.67 1.29 -62.50 138.10 27.92
22 117A 117A N CA 581 582 5.70 38.20 -40.90
23 2041 118A 119A C N 589 591 65.08 55.40 11.62 0.80 -62.50 146.82 29.86
23 119A 119A N CA 591 592 31.77 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 4 4 42 50 66 71 72 83 102 80
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ala_changed.B99990001.pdb 1089.36499
ala_changed.B99990002.pdb 1067.87488
In [39]:
print('ala_changed.B99990001.pdb is green')
display(Image('1a.png', width=600))
print('ala_changed.B99990002.pdb is magenta')
display(Image('2a.png', width=600))
ala_changed.B99990001.pdb is green
ala_changed.B99990002.pdb is magenta
Как можно заметить, даже при использовании в качестве сравниваемой последовательность последовательность аланинов, получается достаточно хорошо сопоставить структуры, при этом Score получается лучше (1089.36499 и 1067.87488), чем в случае, когда положение лиганда было изменено