Гомологичное моделирование комплекса белка с лигандом¶
In [2]:
from IPython.display import Image
def pdb2img(file_name1, file_name2):
command = ''
command += f'load {file_name1}, xxx; load {file_name2}, yyy; align xxx, yyy;'
command += 'as cartoon; as sticks, hetatm; orient; move z, 20;'
command += 'set ray_trace_mode, 3; set antialias, 3;'
command += f'ray {1920//2}, {1080//2}; png tmp.png'
! pymol -Q -c -d "$command"
display(Image('tmp.png'))
1. Загрузим модуль¶
In [3]:
import sys
import modeller
import _modeller
import modeller.automodel
2. Зададим некоторые параметры¶
In [4]:
env=modeller.environ()
env.io.hetatm = True
MODELLER 9.18, 2017/02/17, r11002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 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 srv 4.15.0-46-generic x86_64
Date and time of compilation : 2017/02/17 14:47:45
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2019/04/15 00:33:50
3. Скачаем белок заготовку и последовательность¶
In [4]:
! wget -q http://www.pdb.org/pdb/files/1lmp.pdb
! wget -q http://www.uniprot.org/uniprot/Q7SID7.fasta
LYS_ANTMY.
4. Создадим объект выравнивание¶
In [5]:
alignm = modeller.alignment(env)
In [6]:
alignm.append(file='Q7SID7.fasta', align_codes='all', alignment_format='FASTA')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
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.
5. Делаем выравнивание и сохраняем¶
In [7]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
6. Смотрим на содержимое all_in_one.ali¶
In [8]:
! cat all_in_one.ali
>P1;seq sequence:: : : : :::-1.00:-1.00 KRFTRCGLVNELRKQGFD---ENLMRDWVCLVENESARYTDKIANVNKNGSRDYGLFQINDKYWCSKGSTPGKD- -CNVTCSQLLTDDITVASTCAKKI-YKRTKFDAWSGWDNHCNHSNPDISSC-------* >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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESS-YNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKN VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
7. Построим модель¶
In [ ]:
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
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
----------------------------------------------
18 1 18 22 D E 8.206
74 1 73 76 D C 8.895
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.)
patch_s_522_> Number of disulfides patched in MODEL: 3
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: 10915 10078
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 120
Number of all, selected real atoms : 961 961
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10078 10078
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2077
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 : 1050.9645
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 : 980 0 4 0.010 0.010 28.161 1.000
2 Bond angle potential : 1322 1 8 2.306 2.306 142.37 1.000
3 Stereochemical cosine torsion poten: 631 0 24 46.949 46.949 218.93 1.000
4 Stereochemical improper torsion pot: 405 0 0 1.305 1.305 15.989 1.000
5 Soft-sphere overlap restraints : 2077 0 0 0.003 0.003 2.7686 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) : 2136 0 6 0.415 0.415 138.01 1.000
10 Distance restraints 2 (N-O) : 2283 1 16 0.472 0.472 230.70 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 4.818 4.818 32.575 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 1 66.719 66.719 27.497 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 0 62.952 62.952 29.343 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 66.422 66.422 17.049 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 99.861 99.861 13.954 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.38465 1.000
19 Disulfide angle restraints : 6 0 0 2.505 2.505 0.83154 1.000
20 Disulfide dihedral angle restraints: 3 0 0 26.676 26.676 2.0265 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) : 1319 0 0 0.427 0.427 29.638 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 11 21 29.517 49.402 88.651 1.000
26 Distance restraints 4 (SDCH-SDCH) : 523 0 0 0.801 0.801 32.096 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: 12907.9912
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 1769 71D 71D N CA 573 574 127.43 107.00 20.43 5.87 107.00 20.43 5.87
-------------------------------------------------------------------------------------------------
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 8058 108N 104S N O 864 837 5.48 2.99 2.49 5.89 2.99 2.49 5.89
-------------------------------------------------------------------------------------------------
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 3383 33S 34A C N 276 278 74.25 55.40 83.65 3.62 -62.50 136.77 26.19
1 34A 34A N CA 278 279 -43.30 38.20 -40.90
2 3420 70K 71D C N 571 573 -142.29 -63.30 87.13 14.86 -63.30 87.13 14.86
2 71D 71D N CA 573 574 -76.78 -40.00 -40.00
3 3444 94I 95Y C N 744 746 -41.79 -98.40 57.68 2.61 -63.50 162.17 26.85
3 95Y 95Y N CA 746 747 117.31 128.40 -43.40
4 3447 97R 98T C N 776 778 -93.95 -124.80 69.18 2.20 -63.20 127.45 14.52
4 98T 98T N CA 778 779 81.58 143.50 -42.10
5 3448 98T 99K C N 783 785 -53.25 -62.90 65.72 8.05 -118.00 132.05 6.84
5 99K 99K N CA 785 786 -105.81 -40.80 139.10
6 3453 103W 104S C N 830 832 -72.61 -136.60 65.97 3.04 -64.10 157.97 11.97
6 104S 104S N CA 832 833 167.26 151.20 -35.00
7 3454 104S 105G C N 836 838 95.49 82.20 73.13 2.88 -62.40 159.44 27.49
7 105G 105G N CA 838 839 -63.41 8.50 -41.20
8 3458 108N 109H C N 870 872 -121.55 -63.20 75.69 8.86 -63.20 75.69 8.86
8 109H 109H N CA 872 873 5.91 -42.30 -42.30
9 3459 109H 110C C N 880 882 -121.13 -63.00 59.34 9.18 -63.00 59.34 9.18
9 110C 110C N CA 882 883 -29.17 -41.10 -41.10
10 3467 117I 118S C N 941 943 -67.60 -72.40 55.07 3.08 -64.10 132.59 9.40
10 118S 118S N CA 943 944 97.54 152.40 -35.00
11 3468 118S 119S C N 947 949 64.16 56.90 15.71 1.61 -64.10 154.06 20.07
11 119S 119S N CA 949 950 50.34 36.40 -35.00
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 6 15 42 65 92 108 108 154 138 150
<< 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 : 120
Number of all, selected real atoms : 961 961
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10078 10078
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2017
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 : 931.0333
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 : 980 0 5 0.010 0.010 27.403 1.000
2 Bond angle potential : 1322 1 9 2.271 2.271 138.44 1.000
3 Stereochemical cosine torsion poten: 631 0 19 47.052 47.052 218.65 1.000
4 Stereochemical improper torsion pot: 405 0 0 1.210 1.210 13.882 1.000
5 Soft-sphere overlap restraints : 2017 0 0 0.003 0.003 1.5792 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) : 2136 0 4 0.390 0.390 127.06 1.000
10 Distance restraints 2 (N-O) : 2283 0 6 0.428 0.428 152.54 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 4.910 4.910 33.835 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 70.435 70.435 29.894 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 1 76.585 76.585 37.824 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 67.827 67.827 19.576 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 85.354 85.354 15.438 1.000
18 Disulfide distance restraints : 3 0 0 0.022 0.022 0.26230 1.000
19 Disulfide angle restraints : 6 0 0 2.967 2.967 1.1663 1.000
20 Disulfide dihedral angle restraints: 3 0 0 29.802 29.802 2.4029 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) : 1319 0 0 0.394 0.394 24.019 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 6 19 31.150 45.794 57.648 1.000
26 Distance restraints 4 (SDCH-SDCH) : 523 0 0 0.660 0.660 29.406 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: 12605.9336
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 1769 71D 71D N CA 573 574 126.57 107.00 19.57 5.63 107.00 19.57 5.63
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3355 5R 6C C N 48 50 -67.43 -63.00 4.61 0.69 -117.90 -173.95 7.96
1 6C 6C N CA 50 51 -39.82 -41.10 141.10
2 3383 33S 34A C N 276 278 141.70 -134.00 113.63 3.23 -62.50 -177.05 37.19
2 34A 34A N CA 278 279 -136.81 147.00 -40.90
3 3384 34A 35R C N 281 283 -80.24 -72.10 75.25 5.96 -63.00 109.55 13.72
3 35R 35R N CA 283 284 67.09 141.90 -41.10
4 3420 70K 71D C N 571 573 162.47 -96.50 102.13 4.16 -63.30 -166.59 21.69
4 71D 71D N CA 573 574 99.25 114.20 -40.00
5 3444 94I 95Y C N 744 746 -40.86 -98.40 58.66 2.66 -63.50 161.98 26.87
5 95Y 95Y N CA 746 747 116.99 128.40 -43.40
6 3459 109H 110C C N 880 882 -108.31 -63.00 45.31 7.55 -63.00 45.31 7.55
6 110C 110C N CA 882 883 -41.09 -41.10 -41.10
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 5 10 52 62 96 110 104 131 143 167
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 1050.96448
seq.B99990002.pdb 931.03333
8. Посмотрим результат¶
In [ ]:
pdb2img('seq.B99990001.pdb', '1lmp.pdb')
pdb2img('seq.B99990002.pdb', '1lmp.pdb')
LIGAND??
9. Добавим три остатка лиганда к концу последовательности¶
In [ ]:
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 = 'seq_lig'
del alignm[0]
In [ ]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [ ]:
! 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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESS-YNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKN VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;seq_lig sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 KRFTRCGLVNELRKQGFD---ENLMRDWVCLVENESARYTDKIANVNKNGSRDYGLFQINDKYWCSKGSTPGKD- -CNVTCSQLLTDDITVASTCAKKI-YKRTKFDAWSGWDNHCNH----SNPDISSC...*
In [ ]:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
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_lig 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
----------------------------------------------
18 1 18 22 D E 8.206
74 1 73 76 D C 8.895
118 1 117 122 H S 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 120
atom names : C +N
atom indices : 959 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 120
atom names : C CA +N O
atom indices : 959 956 0 960
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.)
patch_s_522_> Number of disulfides patched in MODEL: 3
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: 12245 11408
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 : 123
Number of all, selected real atoms : 1004 1004
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11408 11408
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2330
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 : 1345.8303
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 : 980 0 5 0.011 0.011 35.380 1.000
2 Bond angle potential : 1322 1 13 2.480 2.480 164.02 1.000
3 Stereochemical cosine torsion poten: 631 0 24 48.272 48.272 226.43 1.000
4 Stereochemical improper torsion pot: 405 0 1 1.507 1.507 20.735 1.000
5 Soft-sphere overlap restraints : 2330 1 2 0.008 0.008 19.116 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) : 2120 1 13 0.536 0.536 202.23 1.000
10 Distance restraints 2 (N-O) : 2267 1 26 0.586 0.586 305.45 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 5.478 5.478 42.119 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 2 75.675 75.675 38.058 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 1 72.896 72.896 45.460 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 77.551 77.551 19.151 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 84.032 84.032 12.880 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.36750 1.000
19 Disulfide angle restraints : 6 0 0 3.843 3.843 1.9571 1.000
20 Disulfide dihedral angle restraints: 3 0 0 20.495 20.495 1.2303 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) : 1289 0 0 0.453 0.453 33.177 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 14 24 35.782 61.009 105.30 1.000
26 Distance restraints 4 (SDCH-SDCH) : 526 0 1 0.775 0.775 50.236 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.044 0.044 22.545 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_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: 15663.0859
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 1769 71D 71D N CA 573 574 128.23 107.00 21.23 6.10 107.00 21.23 6.10
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8050 108N 104S N O 864 837 5.73 2.99 2.74 6.15 2.99 2.74 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 3383 33S 34A C N 276 278 126.95 -134.00 127.07 3.38 -62.50 -165.97 39.46
1 34A 34A N CA 278 279 -133.41 147.00 -40.90
2 3384 34A 35R C N 281 283 -78.82 -72.10 74.08 5.84 -63.00 110.36 13.91
2 35R 35R N CA 283 284 68.12 141.90 -41.10
3 3420 70K 71D C N 571 573 -142.33 -63.30 84.99 14.45 -63.30 84.99 14.45
3 71D 71D N CA 573 574 -71.26 -40.00 -40.00
4 3444 94I 95Y C N 744 746 -47.41 -98.40 56.53 3.44 -63.50 148.26 24.35
4 95Y 95Y N CA 746 747 103.99 128.40 -43.40
5 3453 103W 104S C N 830 832 -70.53 -136.60 66.23 2.75 -64.10 169.32 12.66
5 104S 104S N CA 832 833 155.80 151.20 -35.00
6 3454 104S 105G C N 836 838 104.91 82.20 72.20 2.40 -62.40 168.37 29.25
6 105G 105G N CA 838 839 -60.03 8.50 -41.20
7 3458 108N 109H C N 870 872 -124.12 -63.20 78.79 9.23 -63.20 78.79 9.23
7 109H 109H N CA 872 873 7.66 -42.30 -42.30
8 3459 109H 110C C N 880 882 -103.39 -63.00 93.13 14.39 -63.00 93.13 14.39
8 110C 110C N CA 882 883 -125.01 -41.10 -41.10
9 3461 111N 112H C N 894 896 -155.84 -125.60 62.63 1.75 56.30 -147.34 32.28
9 112H 112H N CA 896 897 -166.36 138.80 40.80
10 3462 112H 113S C N 904 906 -81.73 -72.40 9.45 0.63 -64.10 172.03 13.59
10 113S 113S N CA 906 907 153.88 152.40 -35.00
11 3463 113S 114N C N 910 912 -147.70 -119.90 28.15 1.27 -63.20 -166.83 20.86
11 114N 114N N CA 912 913 132.61 137.00 -41.10
12 3464 114N 115P C N 918 920 -4.93 -64.50 76.62 5.22 -58.70 140.22 15.97
12 115P 115P N CA 920 921 99.00 147.20 -30.50
13 3466 116D 117I C N 933 935 -89.41 -97.30 82.05 8.55 -63.40 92.85 14.43
13 117I 117I N CA 935 936 45.53 127.20 -43.60
14 3468 118S 119S C N 947 949 60.83 56.90 3.94 0.48 -64.10 144.05 18.99
14 119S 119S N CA 949 950 36.70 36.40 -35.00
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 17 12 79 76 123 115 133 149 173 190
<< 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 : 123
Number of all, selected real atoms : 1004 1004
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11408 11408
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2384
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 : 1408.6130
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 : 980 0 6 0.012 0.012 39.170 1.000
2 Bond angle potential : 1322 1 15 2.606 2.606 178.70 1.000
3 Stereochemical cosine torsion poten: 631 0 29 48.400 48.400 232.08 1.000
4 Stereochemical improper torsion pot: 405 0 2 1.686 1.686 26.013 1.000
5 Soft-sphere overlap restraints : 2384 1 2 0.008 0.008 19.108 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) : 2120 0 11 0.533 0.533 212.65 1.000
10 Distance restraints 2 (N-O) : 2267 3 29 0.628 0.628 323.64 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 5 5.649 5.649 44.787 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 69.263 69.263 25.827 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 1 78.032 78.032 46.031 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 79.766 79.766 15.227 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 98.928 98.928 12.044 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27174 1.000
19 Disulfide angle restraints : 6 0 0 3.157 3.157 1.3205 1.000
20 Disulfide dihedral angle restraints: 3 0 0 50.664 50.664 4.6834 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) : 1289 0 0 0.526 0.526 26.719 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 17 24 35.039 64.552 125.40 1.000
26 Distance restraints 4 (SDCH-SDCH) : 526 0 0 0.844 0.844 47.185 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.049 0.049 27.766 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_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: 15766.8105
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 1769 71D 71D N CA 573 574 130.47 107.00 23.47 6.75 107.00 23.47 6.75
-------------------------------------------------------------------------------------------------
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 7341 69G 46N N O 560 382 10.78 7.27 3.51 4.77 7.27 3.51 4.77
2 7351 70K 46N N O 564 382 12.22 8.66 3.56 5.72 8.66 3.56 5.72
-------------------------------------------------------------------------------------------------
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 3368 18D 19E C N 150 152 -178.08 -117.80 60.64 2.39 -63.60 -154.68 23.74
1 19E 19E N CA 152 153 130.14 136.80 -40.30
2 3382 32E 33S C N 270 272 -93.42 -72.40 57.61 2.76 -64.10 122.52 10.88
2 33S 33S N CA 272 273 -153.96 152.40 -35.00
3 3384 34A 35R C N 281 283 -159.61 -63.00 97.97 17.11 -63.00 97.97 17.11
3 35R 35R N CA 283 284 -57.41 -41.10 -41.10
4 3385 35R 36Y C N 292 294 -145.68 -124.30 66.95 4.47 55.90 161.71 19.38
4 36Y 36Y N CA 294 295 71.96 135.40 39.50
5 3395 45K 46N C N 373 375 -72.16 -119.90 75.90 4.12 -63.20 123.22 15.90
5 46N 46N N CA 375 376 -164.00 137.00 -41.10
6 3396 46N 47G C N 381 383 -71.73 -62.40 22.61 3.07 82.20 156.66 11.43
6 47G 47G N CA 383 384 -20.61 -41.20 8.50
7 3420 70K 71D C N 571 573 167.16 -96.50 98.70 4.02 -63.30 -174.51 20.85
7 71D 71D N CA 573 574 92.77 114.20 -40.00
8 3444 94I 95Y C N 744 746 -48.10 -98.40 55.58 3.36 -63.50 148.96 24.43
8 95Y 95Y N CA 746 747 104.76 128.40 -43.40
9 3446 96K 97R C N 765 767 -85.35 -125.20 88.32 3.24 -63.00 105.28 12.86
9 97R 97R N CA 767 768 61.78 140.60 -41.10
10 3447 97R 98T C N 776 778 -154.64 -63.20 95.00 13.25 -63.20 95.00 13.25
10 98T 98T N CA 778 779 -16.34 -42.10 -42.10
11 3448 98T 99K C N 783 785 52.91 -70.20 146.72 12.16 -118.00 -170.82 8.66
11 99K 99K N CA 785 786 -139.79 140.40 139.10
12 3458 108N 109H C N 870 872 -127.87 -63.20 74.63 9.47 -63.20 74.63 9.47
12 109H 109H N CA 872 873 -5.06 -42.30 -42.30
13 3461 111N 112H C N 894 896 -178.46 -125.60 83.75 2.14 56.30 -154.47 29.75
13 112H 112H N CA 896 897 -156.24 138.80 40.80
14 3462 112H 113S C N 904 906 -113.49 -136.60 23.17 0.88 -64.10 -177.75 16.61
14 113S 113S N CA 906 907 149.56 151.20 -35.00
15 3463 113S 114N C N 910 912 -139.70 -119.90 21.97 1.12 -63.20 -174.88 20.06
15 114N 114N N CA 912 913 127.47 137.00 -41.10
16 3464 114N 115P C N 918 920 -7.29 -64.50 75.72 5.04 -58.70 138.03 15.61
16 115P 115P N CA 920 921 97.60 147.20 -30.50
17 3468 118S 119S C N 947 949 52.31 56.90 15.86 0.69 -64.10 145.09 18.67
17 119S 119S N CA 949 950 51.58 36.40 -35.00
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 16 22 79 88 128 107 133 157 164 177
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 1345.83032
seq_lig.B99990002.pdb 1408.61304
In [ ]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
10. Поместим лиганд в другое место¶
In [ ]:
! rm seq_lig.rsr
In [ ]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('N:50','O6:121'), ('N:70', 'O6:123')]:
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 [ ]:
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
----------------------------------------------
18 1 18 22 D E 8.206
74 1 73 76 D C 8.895
118 1 117 122 H S 13.814
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 120
atom names : C +N
atom indices : 959 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 120
atom names : C CA +N O
atom indices : 959 956 0 960
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.)
patch_s_522_> Number of disulfides patched in MODEL: 3
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: 12247 11410
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 : 123
Number of all, selected real atoms : 1004 1004
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11410 11410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2486
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 : 5791.4170
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 : 980 8 16 0.028 0.028 229.13 1.000
2 Bond angle potential : 1322 14 29 3.981 3.981 419.47 1.000
3 Stereochemical cosine torsion poten: 631 0 31 49.164 49.164 234.33 1.000
4 Stereochemical improper torsion pot: 405 0 5 2.144 2.144 43.653 1.000
5 Soft-sphere overlap restraints : 2486 4 7 0.015 0.015 65.633 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) : 2120 20 59 0.664 0.664 582.03 1.000
10 Distance restraints 2 (N-O) : 2267 15 66 0.655 0.655 624.69 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 3 10 9.629 9.629 130.12 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 3 73.392 73.392 53.139 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 0 72.590 72.590 39.816 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 79.607 79.607 18.866 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 66.812 66.812 8.8681 1.000
18 Disulfide distance restraints : 3 0 0 0.010 0.010 0.51714E-01 1.000
19 Disulfide angle restraints : 6 0 0 1.955 1.955 0.50626 1.000
20 Disulfide dihedral angle restraints: 3 0 0 37.672 37.672 2.5574 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) : 1289 0 0 0.543 0.543 53.035 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 18 33 45.686 69.470 196.47 1.000
26 Distance restraints 4 (SDCH-SDCH) : 526 0 0 0.782 0.782 46.657 1.000
27 Distance restraints 5 (X-Y) : 1391 21 84 0.341 0.341 3042.4 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_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: 20071.8223
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
1 407 49R 49R C CA 402 394 1.71 1.49 0.22 6.33 1.49 0.22 6.33
2 408 49R 50D C N 402 404 1.54 1.35 0.20 6.96 1.35 0.20 6.96
3 413 50D 50D N CA 404 405 1.72 1.43 0.29 9.41 1.43 0.29 9.41
4 574 69G 70K C N 562 564 1.51 1.35 0.16 5.81 1.35 0.16 5.81
5 580 70K 70K N CA 564 565 1.77 1.43 0.34 11.20 1.43 0.34 11.20
6 582 70K 70K C CA 571 565 1.87 1.49 0.38 11.02 1.49 0.38 11.02
7 583 70K 71D C N 571 573 1.57 1.35 0.22 7.83 1.35 0.22 7.83
8 588 71D 71D N CA 573 574 1.69 1.43 0.26 8.46 1.43 0.26 8.46
-------------------------------------------------------------------------------------------------
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 1521 49R 49R CA C 394 402 143.54 116.50 27.04 7.78 116.50 27.04 7.78
2 1532 50D 50D N CA 404 405 140.40 107.00 33.40 9.60 107.00 33.40 9.60
3 1649 60Y 60Y N CA 489 490 125.43 107.00 18.43 5.30 107.00 18.43 5.30
4 1650 60Y 60Y CA CB 490 491 129.20 107.50 21.70 5.02 107.50 21.70 5.02
5 1754 69G 69G CA C 561 562 136.64 116.50 20.14 5.79 116.50 20.14 5.79
6 1758 70K 70K N CA 564 565 151.96 107.00 44.96 12.93 107.00 44.96 12.93
7 1766 70K 71D C N 571 573 157.61 120.00 37.61 8.55 120.00 37.61 8.55
8 1769 71D 71D N CA 573 574 128.72 107.00 21.72 6.24 107.00 21.72 6.24
9 1777 71D 72C C N 579 581 142.56 120.00 22.56 5.13 120.00 22.56 5.13
10 1780 72C 72C N CA 581 582 124.21 107.00 17.21 4.95 107.00 17.21 4.95
-------------------------------------------------------------------------------------------------
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 5510 63S 70K CA CA 522 565 9.97 7.04 2.93 5.76 7.04 2.93 5.76
2 5528 64K 70K CA CA 528 565 11.51 8.85 2.66 5.09 8.85 2.66 5.09
3 5542 65G 70K CA CA 537 565 12.29 8.63 3.65 5.13 8.63 3.65 5.13
-------------------------------------------------------------------------------------------------
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 6878 50D 41A N O 404 342 8.61 6.43 2.18 5.11 6.43 2.18 5.11
2 6879 50D 42N N O 404 350 4.80 2.79 2.01 5.39 2.79 2.01 5.39
3 7273 64K 70K N O 527 572 11.79 8.56 3.23 5.58 8.56 3.23 5.58
4 7351 70K 46N N O 564 382 11.80 8.66 3.14 5.05 8.66 3.14 5.05
5 7361 70K 64K N O 564 535 13.86 10.46 3.41 5.39 10.46 3.41 5.39
6 7364 70K 67T N O 564 552 7.98 3.64 4.33 5.35 3.64 4.33 5.35
-------------------------------------------------------------------------------------------------
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 3528 60Y 60Y CA C 490 499 -150.84 -180.00 29.16 5.83 -180.00 29.16 5.83
-------------------------------------------------------------------------------------------------
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 3368 18D 19E C N 150 152 -146.28 -63.60 94.50 16.25 -63.60 94.50 16.25
1 19E 19E N CA 152 153 -86.06 -40.30 -40.30
2 3382 32E 33S C N 270 272 -139.75 -136.60 79.21 4.08 -64.10 131.08 9.21
2 33S 33S N CA 272 273 72.06 151.20 -35.00
3 3383 33S 34A C N 276 278 -42.40 -68.20 25.91 2.28 -62.50 172.49 27.35
3 34A 34A N CA 278 279 147.79 145.30 -40.90
4 3384 34A 35R C N 281 283 70.15 57.30 32.61 1.57 -63.00 141.93 25.59
4 35R 35R N CA 283 284 8.03 38.00 -41.10
5 3395 45K 46N C N 373 375 -76.25 -119.90 74.46 4.03 -63.20 122.27 16.02
5 46N 46N N CA 375 376 -162.67 137.00 -41.10
6 3396 46N 47G C N 381 383 -69.59 -62.40 22.07 3.03 82.20 154.50 11.28
6 47G 47G N CA 383 384 -20.33 -41.20 8.50
7 3409 59K 60Y C N 487 489 -77.21 -63.50 49.17 8.50 -63.50 49.17 8.50
7 60Y 60Y N CA 489 490 -90.62 -43.40 -43.40
8 3415 65G 66S C N 538 540 -140.85 -136.60 60.42 3.15 -64.10 147.48 9.86
8 66S 66S N CA 540 541 90.93 151.20 -35.00
9 3419 69G 70K C N 562 564 117.60 -118.00 125.05 4.95 -70.20 172.77 12.93
9 70K 70K N CA 564 565 126.39 139.10 140.40
10 3420 70K 71D C N 571 573 90.84 -96.50 174.34 7.10 -63.30 -158.30 33.98
10 71D 71D N CA 573 574 90.09 114.20 -40.00
11 3459 109H 110C C N 880 882 -78.78 -63.00 90.25 12.16 -63.00 90.25 12.16
11 110C 110C N CA 882 883 -129.95 -41.10 -41.10
12 3461 111N 112H C N 894 896 -160.08 -125.60 65.20 1.77 56.30 -149.91 31.70
12 112H 112H N CA 896 897 -165.86 138.80 40.80
13 3462 112H 113S C N 904 906 -122.48 -136.60 20.68 0.68 -64.10 -179.22 11.13
13 113S 113S N CA 906 907 136.09 151.20 -35.00
14 3463 113S 114N C N 910 912 -139.42 -63.20 91.38 10.98 -63.20 91.38 10.98
14 114N 114N N CA 912 913 9.30 -41.10 -41.10
15 3465 115P 116D C N 925 927 -54.16 -96.50 43.99 1.81 -63.30 142.54 18.16
15 116D 116D N CA 927 928 102.25 114.20 -40.00
16 3466 116D 117I C N 933 935 151.01 -120.60 153.01 6.29 -63.40 157.93 29.66
16 117I 117I N CA 935 936 -104.80 130.30 -43.60
17 3467 117I 118S C N 941 943 -52.25 -72.40 57.37 2.77 -64.10 134.22 10.47
17 118S 118S N CA 943 944 98.69 152.40 -35.00
18 3468 118S 119S C N 947 949 -66.16 -72.40 37.85 2.02 -64.10 150.08 10.75
18 119S 119S N CA 949 950 115.07 152.40 -35.00
-------------------------------------------------------------------------------------------------
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 10370 96K 121. CA O6 759 974 6.17 5.07 1.10 5.48 5.07 1.10 5.48
2 10386 97R 121. CA O6 768 974 8.07 6.81 1.25 6.26 6.81 1.25 6.26
3 10573 121. 122. C1 O4 962 986 1.62 1.39 0.23 4.61 1.39 0.23 4.61
4 10963 121. 121. O3 O6 971 974 5.12 4.85 0.27 5.43 4.85 0.27 5.43
5 10976 121. 121. O4 O6 972 974 3.71 3.43 0.28 5.54 3.43 0.28 5.54
6 11000 121. 121. O6 O3 974 971 5.12 4.85 0.27 5.43 4.85 0.27 5.43
7 11001 121. 121. O6 O4 974 972 3.71 3.43 0.28 5.54 3.43 0.28 5.54
8 11409 50D 121. N O6 404 974 10.17 3.00 7.17 71.71 3.00 7.17 71.71
9 11410 70K 123. N O6 564 1001 8.10 3.00 5.10 51.00 3.00 5.10 51.00
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 2 15 26 90 99 128 125 136 153 168 199
<< 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 : 123
Number of all, selected real atoms : 1004 1004
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11410 11410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2504
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 : 5687.6299
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 : 980 8 16 0.028 0.028 231.17 1.000
2 Bond angle potential : 1322 15 24 3.954 3.954 411.29 1.000
3 Stereochemical cosine torsion poten: 631 0 32 49.667 49.667 239.97 1.000
4 Stereochemical improper torsion pot: 405 0 4 2.012 2.012 39.177 1.000
5 Soft-sphere overlap restraints : 2504 3 7 0.015 0.015 65.874 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) : 2120 18 57 0.671 0.671 578.23 1.000
10 Distance restraints 2 (N-O) : 2267 14 57 0.648 0.648 568.02 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 3 5 9.191 9.191 118.55 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 4 74.340 74.340 43.369 1.000
15 Sidechain Chi_2 dihedral restraints: 76 0 1 77.527 77.527 36.353 1.000
16 Sidechain Chi_3 dihedral restraints: 28 0 0 81.095 81.095 18.277 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 85.723 85.723 11.732 1.000
18 Disulfide distance restraints : 3 0 0 0.009 0.009 0.42862E-01 1.000
19 Disulfide angle restraints : 6 0 0 2.213 2.213 0.64894 1.000
20 Disulfide dihedral angle restraints: 3 0 0 23.594 23.594 1.7186 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) : 1289 0 0 0.581 0.581 59.321 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 17 30 42.202 67.288 159.38 1.000
26 Distance restraints 4 (SDCH-SDCH) : 526 0 0 0.814 0.814 51.442 1.000
27 Distance restraints 5 (X-Y) : 1391 21 86 0.342 0.342 3053.1 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_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: 20154.2812
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
1 407 49R 49R C CA 402 394 1.70 1.49 0.21 6.08 1.49 0.21 6.08
2 408 49R 50D C N 402 404 1.53 1.35 0.19 6.73 1.35 0.19 6.73
3 413 50D 50D N CA 404 405 1.72 1.43 0.29 9.41 1.43 0.29 9.41
4 574 69G 70K C N 562 564 1.51 1.35 0.16 5.82 1.35 0.16 5.82
5 580 70K 70K N CA 564 565 1.77 1.43 0.34 11.15 1.43 0.34 11.15
6 582 70K 70K C CA 571 565 1.87 1.49 0.38 10.93 1.49 0.38 10.93
7 583 70K 71D C N 571 573 1.57 1.35 0.23 8.00 1.35 0.23 8.00
8 588 71D 71D N CA 573 574 1.69 1.43 0.26 8.62 1.43 0.26 8.62
-------------------------------------------------------------------------------------------------
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 1521 49R 49R CA C 394 402 143.36 116.50 26.86 7.72 116.50 26.86 7.72
2 1532 50D 50D N CA 404 405 141.03 107.00 34.03 9.78 107.00 34.03 9.78
3 1649 60Y 60Y N CA 489 490 124.85 107.00 17.85 5.13 107.00 17.85 5.13
4 1650 60Y 60Y CA CB 490 491 135.84 107.50 28.34 6.55 107.50 28.34 6.55
5 1754 69G 69G CA C 561 562 136.82 116.50 20.32 5.84 116.50 20.32 5.84
6 1758 70K 70K N CA 564 565 151.81 107.00 44.81 12.88 107.00 44.81 12.88
7 1766 70K 71D C N 571 573 158.24 120.00 38.24 8.69 120.00 38.24 8.69
8 1769 71D 71D N CA 573 574 129.22 107.00 22.22 6.39 107.00 22.22 6.39
9 1777 71D 72C C N 579 581 141.75 120.00 21.75 4.94 120.00 21.75 4.94
10 1780 72C 72C N CA 581 582 123.56 107.00 16.56 4.76 107.00 16.56 4.76
-------------------------------------------------------------------------------------------------
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 5510 63S 70K CA CA 522 565 10.06 7.04 3.02 5.94 7.04 3.02 5.94
2 5528 64K 70K CA CA 528 565 11.49 8.85 2.64 5.05 8.85 2.64 5.05
3 5542 65G 70K CA CA 537 565 12.38 8.63 3.75 5.26 8.63 3.75 5.26
-------------------------------------------------------------------------------------------------
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 6878 50D 41A N O 404 342 8.59 6.43 2.16 5.06 6.43 2.16 5.06
2 6879 50D 42N N O 404 350 4.81 2.79 2.02 5.41 2.79 2.02 5.41
3 7273 64K 70K N O 527 572 11.83 8.56 3.27 5.65 8.56 3.27 5.65
4 7292 65G 70K N O 536 572 12.74 9.02 3.72 4.54 9.02 3.72 4.54
5 7361 70K 64K N O 564 535 13.88 10.46 3.42 5.41 10.46 3.42 5.41
6 7364 70K 67T N O 564 552 8.01 3.64 4.37 5.39 3.64 4.37 5.39
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3528 60Y 60Y CA C 490 499 -153.27 -180.00 26.73 5.34 -180.00 26.73 5.34
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3383 33S 34A C N 276 278 63.72 55.40 88.98 6.05 -62.50 -150.12 41.02
1 34A 34A N CA 278 279 126.79 38.20 -40.90
2 3384 34A 35R C N 281 283 61.29 57.30 26.72 1.50 -63.00 134.99 24.46
2 35R 35R N CA 283 284 11.58 38.00 -41.10
3 3409 59K 60Y C N 487 489 -77.86 -63.50 47.13 8.21 -63.50 47.13 8.21
3 60Y 60Y N CA 489 490 -88.29 -43.40 -43.40
4 3415 65G 66S C N 538 540 -140.27 -136.60 59.54 3.09 -64.10 147.90 9.84
4 66S 66S N CA 540 541 91.78 151.20 -35.00
5 3419 69G 70K C N 562 564 116.32 -118.00 126.55 5.04 -70.20 174.23 13.09
5 70K 70K N CA 564 565 124.28 139.10 140.40
6 3420 70K 71D C N 571 573 96.05 -96.50 168.58 6.87 -63.30 -151.36 35.15
6 71D 71D N CA 573 574 94.67 114.20 -40.00
7 3444 94I 95Y C N 744 746 -54.15 -98.40 49.42 3.06 -63.50 150.07 24.29
7 95Y 95Y N CA 746 747 106.38 128.40 -43.40
8 3447 97R 98T C N 776 778 -89.52 -124.80 56.42 1.76 -63.20 143.99 16.85
8 98T 98T N CA 778 779 99.47 143.50 -42.10
9 3448 98T 99K C N 783 785 -61.17 -62.90 64.57 8.29 -118.00 128.77 6.67
9 99K 99K N CA 785 786 -105.35 -40.80 139.10
10 3458 108N 109H C N 870 872 -124.08 -63.20 76.57 9.12 -63.20 76.57 9.12
10 109H 109H N CA 872 873 4.14 -42.30 -42.30
11 3459 109H 110C C N 880 882 -103.52 -117.90 91.44 3.80 -63.00 96.42 14.80
11 110C 110C N CA 882 883 -128.59 141.10 -41.10
12 3461 111N 112H C N 894 896 -152.49 -125.60 63.48 1.85 56.30 -143.10 32.96
12 112H 112H N CA 896 897 -163.70 138.80 40.80
13 3462 112H 113S C N 904 906 -125.24 -136.60 23.66 0.91 -64.10 176.38 10.88
13 113S 113S N CA 906 907 130.45 151.20 -35.00
14 3463 113S 114N C N 910 912 -135.13 -63.20 99.38 11.18 -63.20 99.38 11.18
14 114N 114N N CA 912 913 27.48 -41.10 -41.10
15 3465 115P 116D C N 925 927 -22.45 -70.90 60.86 2.83 -63.30 158.80 22.23
15 116D 116D N CA 927 928 113.46 150.30 -40.00
16 3466 116D 117I C N 933 935 16.23 -97.30 124.32 7.51 -63.40 144.15 26.46
16 117I 117I N CA 935 936 76.55 127.20 -43.60
17 3468 118S 119S C N 947 949 63.97 56.90 8.13 0.67 -64.10 144.72 19.17
17 119S 119S N CA 949 950 32.38 36.40 -35.00
-------------------------------------------------------------------------------------------------
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 10370 96K 121. CA O6 759 974 6.29 5.07 1.21 6.06 5.07 1.21 6.06
2 10386 97R 121. CA O6 768 974 8.17 6.81 1.36 6.78 6.81 1.36 6.78
3 10573 121. 122. C1 O4 962 986 1.62 1.39 0.23 4.65 1.39 0.23 4.65
4 10963 121. 121. O3 O6 971 974 5.12 4.85 0.27 5.46 4.85 0.27 5.46
5 10976 121. 121. O4 O6 972 974 3.71 3.43 0.28 5.51 3.43 0.28 5.51
6 11000 121. 121. O6 O3 974 971 5.12 4.85 0.27 5.46 4.85 0.27 5.46
7 11001 121. 121. O6 O4 974 972 3.71 3.43 0.28 5.51 3.43 0.28 5.51
8 11409 50D 121. N O6 404 974 10.18 3.00 7.18 71.79 3.00 7.18 71.79
9 11410 70K 123. N O6 564 1001 8.10 3.00 5.10 50.98 3.00 5.10 50.98
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 24 24 80 91 134 129 131 169 183 183
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 5791.41699
seq_lig.B99990002.pdb 5687.62988
In [5]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
Before After
1345.83032 5791.41699
1408.61304 5687.62988
11. Аланиновый лизоцим¶
In [7]:
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' * 120 + '...'
alignm.append_sequence(seq_ala)
alignm[0].code = 'pdb'
alignm[1].code = 'seq_ala'
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 [8]:
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [9]:
! 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 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...* >P1;seq_ala sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [10]:
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
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
read_to_681_> topology.submodel read from topology file: 3
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): 1121
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 : 997.4510
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 12.639 1.000
2 Bond angle potential : 839 0 2 2.046 2.046 73.649 1.000
3 Stereochemical cosine torsion poten: 244 0 32 74.759 74.759 225.05 1.000
4 Stereochemical improper torsion pot: 240 0 0 0.799 0.799 4.1371 1.000
5 Soft-sphere overlap restraints : 1121 1 2 0.011 0.011 15.732 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 8 25 0.756 0.756 256.68 1.000
10 Distance restraints 2 (N-O) : 2093 7 31 0.745 0.745 337.73 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 2 4.466 4.466 27.989 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 0.293 0.293 6.0921 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 21 15 29.787 69.049 16.727 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.014 1.014 3.8909 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.040 0.040 17.139 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: 11533.6406
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 13.35 7.04 6.31 5.95 7.04 6.31 5.95
2 3584 56A 64A CA CA 277 317 13.90 7.69 6.22 4.84 7.69 6.22 4.84
3 3585 56A 65A CA CA 277 322 11.15 5.45 5.70 6.56 5.45 5.70 6.56
4 3588 56A 68A CA CA 277 337 12.30 7.46 4.84 4.70 7.46 4.84 4.70
5 3589 56A 69A CA CA 277 342 10.11 6.07 4.03 5.67 6.07 4.03 5.67
6 3590 56A 70A CA CA 277 347 9.69 4.69 5.00 7.13 4.69 5.00 7.13
-------------------------------------------------------------------------------------------------
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 8.30 5.51 2.79 4.76 5.51 2.79 4.76
2 5216 56A 63A N O 276 315 14.37 7.89 6.48 5.26 7.89 6.48 5.26
3 5217 56A 64A N O 276 320 13.31 7.21 6.09 4.63 7.21 6.09 4.63
4 5218 56A 65A N O 276 325 13.65 6.37 7.29 6.89 6.37 7.29 6.89
5 5221 56A 68A N O 276 340 12.54 7.02 5.52 5.15 7.02 5.52 5.15
6 5222 56A 69A N O 276 345 9.02 2.70 6.33 12.36 2.70 6.33 12.36
7 5389 71A 56A N O 351 280 5.73 2.97 2.76 5.84 2.97 2.76 5.84
-------------------------------------------------------------------------------------------------
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 78.88 55.40 27.01 2.01 -62.50 155.91 31.67
1 16A 16A N CA 76 77 24.84 38.20 -40.90
2 1941 18A 19A C N 89 91 58.32 55.40 3.79 0.23 -62.50 143.10 29.08
2 19A 19A N CA 91 92 35.79 38.20 -40.90
3 1942 19A 20A C N 94 96 -60.66 -62.50 18.52 2.95 -68.20 155.55 12.81
3 20A 20A N CA 96 97 -59.33 -40.90 145.30
4 1943 20A 21A C N 99 101 -124.94 -134.00 75.94 4.09 -62.50 128.66 19.27
4 21A 21A N CA 101 102 71.60 147.00 -40.90
5 1944 21A 22A C N 104 106 60.09 55.40 15.41 0.60 -62.50 138.49 28.16
5 22A 22A N CA 106 107 23.52 38.20 -40.90
6 1959 36A 37A C N 179 181 66.41 55.40 14.37 0.86 -62.50 146.62 29.82
6 37A 37A N CA 181 182 28.96 38.20 -40.90
7 1960 37A 38A C N 184 186 60.98 55.40 9.05 0.40 -62.50 142.92 29.06
7 38A 38A N CA 186 187 31.07 38.20 -40.90
8 1971 48A 49A C N 239 241 163.56 -134.00 64.03 1.64 -62.50 -152.92 40.88
8 49A 49A N CA 241 242 161.17 147.00 -40.90
9 1972 49A 50A C N 244 246 91.06 -134.00 135.62 4.00 -68.20 159.99 14.06
9 50A 50A N CA 246 247 160.51 147.00 145.30
10 1976 53A 54A C N 264 266 58.49 -68.20 142.70 13.83 -62.50 162.27 25.41
10 54A 54A N CA 266 267 -149.03 145.30 -40.90
11 1979 56A 57A C N 279 281 -151.24 -134.00 29.94 1.10 -62.50 172.25 32.96
11 57A 57A N CA 281 282 171.47 147.00 -40.90
12 1980 57A 58A C N 284 286 -67.21 -68.20 5.56 0.48 -62.50 168.39 27.83
12 58A 58A N CA 286 287 150.77 145.30 -40.90
13 1984 61A 62A C N 304 306 60.85 55.40 19.38 0.78 -62.50 137.38 27.93
13 62A 62A N CA 306 307 19.60 38.20 -40.90
14 1986 63A 64A C N 314 316 -79.05 -68.20 11.68 1.11 -62.50 178.90 30.16
14 64A 64A N CA 316 317 140.97 145.30 -40.90
15 1987 64A 65A C N 319 321 -91.69 -68.20 43.21 4.17 -62.50 152.74 23.77
15 65A 65A N CA 321 322 109.03 145.30 -40.90
16 1989 66A 67A C N 329 331 -92.69 -68.20 46.10 4.44 -62.50 150.21 23.32
16 67A 67A N CA 331 332 106.24 145.30 -40.90
17 1990 67A 68A C N 334 336 -61.51 -68.20 39.26 2.93 -62.50 147.52 24.22
17 68A 68A N CA 336 337 106.62 145.30 -40.90
18 2017 94A 95A C N 469 471 80.11 -134.00 160.28 3.64 -62.50 177.53 28.47
18 95A 95A N CA 471 472 -146.62 147.00 -40.90
19 2030 107A 108A C N 534 536 49.18 55.40 10.38 0.44 -62.50 141.82 28.68
19 108A 108A N CA 536 537 46.51 38.20 -40.90
20 2039 116A 117A C N 579 581 72.60 55.40 40.93 1.48 -62.50 141.46 28.50
20 117A 117A N CA 581 582 1.05 38.20 -40.90
21 2041 118A 119A C N 589 591 66.24 55.40 16.56 0.78 -62.50 144.94 29.47
21 119A 119A N CA 591 592 25.69 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 3 34 57 66 53 81 97 90 67
<< 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): 1134
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 : 1177.2844
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 11.259 1.000
2 Bond angle potential : 839 0 3 2.232 2.232 86.037 1.000
3 Stereochemical cosine torsion poten: 244 0 34 77.402 77.402 237.34 1.000
4 Stereochemical improper torsion pot: 240 0 0 1.137 1.137 7.6996 1.000
5 Soft-sphere overlap restraints : 1134 1 2 0.011 0.011 15.836 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 28 0.785 0.785 281.47 1.000
10 Distance restraints 2 (N-O) : 2093 9 36 0.799 0.799 391.53 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 5 5.185 5.185 37.733 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 0.331 0.331 7.7654 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 25 18 35.239 78.101 74.580 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.087 1.087 4.5952 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.045 0.045 21.447 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: 12626.5547
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 12.97 7.04 5.93 5.60 7.04 5.93 5.60
2 3584 56A 64A CA CA 277 317 14.14 7.69 6.45 5.02 7.69 6.45 5.02
3 3585 56A 65A CA CA 277 322 10.79 5.45 5.34 6.14 5.45 5.34 6.14
4 3588 56A 68A CA CA 277 337 12.25 7.46 4.78 4.64 7.46 4.78 4.64
5 3589 56A 69A CA CA 277 342 9.87 6.07 3.79 5.33 6.07 3.79 5.33
6 3590 56A 70A CA CA 277 347 9.04 4.69 4.35 6.21 4.69 4.35 6.21
-------------------------------------------------------------------------------------------------
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 8.19 5.51 2.68 4.57 5.51 2.68 4.57
2 5033 44A 52A N O 216 260 5.84 3.15 2.69 4.70 3.15 2.69 4.70
3 5216 56A 63A N O 276 315 14.44 7.89 6.56 5.32 7.89 6.56 5.32
4 5217 56A 64A N O 276 320 14.37 7.21 7.15 5.43 7.21 7.15 5.43
5 5218 56A 65A N O 276 325 12.56 6.37 6.19 5.85 6.37 6.19 5.85
6 5221 56A 68A N O 276 340 12.58 7.02 5.56 5.19 7.02 5.56 5.19
7 5222 56A 69A N O 276 345 8.45 2.70 5.75 11.24 2.70 5.75 11.24
8 5389 71A 56A N O 351 280 5.75 2.97 2.78 5.86 2.97 2.78 5.86
9 5427 73A 70A N O 361 350 6.06 3.17 2.89 4.70 3.17 2.89 4.70
-------------------------------------------------------------------------------------------------
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 1924 1A 2A C N 4 6 -66.25 -62.50 7.80 1.17 -134.00 -168.67 11.78
1 2A 2A N CA 6 7 -34.06 -40.90 147.00
2 1925 2A 3A C N 9 11 57.57 -68.20 127.17 10.12 -68.20 127.17 10.12
2 3A 3A N CA 11 12 126.47 145.30 145.30
3 1938 15A 16A C N 74 76 78.89 55.40 26.03 2.09 -62.50 156.84 31.88
3 16A 16A N CA 76 77 26.99 38.20 -40.90
4 1940 17A 18A C N 84 86 -52.28 -62.50 10.23 1.99 -134.00 -168.93 11.79
4 18A 18A N CA 86 87 -40.29 -40.90 147.00
5 1941 18A 19A C N 89 91 -138.23 -134.00 80.59 4.67 -62.50 131.43 19.79
5 19A 19A N CA 91 92 66.52 147.00 -40.90
6 1943 20A 21A C N 99 101 57.09 55.40 6.22 0.25 -62.50 140.17 28.49
6 21A 21A N CA 101 102 32.21 38.20 -40.90
7 1944 21A 22A C N 104 106 65.10 55.40 14.29 0.71 -62.50 144.87 29.46
7 22A 22A N CA 106 107 27.71 38.20 -40.90
8 1959 36A 37A C N 179 181 64.76 55.40 12.17 0.73 -62.50 145.89 29.67
8 37A 37A N CA 181 182 30.43 38.20 -40.90
9 1960 37A 38A C N 184 186 61.66 55.40 13.15 0.48 -62.50 141.34 28.75
9 38A 38A N CA 186 187 26.64 38.20 -40.90
10 1971 48A 49A C N 239 241 152.34 -134.00 75.68 1.93 -62.50 -147.83 42.20
10 49A 49A N CA 241 242 164.37 147.00 -40.90
11 1972 49A 50A C N 244 246 92.38 -134.00 134.19 3.99 -68.20 161.20 14.13
11 50A 50A N CA 246 247 159.38 147.00 145.30
12 1974 51A 52A C N 254 256 -68.05 -62.50 6.29 1.28 -134.00 -178.44 11.19
12 52A 52A N CA 256 257 -43.84 -40.90 147.00
13 1979 56A 57A C N 279 281 -168.59 -134.00 36.18 1.61 -62.50 -153.38 30.97
13 57A 57A N CA 281 282 136.40 147.00 -40.90
14 1980 57A 58A C N 284 286 -54.14 -68.20 14.23 1.13 -62.50 176.23 28.48
14 58A 58A N CA 286 287 143.07 145.30 -40.90
15 1984 61A 62A C N 304 306 55.84 55.40 7.01 0.39 -62.50 138.57 28.17
15 62A 62A N CA 306 307 31.21 38.20 -40.90
16 1987 64A 65A C N 319 321 54.66 55.40 28.31 1.65 -62.50 158.94 31.91
16 65A 65A N CA 321 322 66.50 38.20 -40.90
17 1988 65A 66A C N 324 326 -56.39 -68.20 15.21 1.50 -62.50 164.33 26.64
17 66A 66A N CA 326 327 154.89 145.30 -40.90
18 1989 66A 67A C N 329 331 58.10 -68.20 137.38 9.72 -62.50 178.92 35.52
18 67A 67A N CA 331 332 91.27 145.30 -40.90
19 1990 67A 68A C N 334 336 -79.62 -68.20 46.56 4.14 -62.50 142.10 22.51
19 68A 68A N CA 336 337 100.16 145.30 -40.90
20 1992 69A 70A C N 344 346 -65.88 -62.50 21.05 3.62 -134.00 165.95 10.24
20 70A 70A N CA 346 347 -61.67 -40.90 147.00
21 1993 70A 71A C N 349 351 -177.98 -62.50 116.96 21.63 -62.50 116.96 21.63
21 71A 71A N CA 351 352 -22.35 -40.90 -40.90
22 2017 94A 95A C N 469 471 83.05 -134.00 158.80 3.61 -62.50 178.28 28.77
22 95A 95A N CA 471 472 -143.85 147.00 -40.90
23 2030 107A 108A C N 534 536 53.30 55.40 6.64 0.26 -62.50 143.88 29.15
23 108A 108A N CA 536 537 44.50 38.20 -40.90
24 2039 116A 117A C N 579 581 72.19 55.40 45.46 1.67 -62.50 139.64 28.04
24 117A 117A N CA 581 582 -4.05 38.20 -40.90
25 2041 118A 119A C N 589 591 62.82 55.40 10.13 0.56 -62.50 144.63 29.41
25 119A 119A N CA 591 592 31.30 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 5 3 39 55 59 57 82 101 94 81
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 997.45105
seq_ala.B99990002.pdb 1177.28442
In [11]:
pdb2img('seq_ala.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_ala.B99990002.pdb', '1lmp.pdb')
