Гомологичное моделирование комплекса белка с лигандом¶
In [1]:
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'))
In [2]:
#загрузка модулей
import sys
import modeller
import _modeller
import modeller.automodel
In [3]:
env=modeller.environ()
env.io.hetatm = True
MODELLER 9.20, 2018/05/30, r11208
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2018 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 emkeller 4.15.0-142-generic x86_64
Date and time of compilation : 2018/05/30 15:42:57
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/09/15 16:53:21
In [4]:
! wget -q http://www.pdb.org/pdb/files/1lmp.pdb
! wget -q http://www.uniprot.org/uniprot/P82174.fasta #Galleria mellonella (Greater wax moth)
In [5]:
alignm = modeller.alignment(env)
In [6]:
#добавим последовательность для моделирования и структуру известного лизоцима
alignm.append(file='P82174.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')
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
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, не блещет
! cat all_in_one.ali
>P1;seq sequence:: : : : :::-1.00:-1.00 KTFTRCELVQALRRQGFD---EAKLRDWVCLVENESRGRTDIVGKPNKNGSRDYGLFQINDKYWCSN--TSKAGK DCNITCSQLLTDDITVASKCAKKVYKRHNFM-AWYGWRNHCQNKPLPDISK---C* >P1;pdb structureX:1lmp.pdb: 1 :A:+129 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQINSRYWCDDGRTPGAKN VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV*
In [9]:
#построим модель и выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
#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()
seq pdb
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
126 1 125 129 K C 8.792
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
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.
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: 11271 10410
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 121
Number of all, selected real atoms : 982 982
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10410 10410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2088
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 : 856.7200
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 : 1002 0 0 0.006 0.006 9.7052 1.000
2 Bond angle potential : 1348 0 7 2.186 2.186 126.77 1.000
3 Stereochemical cosine torsion poten: 641 0 22 46.695 46.695 213.17 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.258 1.258 14.180 1.000
5 Soft-sphere overlap restraints : 2088 0 0 0.002 0.002 0.83720 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) : 2171 0 3 0.387 0.387 96.632 1.000
10 Distance restraints 2 (N-O) : 2309 0 2 0.406 0.406 105.90 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: 120 0 3 4.915 4.915 34.180 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 66.290 66.290 18.879 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 67.940 67.940 36.520 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 69.962 69.962 23.802 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 106.181 106.181 17.479 1.000
18 Disulfide distance restraints : 3 0 0 0.004 0.004 0.95775E-02 1.000
19 Disulfide angle restraints : 6 0 0 1.662 1.662 0.36604 1.000
20 Disulfide dihedral angle restraints: 3 0 0 32.895 32.895 3.0775 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) : 1404 0 0 0.382 0.382 24.573 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: 119 7 18 30.586 42.507 96.255 1.000
26 Distance restraints 4 (SDCH-SDCH) : 632 0 0 0.654 0.654 34.380 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: 12062.8770
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 3442 32E 33S C N 268 270 -138.18 -64.10 84.50 8.55 -64.10 84.50 8.55
1 33S 33S N CA 270 271 5.66 -35.00 -35.00
2 3452 42K 43P C N 343 345 -76.01 -58.70 24.96 1.72 -64.50 160.13 12.57
2 43P 43P N CA 345 346 -12.52 -30.50 147.20
3 3473 63S 64N C N 519 521 -142.70 -63.20 95.34 15.67 -63.20 95.34 15.67
3 64N 64N N CA 521 522 -93.72 -41.10 -41.10
4 3478 68A 69G C N 554 556 167.65 82.20 94.38 4.46 -62.40 130.31 22.87
4 69G 69G N CA 556 557 -31.57 8.50 -41.20
5 3510 100F 101M C N 803 805 -66.49 -63.40 51.31 7.43 -63.40 51.31 7.43
5 101M 101M N CA 805 806 10.72 -40.50 -40.50
6 3528 118I 119S C N 959 961 -112.82 -64.10 83.99 9.60 -64.10 83.99 9.60
6 119S 119S N CA 961 962 -103.42 -35.00 -35.00
7 3529 119S 120K C N 965 967 66.68 56.60 12.98 1.62 -118.00 -161.86 9.20
7 120K 120K N CA 967 968 46.79 38.60 139.10
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 6 12 44 62 113 84 121 141 189 154
<< 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 : 121
Number of all, selected real atoms : 982 982
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10410 10410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2030
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 : 825.1884
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 : 1002 0 0 0.006 0.006 10.217 1.000
2 Bond angle potential : 1348 0 9 2.166 2.166 125.04 1.000
3 Stereochemical cosine torsion poten: 641 0 19 46.208 46.208 210.81 1.000
4 Stereochemical improper torsion pot: 407 0 0 1.243 1.243 14.239 1.000
5 Soft-sphere overlap restraints : 2030 0 0 0.002 0.002 1.0609 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) : 2171 0 3 0.408 0.408 96.494 1.000
10 Distance restraints 2 (N-O) : 2309 0 2 0.434 0.434 110.85 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: 120 0 2 4.659 4.659 30.711 1.000
14 Sidechain Chi_1 dihedral restraints: 108 0 0 63.975 63.975 16.796 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 59.990 59.990 28.866 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 69.012 69.012 24.022 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 90.823 90.823 14.330 1.000
18 Disulfide distance restraints : 3 0 0 0.005 0.005 0.13564E-01 1.000
19 Disulfide angle restraints : 6 0 0 1.669 1.669 0.36917 1.000
20 Disulfide dihedral angle restraints: 3 0 0 33.278 33.278 3.0280 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) : 1404 0 0 0.462 0.462 24.474 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: 119 5 13 28.491 38.605 77.855 1.000
26 Distance restraints 4 (SDCH-SDCH) : 632 0 0 0.726 0.726 36.012 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: 11271.9893
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 3442 32E 33S C N 268 270 -142.20 -64.10 90.34 8.98 -64.10 90.34 8.98
1 33S 33S N CA 270 271 10.42 -35.00 -35.00
2 3473 63S 64N C N 519 521 -149.01 -63.20 101.06 16.62 -63.20 101.06 16.62
2 64N 64N N CA 521 522 -94.47 -41.10 -41.10
3 3510 100F 101M C N 803 805 -67.52 -63.40 55.95 8.04 -63.40 55.95 8.04
3 101M 101M N CA 805 806 15.30 -40.50 -40.50
4 3528 118I 119S C N 959 961 -108.49 -64.10 82.40 9.17 -64.10 82.40 9.17
4 119S 119S N CA 961 962 -104.42 -35.00 -35.00
5 3529 119S 120K C N 965 967 68.22 56.60 13.19 1.69 -118.00 -162.31 9.22
5 120K 120K N CA 967 968 44.85 38.60 139.10
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 18 45 62 100 95 121 125 167 153
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 856.71997
seq.B99990002.pdb 825.18842
In [10]:
pdb2img('seq.B99990001.pdb', '1lmp.pdb')
pdb2img('seq.B99990002.pdb', '1lmp.pdb')
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 = 'seq_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;pdb structureX:1lmp.pdb: 1 :A:+129 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQINSRYWCDDGRTPGAKN VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV* >P1;seq_lig sequence::1 : :+124 : :undefined:undefined:-1.00:-1.00 KTFTRCELVQALRRQGFDE---AKLRDWVCLVENESRGRTDIVGKPNKNGSRDYGLFQINDKYWCSN--TSKAGK DCNITCSQLLTDDITVASKCAKKVYKRHNFM-AWYGWRNHCQNKPLPDISKCCGV*
In [14]:
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()
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
patch_s_522_> Number of disulfides patched in MODEL: 4
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.
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: 11555 10675
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 : 124
Number of all, selected real atoms : 999 999
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10675 10675
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2085
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 : 840.3017
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 : 1019 0 0 0.006 0.006 10.866 1.000
2 Bond angle potential : 1371 0 10 2.196 2.196 130.71 1.000
3 Stereochemical cosine torsion poten: 651 0 22 46.495 46.495 217.59 1.000
4 Stereochemical improper torsion pot: 413 0 0 1.221 1.221 14.061 1.000
5 Soft-sphere overlap restraints : 2085 0 0 0.003 0.003 1.6726 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) : 2234 0 1 0.302 0.302 79.556 1.000
10 Distance restraints 2 (N-O) : 2382 0 1 0.355 0.355 100.50 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: 123 0 3 4.980 4.980 35.967 1.000
14 Sidechain Chi_1 dihedral restraints: 110 0 0 69.313 69.313 22.655 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 69.647 69.647 27.497 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 73.194 73.194 25.207 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 99.010 99.010 16.269 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.41937E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.861 2.861 1.4460 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.457 27.457 2.6330 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) : 1449 0 0 0.555 0.555 29.371 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: 122 4 15 28.980 35.479 85.617 1.000
26 Distance restraints 4 (SDCH-SDCH) : 648 0 0 0.757 0.757 38.643 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_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: 12067.2764
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 3502 32E 33S C N 268 270 -135.16 -64.10 78.44 8.28 -64.10 78.44 8.28
1 33S 33S N CA 270 271 -1.78 -35.00 -35.00
2 3533 63S 64N C N 519 521 -147.46 -63.20 100.47 16.51 -63.20 100.47 16.51
2 64N 64N N CA 521 522 -95.81 -41.10 -41.10
3 3538 68A 69G C N 554 556 168.11 82.20 94.87 4.48 -62.40 129.83 22.79
3 69G 69G N CA 556 557 -31.73 8.50 -41.20
4 3570 100F 101M C N 803 805 -67.29 -63.40 55.07 7.93 -63.40 55.07 7.93
4 101M 101M N CA 805 806 14.43 -40.50 -40.50
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 48 74 103 91 125 148 160 163
<< 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 : 124
Number of all, selected real atoms : 999 999
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10675 10675
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2155
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 : 851.0093
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 : 1019 0 0 0.006 0.006 11.861 1.000
2 Bond angle potential : 1371 0 8 2.325 2.325 146.87 1.000
3 Stereochemical cosine torsion poten: 651 0 24 47.146 47.146 225.00 1.000
4 Stereochemical improper torsion pot: 413 0 0 1.399 1.399 17.499 1.000
5 Soft-sphere overlap restraints : 2155 0 0 0.003 0.003 2.2949 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) : 2234 0 5 0.314 0.314 89.397 1.000
10 Distance restraints 2 (N-O) : 2382 0 2 0.355 0.355 106.98 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: 123 0 4 5.019 5.019 36.542 1.000
14 Sidechain Chi_1 dihedral restraints: 110 0 1 62.051 62.051 21.715 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 2 60.548 60.548 31.757 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 74.738 74.738 26.250 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 94.457 94.457 15.277 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.36006E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.253 2.253 0.89662 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.226 27.226 2.9566 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) : 1449 0 0 0.461 0.461 27.485 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: 122 6 14 25.288 39.822 55.176 1.000
26 Distance restraints 4 (SDCH-SDCH) : 648 0 0 0.700 0.700 33.017 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_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: 12008.0938
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 3488 18D 19E C N 150 152 -170.54 -63.60 119.75 20.57 -63.60 119.75 20.57
1 19E 19E N CA 152 153 -94.17 -40.30 -40.30
2 3502 32E 33S C N 268 270 -139.09 -64.10 87.58 8.61 -64.10 87.58 8.61
2 33S 33S N CA 270 271 10.25 -35.00 -35.00
3 3533 63S 64N C N 519 521 -146.35 -63.20 97.10 15.97 -63.20 97.10 15.97
3 64N 64N N CA 521 522 -91.23 -41.10 -41.10
4 3568 98H 99N C N 784 786 -91.93 -119.90 54.89 1.79 -63.20 133.98 15.34
4 99N 99N N CA 786 787 89.76 137.00 -41.10
5 3569 99N 100F C N 792 794 -57.38 -63.20 8.63 0.99 -124.20 178.96 9.68
5 100F 100F N CA 794 795 -50.68 -44.30 143.30
6 3570 100F 101M C N 803 805 -75.80 -63.40 50.78 6.72 -63.40 50.78 6.72
6 101M 101M N CA 805 806 8.74 -40.50 -40.50
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 7 12 46 67 105 93 151 151 149 163
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 840.30170
seq_lig.B99990002.pdb 851.00928
In [15]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
In [19]:
! rm seq_lig.rsr
rm: cannot remove 'seq_lig.rsr': No such file or directory
In [21]:
#Переместим лиганд в другое место
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 [22]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
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
patch_s_522_> Number of disulfides patched in MODEL: 4
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.
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: 11556 10676
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 : 124
Number of all, selected real atoms : 999 999
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10676 10676
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2116
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 : 1526.7205
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 : 1019 0 4 0.010 0.010 30.101 1.000
2 Bond angle potential : 1371 3 14 2.654 2.654 188.09 1.000
3 Stereochemical cosine torsion poten: 651 0 23 46.774 46.774 222.08 1.000
4 Stereochemical improper torsion pot: 413 0 0 1.442 1.442 20.662 1.000
5 Soft-sphere overlap restraints : 2116 0 0 0.003 0.003 2.6018 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) : 2234 10 37 0.587 0.587 333.73 1.000
10 Distance restraints 2 (N-O) : 2382 2 28 0.516 0.516 294.81 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: 123 0 5 5.390 5.390 42.148 1.000
14 Sidechain Chi_1 dihedral restraints: 110 0 0 60.634 60.634 21.247 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 71.351 71.351 36.609 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 76.328 76.328 24.150 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 76.236 76.236 13.544 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.37613E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.538 2.538 1.1382 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.842 28.842 3.2781 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) : 1449 0 0 0.540 0.540 30.631 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: 122 10 18 32.976 48.647 126.36 1.000
26 Distance restraints 4 (SDCH-SDCH) : 648 0 1 0.776 0.776 46.544 1.000
27 Distance restraints 5 (X-Y) : 1 1 1 1.736 1.736 88.957 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: 13874.0293
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 2306 114P 115L C N 928 930 141.46 120.00 21.46 4.88 120.00 21.46 4.88
2 2392 123G 124V C N 990 992 145.77 120.00 25.77 5.86 120.00 25.77 5.86
-------------------------------------------------------------------------------------------------
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 6130 109H 113K CA CA 882 915 9.58 7.42 2.16 4.68 7.42 2.16 4.68
-------------------------------------------------------------------------------------------------
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 6312 7E 122C N O 52 987 9.84 6.99 2.84 5.24 6.99 2.84 5.24
-------------------------------------------------------------------------------------------------
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 3502 32E 33S C N 268 270 -138.12 -64.10 82.33 8.60 -64.10 82.33 8.60
1 33S 33S N CA 270 271 1.05 -35.00 -35.00
2 3511 41G 42K C N 334 336 -66.40 -62.90 5.16 0.62 -118.00 -176.49 8.07
2 42K 42K N CA 336 337 -37.01 -40.80 139.10
3 3533 63S 64N C N 519 521 -143.21 -63.20 89.60 14.71 -63.20 89.60 14.71
3 64N 64N N CA 521 522 -81.42 -41.10 -41.10
4 3570 100F 101M C N 803 805 -68.79 -63.40 53.70 7.61 -63.40 53.70 7.61
4 101M 101M N CA 805 806 12.92 -40.50 -40.50
5 3580 110C 111Q C N 895 897 -50.91 -63.80 13.03 2.25 -73.00 -179.55 11.36
5 111Q 111Q N CA 897 898 -38.39 -40.30 140.70
6 3581 111Q 112N C N 904 906 -58.82 -63.20 17.97 2.04 55.90 150.89 18.17
6 112N 112N N CA 906 907 -58.52 -41.10 39.50
7 3582 112N 113K C N 912 914 178.17 -118.00 70.49 2.33 -70.20 115.24 7.73
7 113K 113K N CA 914 915 169.02 139.10 140.40
8 3584 114P 115L C N 928 930 -77.61 -63.50 90.74 11.86 -63.50 90.74 11.86
8 115L 115L N CA 930 931 48.43 -41.20 -41.20
9 3589 119S 120K C N 965 967 52.87 -62.90 145.93 18.64 -118.00 -166.28 9.02
9 120K 120K N CA 967 968 -129.64 -40.80 139.10
10 3590 120K 121C C N 974 976 -53.67 -63.00 14.85 2.49 57.40 128.96 16.64
10 121C 121C N CA 976 977 -29.54 -41.10 36.00
-------------------------------------------------------------------------------------------------
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 10676 123G 114P O CA 991 924 4.74 3.00 1.74 17.36 3.00 1.74 17.36
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 15 49 66 95 110 136 132 176 150
<< 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 : 124
Number of all, selected real atoms : 999 999
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10676 10676
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2163
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 : 1535.6798
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 : 1019 0 3 0.009 0.009 28.212 1.000
2 Bond angle potential : 1371 4 15 2.690 2.690 187.67 1.000
3 Stereochemical cosine torsion poten: 651 0 23 48.269 48.269 228.04 1.000
4 Stereochemical improper torsion pot: 413 0 0 1.385 1.385 18.928 1.000
5 Soft-sphere overlap restraints : 2163 0 0 0.003 0.003 2.1639 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) : 2234 7 34 0.556 0.556 307.59 1.000
10 Distance restraints 2 (N-O) : 2382 5 23 0.500 0.500 284.49 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: 123 0 5 5.625 5.625 45.897 1.000
14 Sidechain Chi_1 dihedral restraints: 110 0 0 64.802 64.802 21.928 1.000
15 Sidechain Chi_2 dihedral restraints: 80 0 0 69.098 69.098 28.286 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 78.349 78.349 22.798 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 87.516 87.516 14.106 1.000
18 Disulfide distance restraints : 4 0 0 0.011 0.011 0.80539E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.427 2.427 1.0409 1.000
20 Disulfide dihedral angle restraints: 4 0 0 31.081 31.081 3.6825 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) : 1449 0 0 0.457 0.457 30.770 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: 122 15 19 37.537 51.952 169.52 1.000
26 Distance restraints 4 (SDCH-SDCH) : 648 0 2 0.795 0.795 45.037 1.000
27 Distance restraints 5 (X-Y) : 1 1 1 1.799 1.799 95.445 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: 14316.8428
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 2387 122C 123G C N 986 988 140.39 120.00 20.39 4.63 120.00 20.39 4.63
2 2389 123G 123G N CA 988 989 123.52 107.00 16.52 4.75 107.00 16.52 4.75
3 2392 123G 124V C N 990 992 146.55 120.00 26.55 6.03 120.00 26.55 6.03
-------------------------------------------------------------------------------------------------
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 4289 10Q 124V CA CA 77 993 9.18 6.74 2.44 4.75 6.74 2.44 4.75
-------------------------------------------------------------------------------------------------
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 6312 7E 122C N O 52 987 9.54 6.99 2.55 4.70 6.99 2.55 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 3488 18D 19E C N 150 152 -156.47 -63.60 102.72 17.62 -63.60 102.72 17.62
1 19E 19E N CA 152 153 -84.19 -40.30 -40.30
2 3502 32E 33S C N 268 270 -134.77 -64.10 77.38 8.26 -64.10 77.38 8.26
2 33S 33S N CA 270 271 -3.47 -35.00 -35.00
3 3512 42K 43P C N 343 345 -62.62 -58.70 9.12 0.53 -64.50 169.47 12.55
3 43P 43P N CA 345 346 -22.26 -30.50 147.20
4 3533 63S 64N C N 519 521 -149.86 -63.20 94.38 15.44 -63.20 94.38 15.44
4 64N 64N N CA 521 522 -78.48 -41.10 -41.10
5 3535 65T 66S C N 534 536 -58.20 -64.10 45.63 3.00 -72.40 128.14 8.03
5 66S 66S N CA 536 537 -80.25 -35.00 152.40
6 3536 66S 67K C N 540 542 -54.29 -62.90 16.02 1.85 56.60 144.67 18.04
6 67K 67K N CA 542 543 -54.31 -40.80 38.60
7 3537 67K 68A C N 549 551 72.85 -68.20 147.27 13.74 -68.20 147.27 13.74
7 68A 68A N CA 551 552 -172.36 145.30 145.30
8 3538 68A 69G C N 554 556 151.00 82.20 84.22 3.24 -62.40 146.60 26.14
8 69G 69G N CA 556 557 -40.07 8.50 -41.20
9 3570 100F 101M C N 803 805 -68.91 -63.40 58.39 8.30 -63.40 58.39 8.30
9 101M 101M N CA 805 806 17.63 -40.50 -40.50
10 3580 110C 111Q C N 895 897 19.33 -63.80 115.58 15.13 -73.00 135.15 10.46
10 111Q 111Q N CA 897 898 -120.61 -40.30 140.70
11 3581 111Q 112N C N 904 906 -101.98 -119.90 40.59 1.39 55.90 169.28 15.26
11 112N 112N N CA 906 907 100.59 137.00 39.50
12 3582 112N 113K C N 912 914 -165.62 -118.00 48.41 1.70 -70.20 95.71 6.81
12 113K 113K N CA 914 915 147.83 139.10 140.40
13 3584 114P 115L C N 928 930 -85.82 -63.50 84.00 10.61 -63.50 84.00 10.61
13 115L 115L N CA 930 931 39.77 -41.20 -41.20
14 3588 118I 119S C N 959 961 -139.34 -136.60 84.66 4.35 -64.10 126.41 9.04
14 119S 119S N CA 961 962 66.58 151.20 -35.00
15 3591 121C 122C C N 980 982 -162.37 -63.00 101.49 15.69 -63.00 101.49 15.69
15 122C 122C N CA 982 983 -20.45 -41.10 -41.10
-------------------------------------------------------------------------------------------------
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 10676 123G 114P O CA 991 924 4.80 3.00 1.80 17.99 3.00 1.80 17.99
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 13 62 77 96 102 132 126 164 175
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 1526.72046
seq_lig.B99990002.pdb 1535.67981
In [26]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
In [ ]:
#на вид ничего не изменилось, но скоры сильно просели
In [28]:
# заменим всех аминокислот на Ala
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'
In [29]:
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [30]:
! cat all_in_one3.ali
>P1;pdb structureX:1lmp.pdb: 1 :A:+129 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV* >P1;seq_ala sequence::1 : :+123 : :undefined:undefined:-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA------AAAAAAAAAA...*
In [31]:
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_ala pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
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
----------------------------------------------
110 1 110 117 A A 12.552
END OF TABLE
buildc__467W> All coordinates in MODEL have been assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
buildc__467W> All coordinates in MODEL have been assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
invent__526W> Inventing the mainchain model coordinates.
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF
IUPAC atoms : C N
Atom indices : 599 601
Residues : ALA CYS
addprm__440W> Adding params (mean,force,period): 1.3258 300.0000 0
For atoms: C UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF
IUPAC atoms : CB CA
Atom indices : 605 602
Residues : CYS CYS
addprm__440W> Adding params (mean,force,period): 1.5447 300.0000 0
For atoms: UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CC UNDF
IUPAC atoms : C CA
Atom indices : 613 612
Residues : VAL VAL
addprm__440W> Adding params (mean,force,period): 1.5664 300.0000 0
For atoms: CC UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CT1 C UNDF
IUPAC atoms : CA C N
Atom indices : 597 599 601
Residues : ALA ALA CYS
addprm__440W> Adding params (mean,force,period): 121.2296 60.0000 0
For atoms: CT1 C UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF UNDF
IUPAC atoms : C N CA
Atom indices : 599 601 602
Residues : ALA CYS CYS
addprm__440W> Adding params (mean,force,period): 119.8740 60.0000 0
For atoms: C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C O
IUPAC atoms : N C O
Atom indices : 601 599 600
Residues : CYS ALA ALA
addprm__440W> Adding params (mean,force,period): 126.2406 60.0000 0
For atoms: UNDF C O
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF
IUPAC atoms : N CA CB
Atom indices : 601 602 605
Residues : CYS CYS CYS
addprm__440W> Adding params (mean,force,period): 108.4854 60.0000 0
For atoms: UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF CC
IUPAC atoms : N CA C
Atom indices : 611 612 613
Residues : VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 104.5036 60.0000 0
For atoms: UNDF UNDF CC
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF CC OC
IUPAC atoms : CA C O
Atom indices : 612 613 614
Residues : VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 110.1571 60.0000 0
For atoms: UNDF CC OC
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C CT1 CT3
IUPAC atoms : N C CA CB
Atom indices : 601 599 597 598
Residues : CYS ALA ALA ALA
addprm__440W> Adding params (mean,force,period): 131.0444 10.0000 3
For atoms: UNDF C CT1 CT3
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C CT1 NH1
IUPAC atoms : N C CA N
Atom indices : 601 599 597 596
Residues : CYS ALA ALA ALA
addprm__440W> Adding params (mean,force,period): 7.8145 10.0000 3
For atoms: UNDF C CT1 NH1
generat_607W> Cannot find params in params file:
CHARMM atoms : O C UNDF UNDF
IUPAC atoms : O C N CA
Atom indices : 600 599 601 602
Residues : ALA ALA CYS CYS
addprm__440W> Adding params (mean,force,period): 4.1120 10.0000 3
For atoms: O C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CT1 C UNDF UNDF
IUPAC atoms : CA C N CA
Atom indices : 597 599 601 602
Residues : ALA ALA CYS CYS
addprm__440W> Adding params (mean,force,period): -174.0557 10.0000 3
For atoms: CT1 C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF UNDF
IUPAC atoms : SG CB CA N
Atom indices : 606 605 602 601
Residues : CYS CYS CYS CYS
addprm__440W> Adding params (mean,force,period): -64.4538 10.0000 3
For atoms: UNDF UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF UNDF UNDF
IUPAC atoms : C N CA CB
Atom indices : 599 601 602 605
Residues : ALA CYS CYS CYS
addprm__440W> Adding params (mean,force,period): 144.4096 10.0000 3
For atoms: C UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF CC
IUPAC atoms : CG1 CB CA C
Atom indices : 616 615 612 613
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): -175.3415 10.0000 3
For atoms: UNDF UNDF UNDF CC
generat_607W> Cannot find params in params file:
CHARMM atoms : OC CC UNDF UNDF
IUPAC atoms : O C CA CB
Atom indices : 614 613 612 615
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): -99.4752 10.0000 3
For atoms: OC CC UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF UNDF
IUPAC atoms : C CA N O
Atom indices : 603 602 607 604
Residues : CYS CYS GLY CYS
addprm__440W> Adding params (mean,force,period): 1.0526 60.0000 0
For atoms: UNDF UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF CC UNDF
IUPAC atoms : CA N C CB
Atom indices : 612 611 613 615
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 29.9746 60.0000 0
For atoms: UNDF UNDF CC UNDF
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.
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: 8209 7602
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 618 618
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 7602 7602
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1076
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 : 712.5024
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 : 617 0 0 0.006 0.006 6.5539 1.000
2 Bond angle potential : 862 0 7 2.504 2.504 106.17 1.000
3 Stereochemical cosine torsion poten: 256 1 37 76.272 76.272 269.66 1.000
4 Stereochemical improper torsion pot: 246 3 5 3.084 3.084 48.694 1.000
5 Soft-sphere overlap restraints : 1076 0 0 0.002 0.002 0.38818 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) : 2233 0 3 0.410 0.410 87.959 1.000
10 Distance restraints 2 (N-O) : 2371 0 4 0.420 0.420 107.43 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: 122 0 3 4.665 4.665 31.310 1.000
14 Sidechain Chi_1 dihedral restraints: 2 0 2 61.091 61.091 7.8715 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) : 708 0 0 0.339 0.339 5.2870 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: 121 22 15 31.491 69.806 32.288 1.000
26 Distance restraints 4 (SDCH-SDCH) : 64 0 2 1.219 1.219 8.8948 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_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: 11199.0078
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 3 : Stereochemical cosine torsion 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 1729 123V 123V CG2 CB 617 615 -23.93 -4.66 -19.27 6.11 -4.66 -19.27 6.11
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1976 121C 121C C CA 603 602 25.86 1.05 24.81 6.18 1.05 24.81 6.18
2 1977 121C 121C CA N 602 601 28.44 1.05 27.39 6.82 1.05 27.39 6.82
-------------------------------------------------------------------------------------------------
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 1996 15A 16A C N 74 76 78.97 55.40 27.54 1.99 -62.50 155.62 31.61
1 16A 16A N CA 76 77 23.95 38.20 -40.90
2 1999 18A 19A C N 89 91 65.35 55.40 23.11 0.83 -62.50 140.48 28.53
2 19A 19A N CA 91 92 17.34 38.20 -40.90
3 2001 20A 21A C N 99 101 53.89 55.40 3.69 0.34 -62.50 138.86 28.21
3 21A 21A N CA 101 102 34.83 38.20 -40.90
4 2002 21A 22A C N 104 106 61.95 55.40 8.26 0.52 -62.50 144.81 29.45
4 22A 22A N CA 106 107 33.16 38.20 -40.90
5 2017 36A 37A C N 179 181 66.39 55.40 13.79 0.88 -62.50 147.03 29.90
5 37A 37A N CA 181 182 29.86 38.20 -40.90
6 2018 37A 38A C N 184 186 62.33 55.40 11.66 0.49 -62.50 142.98 29.08
6 38A 38A N CA 186 187 28.82 38.20 -40.90
7 2029 48A 49A C N 239 241 86.02 55.40 44.31 2.26 -62.50 155.80 31.41
7 49A 49A N CA 241 242 6.18 38.20 -40.90
8 2034 53A 54A C N 264 266 90.71 -134.00 140.74 3.43 -62.50 -156.91 31.90
8 54A 54A N CA 266 267 -174.21 147.00 -40.90
9 2037 56A 57A C N 279 281 59.00 55.40 13.04 1.08 -62.50 152.18 30.81
9 57A 57A N CA 281 282 50.73 38.20 -40.90
10 2047 66A 67A C N 329 331 82.44 55.40 60.31 2.18 -62.50 147.11 29.18
10 67A 67A N CA 331 332 -15.71 38.20 -40.90
11 2050 69A 70A C N 344 346 -62.86 -62.50 22.04 3.63 -68.20 151.86 12.44
11 70A 70A N CA 346 347 -62.93 -40.90 145.30
12 2051 70A 71A C N 349 351 -117.37 -134.00 49.48 2.32 -62.50 151.57 22.88
12 71A 71A N CA 351 352 100.39 147.00 -40.90
13 2054 73A 74A C N 364 366 52.71 55.40 18.55 0.91 -62.50 150.89 30.42
13 74A 74A N CA 366 367 56.55 38.20 -40.90
14 2057 76A 77A C N 379 381 65.16 55.40 10.13 1.19 -62.50 151.63 30.81
14 77A 77A N CA 381 382 40.92 38.20 -40.90
15 2084 103A 104A C N 514 516 79.03 -134.00 158.33 3.63 -62.50 -178.75 28.77
15 104A 104A N CA 516 517 -154.13 147.00 -40.90
16 2089 108A 109A C N 539 541 -111.08 -134.00 62.51 2.85 -62.50 138.53 20.94
16 109A 109A N CA 541 542 88.84 147.00 -40.90
17 2090 109A 110A C N 544 546 -147.17 -134.00 19.50 1.15 -62.50 -166.93 28.95
17 110A 110A N CA 546 547 132.62 147.00 -40.90
18 2091 110A 111A C N 549 551 -144.97 -134.00 15.16 0.44 -62.50 -178.54 34.15
18 111A 111A N CA 551 552 157.47 147.00 -40.90
19 2092 111A 112A C N 554 556 158.19 -134.00 78.57 1.84 -68.20 139.87 10.38
19 112A 112A N CA 556 557 -173.33 147.00 145.30
20 2094 113A 114A C N 564 566 -134.60 -134.00 60.20 3.43 -62.50 146.64 21.97
20 114A 114A N CA 566 567 86.80 147.00 -40.90
21 2100 119A 120A C N 594 596 73.22 55.40 39.01 1.42 -62.50 142.79 28.81
21 120A 120A N CA 596 597 3.50 38.20 -40.90
22 2101 120A 121C C N 599 601 17.74 -63.00 144.12 15.21 -63.00 144.12 15.21
22 121C 121C N CA 601 602 -160.48 -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 0 4 27 43 64 52 67 89 89 64
<< 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 : 618 618
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 7602 7602
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1057
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 : 677.4470
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 : 617 0 0 0.006 0.006 7.0978 1.000
2 Bond angle potential : 862 0 10 2.478 2.478 105.58 1.000
3 Stereochemical cosine torsion poten: 256 2 36 75.930 75.930 271.63 1.000
4 Stereochemical improper torsion pot: 246 3 5 2.840 2.840 42.143 1.000
5 Soft-sphere overlap restraints : 1057 0 0 0.001 0.001 0.24437 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) : 2233 1 5 0.386 0.386 84.970 1.000
10 Distance restraints 2 (N-O) : 2371 0 4 0.379 0.379 106.17 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: 122 0 4 4.651 4.651 31.116 1.000
14 Sidechain Chi_1 dihedral restraints: 2 0 1 62.649 62.649 7.3155 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) : 708 0 0 0.337 0.337 5.1524 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: 121 20 13 27.203 66.025 14.607 1.000
26 Distance restraints 4 (SDCH-SDCH) : 64 0 0 0.502 0.502 1.4154 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_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: 10813.0518
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 3 : Stereochemical cosine torsion 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 1729 123V 123V CG2 CB 617 615 -28.59 -4.66 -23.93 8.45 -4.66 -23.93 8.45
2 1731 122G 123V C N 609 611 -26.26 -4.66 -21.60 7.26 -4.66 -21.60 7.26
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1977 121C 121C CA N 602 601 22.70 1.05 21.65 5.39 1.05 21.65 5.39
2 1981 123V 123V O CA 614 612 19.96 0.00 19.96 6.29 0.00 19.96 6.29
-------------------------------------------------------------------------------------------------
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 1996 15A 16A C N 74 76 78.26 55.40 26.53 1.95 -62.50 155.30 31.55
1 16A 16A N CA 76 77 24.74 38.20 -40.90
2 1999 18A 19A C N 89 91 58.31 55.40 3.65 0.23 -62.50 143.21 29.10
2 19A 19A N CA 91 92 36.00 38.20 -40.90
3 2000 19A 20A C N 94 96 -60.69 -62.50 19.37 3.09 -68.20 154.70 12.74
3 20A 20A N CA 96 97 -60.18 -40.90 145.30
4 2001 20A 21A C N 99 101 -122.02 -134.00 77.69 4.11 -62.50 126.07 18.89
4 21A 21A N CA 101 102 70.24 147.00 -40.90
5 2002 21A 22A C N 104 106 59.45 55.40 14.12 0.56 -62.50 138.46 28.16
5 22A 22A N CA 106 107 24.67 38.20 -40.90
6 2017 36A 37A C N 179 181 67.36 55.40 14.78 0.97 -62.50 147.71 30.04
6 37A 37A N CA 181 182 29.51 38.20 -40.90
7 2018 37A 38A C N 184 186 63.22 55.40 12.54 0.56 -62.50 143.55 29.20
7 38A 38A N CA 186 187 28.40 38.20 -40.90
8 2029 48A 49A C N 239 241 85.44 55.40 43.59 2.21 -62.50 155.38 31.33
8 49A 49A N CA 241 242 6.61 38.20 -40.90
9 2034 53A 54A C N 264 266 91.22 -134.00 140.36 3.41 -62.50 -156.78 31.95
9 54A 54A N CA 266 267 -173.82 147.00 -40.90
10 2037 56A 57A C N 279 281 59.59 55.40 12.09 1.07 -62.50 151.94 30.78
10 57A 57A N CA 281 282 49.55 38.20 -40.90
11 2047 66A 67A C N 329 331 82.04 55.40 59.12 2.14 -62.50 146.91 29.18
11 67A 67A N CA 331 332 -14.58 38.20 -40.90
12 2051 70A 71A C N 349 351 54.86 55.40 5.67 0.30 -62.50 144.76 29.34
12 71A 71A N CA 351 352 43.85 38.20 -40.90
13 2054 73A 74A C N 364 366 53.38 55.40 15.34 0.76 -62.50 149.40 30.16
13 74A 74A N CA 366 367 53.40 38.20 -40.90
14 2057 76A 77A C N 379 381 64.62 55.40 9.95 1.18 -62.50 151.73 30.82
14 77A 77A N CA 381 382 41.95 38.20 -40.90
15 2084 103A 104A C N 514 516 80.44 -134.00 157.46 3.60 -62.50 -178.38 28.91
15 104A 104A N CA 516 517 -152.94 147.00 -40.90
16 2089 108A 109A C N 539 541 -110.23 -134.00 54.57 2.34 -62.50 146.75 22.26
16 109A 109A N CA 541 542 97.87 147.00 -40.90
17 2090 109A 110A C N 544 546 -153.75 -134.00 20.07 0.80 -62.50 -162.08 37.32
17 110A 110A N CA 546 547 143.48 147.00 -40.90
18 2091 110A 111A C N 549 551 -145.24 -134.00 18.86 0.67 -62.50 177.43 33.50
18 111A 111A N CA 551 552 162.14 147.00 -40.90
19 2092 111A 112A C N 554 556 166.73 -134.00 72.90 1.83 -68.20 132.63 9.66
19 112A 112A N CA 556 557 -170.57 147.00 145.30
20 2100 119A 120A C N 594 596 67.91 55.40 32.93 1.20 -62.50 139.18 28.17
20 120A 120A N CA 596 597 7.73 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 0 7 23 41 63 50 65 101 87 71
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 712.50244
seq_ala.B99990002.pdb 677.44702
In [32]:
pdb2img('seq_ala.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_ala.B99990002.pdb', '1lmp.pdb')
In [ ]:
#аланины всему голова, скор лучше чем у изначального выравнивания