Гомологичное моделирование комплекса белка с лигандом¶
Импортируем модули и инициализируем программу
In [29]:
import sys
import os
import modeller
import _modeller
import modeller.automodel
In [36]:
env=modeller.environ()
env.io.hetatm = True
Вручную скачаем необходимые для работы файлы: исходную трехмерную структуру 1lmp.pdb и аминокислотную последовательность лизоцима жабы LYS_BUFGA. Затем создадим объект выравнивания, в котором объединим последвательность и структуру, подправив их идентификаторы
In [37]:
alignm = modeller.alignment(env)
In [40]:
alignm.append(file='P85045.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.
Проведем выравнивание, сохраним его и посмотрим итоговый файл, осуществим моделирование и визуализируем. Здесь и далее белок жабы зеленого цвета, белок форели - голубого.
In [21]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [22]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq pdb
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
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.
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: 13044 12008
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 : 146
Number of all, selected real atoms : 1166 1166
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12008 12008
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2424
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 : 832.4334
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 : 1197 0 0 0.006 0.006 11.839 1.000
2 Bond angle potential : 1618 0 6 2.213 2.213 154.77 1.000
3 Stereochemical cosine torsion poten: 814 0 28 47.426 47.426 278.22 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.235 1.235 17.705 1.000
5 Soft-sphere overlap restraints : 2424 0 0 0.002 0.002 1.0354 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.134 0.134 40.620 1.000
10 Distance restraints 2 (N-O) : 2564 0 2 0.190 0.190 79.238 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: 145 0 2 4.504 4.504 34.693 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 1 66.485 66.485 19.359 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 71.574 71.574 32.975 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 80.978 80.978 22.803 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 101.703 101.703 13.681 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.23926E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.736 2.736 1.3228 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.361 28.361 2.7418 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) : 1582 0 0 0.431 0.431 33.701 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: 144 18 11 22.155 61.166 41.702 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.675 0.675 45.999 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: 15140.6514
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 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 4148 1S 2G C N 5 7 -66.31 -80.20 33.15 0.78 82.20 -158.96 6.63
1 2G 2G N CA 7 8 144.00 174.10 8.50
2 4149 2G 3K C N 9 11 -79.10 -70.20 10.18 0.63 -62.90 174.62 23.60
2 3K 3K N CA 11 12 145.33 140.40 -40.80
3 4150 3K 4Y C N 18 20 -76.43 -98.40 22.02 0.84 -63.50 173.80 26.92
3 4Y 4Y N CA 20 21 129.92 128.40 -43.40
4 4152 5I 6S C N 38 40 -80.53 -72.40 8.41 0.53 -64.10 171.24 13.45
4 6S 6S N CA 40 41 154.55 152.40 -35.00
5 4153 6S 7W C N 44 46 -145.21 -124.90 38.59 1.36 -63.00 161.99 25.78
5 7W 7W N CA 46 47 176.22 143.40 -44.20
6 4154 7W 8E C N 58 60 -61.86 -69.30 9.26 0.52 -63.60 177.29 23.73
6 8E 8E N CA 60 61 136.98 142.50 -40.30
7 4155 8E 9D C N 67 69 -104.91 -96.50 10.08 0.41 -63.30 154.36 16.97
7 9D 9D N CA 69 70 108.65 114.20 -40.00
8 4156 9D 10S C N 75 77 -130.98 -136.60 6.63 0.35 -64.10 -177.06 17.99
8 10S 10S N CA 77 78 154.73 151.20 -35.00
9 4158 11C 12S C N 87 89 -81.10 -72.40 21.21 1.00 -64.10 154.20 12.26
9 12S 12S N CA 89 90 171.74 152.40 -35.00
10 4159 12S 13Y C N 93 95 -130.84 -124.30 34.43 1.56 -63.50 162.05 29.04
10 13Y 13Y N CA 95 96 169.20 135.40 -43.40
11 4160 13Y 14L C N 105 107 -65.19 -70.70 7.80 0.78 -63.50 171.68 23.93
11 14L 14L N CA 107 108 147.13 141.60 -41.20
12 4161 14L 15Q C N 113 115 -54.06 -73.00 24.09 1.42 -63.80 166.41 24.98
12 15Q 15Q N CA 115 116 125.82 140.70 -40.30
13 4162 15Q 16L C N 122 124 -111.34 -108.50 24.57 1.30 -63.50 168.81 26.39
13 16L 16L N CA 124 125 156.91 132.50 -41.20
14 4163 16L 17Q C N 130 132 -115.52 -121.10 19.26 0.81 -63.80 169.65 22.59
14 17Q 17Q N CA 132 133 121.27 139.70 -40.30
15 4198 51E 52S C N 414 416 -137.92 -64.10 82.32 8.57 -64.10 82.32 8.57
15 52S 52S N CA 416 417 1.44 -35.00 -35.00
16 4210 63P 64P C N 504 506 -76.20 -58.70 17.84 2.08 -64.50 174.63 13.66
16 64P 64P N CA 506 507 -27.04 -30.50 147.20
17 4288 141T 142Q C N 1128 1130 24.18 -63.80 128.28 16.65 -73.00 129.53 10.09
17 142Q 142Q N CA 1130 1131 -133.66 -40.30 140.70
18 4289 142Q 143G C N 1137 1139 -59.26 -62.40 26.20 4.07 82.20 143.43 10.39
18 143G 143G N CA 1139 1140 -15.19 -41.20 8.50
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 4 11 47 82 118 123 134 156 192 185
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 146
Number of all, selected real atoms : 1166 1166
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12008 12008
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2382
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 : 777.5758
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 : 1197 0 0 0.006 0.006 11.337 1.000
2 Bond angle potential : 1618 0 5 2.092 2.092 139.72 1.000
3 Stereochemical cosine torsion poten: 814 0 30 47.513 47.513 279.23 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.240 1.240 17.751 1.000
5 Soft-sphere overlap restraints : 2382 0 0 0.002 0.002 0.92328 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.117 0.117 33.532 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.166 0.166 67.029 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: 145 0 1 4.125 4.125 29.089 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 63.071 63.071 14.641 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 75.695 75.695 33.398 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 88.212 88.212 27.347 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 90.711 90.711 11.262 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.38517E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.777 1.777 0.55776 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.777 29.777 3.3456 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) : 1582 0 0 0.339 0.339 28.551 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: 144 16 15 22.842 57.616 40.922 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.564 0.564 38.894 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: 14222.7178
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 4148 1S 2G C N 5 7 -81.90 -80.20 11.05 0.35 82.20 -118.98 7.26
1 2G 2G N CA 7 8 -174.98 174.10 8.50
2 4149 2G 3K C N 9 11 -62.65 -70.20 18.85 1.52 -62.90 161.53 20.96
2 3K 3K N CA 11 12 157.67 140.40 -40.80
3 4150 3K 4Y C N 18 20 -98.65 -98.40 23.38 2.49 -63.50 152.52 22.51
3 4Y 4Y N CA 20 21 105.02 128.40 -43.40
4 4152 5I 6S C N 38 40 -74.80 -72.40 3.24 0.26 -64.10 175.10 13.35
4 6S 6S N CA 40 41 150.22 152.40 -35.00
5 4153 6S 7W C N 44 46 -118.48 -124.90 16.02 0.61 -63.00 -178.40 20.22
5 7W 7W N CA 46 47 128.72 143.40 -44.20
6 4154 7W 8E C N 58 60 -77.84 -69.30 9.48 0.84 -63.60 179.26 23.15
6 8E 8E N CA 60 61 138.39 142.50 -40.30
7 4155 8E 9D C N 67 69 -109.48 -70.90 39.03 2.74 -63.30 170.16 23.98
7 9D 9D N CA 69 70 156.22 150.30 -40.00
8 4158 11C 12S C N 87 89 -99.32 -72.40 64.79 4.71 -64.10 133.21 8.26
8 12S 12S N CA 89 90 93.47 152.40 -35.00
9 4159 12S 13Y C N 93 95 -134.28 -124.30 10.04 0.78 -63.50 -168.68 27.20
9 13Y 13Y N CA 95 96 134.34 135.40 -43.40
10 4160 13Y 14L C N 105 107 -114.61 -108.50 18.92 1.07 -63.50 163.96 20.48
10 14L 14L N CA 107 108 114.59 132.50 -41.20
11 4161 14L 15Q C N 113 115 -103.61 -121.10 75.84 3.28 -63.80 113.42 14.93
11 15Q 15Q N CA 115 116 65.90 139.70 -40.30
12 4162 15Q 16L C N 122 124 -147.60 -108.50 59.61 2.72 -63.50 164.43 28.00
12 16L 16L N CA 124 125 177.50 132.50 -41.20
13 4163 16L 17Q C N 130 132 -89.69 -73.00 37.21 2.76 -63.80 150.00 20.78
13 17Q 17Q N CA 132 133 107.45 140.70 -40.30
14 4198 51E 52S C N 414 416 -138.68 -64.10 83.52 8.65 -64.10 83.52 8.65
14 52S 52S N CA 416 417 2.61 -35.00 -35.00
15 4209 62N 63P C N 497 499 -74.84 -64.50 85.97 5.89 -58.70 98.29 9.46
15 63P 63P N CA 499 500 -127.46 147.20 -30.50
16 4210 63P 64P C N 504 506 -54.75 -58.70 13.84 1.47 -64.50 164.73 11.79
16 64P 64P N CA 506 507 -17.24 -30.50 147.20
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 11 41 75 110 127 131 156 189 176
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 832.43341
seq.B99990002.pdb 777.57581
In [23]:
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 [24]:
pdb2img('seq.B99990001.pdb', '1lmp.pdb')
pdb2img('seq.B99990002.pdb', '1lmp.pdb')
Проведем все те же манипуляции, но добавив три остатка лиганда на конец последовательности
In [41]:
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 [26]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [27]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_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
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C +N
atom indices : 1164 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C CA +N O
atom indices : 1164 1159 0 1165
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: 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.
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: 14445 13409
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 : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13409 13409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2634
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 : 948.2318
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 : 1197 0 0 0.006 0.006 13.172 1.000
2 Bond angle potential : 1618 0 8 2.366 2.366 176.45 1.000
3 Stereochemical cosine torsion poten: 814 0 30 47.239 47.239 278.13 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.435 1.435 22.350 1.000
5 Soft-sphere overlap restraints : 2634 1 2 0.008 0.008 17.643 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.131 0.131 41.007 1.000
10 Distance restraints 2 (N-O) : 2564 0 3 0.187 0.187 90.729 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: 145 0 3 4.825 4.825 39.803 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 2 70.101 70.101 28.717 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 1 69.942 69.942 35.796 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 89.628 89.628 26.968 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 1 68.427 68.427 15.524 1.000
18 Disulfide distance restraints : 4 0 0 0.011 0.011 0.90381E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.938 1.938 0.66342 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.919 27.919 2.9395 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) : 1582 0 0 0.448 0.448 42.336 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: 144 13 18 21.688 56.543 35.990 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.748 0.748 65.565 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 14.358 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: 15338.5469
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 4148 1S 2G C N 5 7 -72.92 -80.20 22.71 0.58 82.20 -148.29 6.91
1 2G 2G N CA 7 8 152.58 174.10 8.50
2 4149 2G 3K C N 9 11 -114.87 -118.00 10.37 0.53 -62.90 177.97 26.20
2 3K 3K N CA 11 12 148.99 139.10 -40.80
3 4150 3K 4Y C N 18 20 -134.71 -124.30 15.35 0.66 -63.50 -175.75 32.78
3 4Y 4Y N CA 20 21 146.67 135.40 -43.40
4 4152 5I 6S C N 38 40 -162.46 -136.60 64.23 2.61 -64.10 151.34 18.05
4 6S 6S N CA 40 41 -150.01 151.20 -35.00
5 4153 6S 7W C N 44 46 -61.83 -71.30 12.20 1.04 -63.00 169.12 21.07
5 7W 7W N CA 46 47 146.69 139.00 -44.20
6 4160 13Y 14L C N 105 107 -165.15 -108.50 56.97 2.65 -63.50 -153.53 25.30
6 14L 14L N CA 107 108 138.52 132.50 -41.20
7 4161 14L 15Q C N 113 115 -141.41 -121.10 56.25 2.91 -63.80 149.30 19.16
7 15Q 15Q N CA 115 116 87.24 139.70 -40.30
8 4162 15Q 16L C N 122 124 -175.87 -108.50 67.91 3.34 -63.50 -160.21 24.64
8 16L 16L N CA 124 125 123.99 132.50 -41.20
9 4163 16L 17Q C N 130 132 -86.57 -73.00 37.86 2.75 -63.80 147.43 20.55
9 17Q 17Q N CA 132 133 105.36 140.70 -40.30
10 4198 51E 52S C N 414 416 -137.23 -64.10 78.48 8.62 -64.10 78.48 8.62
10 52S 52S N CA 416 417 -6.51 -35.00 -35.00
11 4210 63P 64P C N 504 506 -77.08 -58.70 19.61 2.05 -64.50 171.33 13.46
11 64P 64P N CA 506 507 -23.67 -30.50 147.20
12 4279 132C 133K C N 1054 1056 -49.69 -62.90 31.17 3.58 -70.20 151.96 11.48
12 133K 133K N CA 1056 1057 -69.03 -40.80 140.40
13 4280 133K 134G C N 1063 1065 -74.41 -62.40 14.02 2.13 82.20 162.27 12.14
13 134G 134G N CA 1065 1066 -33.96 -41.20 8.50
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 12 11 54 76 138 131 164 183 189 218
<< 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 : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13409 13409
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2552
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 : 998.4572
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 : 1197 0 0 0.006 0.006 13.021 1.000
2 Bond angle potential : 1618 0 7 2.223 2.223 161.52 1.000
3 Stereochemical cosine torsion poten: 814 0 30 47.514 47.514 284.45 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.288 1.288 19.598 1.000
5 Soft-sphere overlap restraints : 2552 2 2 0.008 0.008 17.713 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.137 0.137 44.589 1.000
10 Distance restraints 2 (N-O) : 2564 3 11 0.236 0.236 141.60 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: 145 1 4 5.226 5.226 46.707 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 67.282 67.282 24.807 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 2 74.039 74.039 31.255 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 73.065 73.065 22.301 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 71.293 71.293 10.626 1.000
18 Disulfide distance restraints : 4 0 0 0.009 0.009 0.55523E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.795 1.795 0.56890 1.000
20 Disulfide dihedral angle restraints: 4 0 0 33.618 33.618 3.9140 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) : 1582 0 0 0.350 0.350 33.515 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: 144 23 20 28.491 68.803 90.918 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.583 0.583 39.443 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.030 0.030 11.859 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: 16198.7939
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9264 121G 37K N O 959 298 10.28 7.92 2.35 4.66 7.92 2.35 4.66
2 9279 122M 37K N O 963 298 9.27 6.93 2.35 5.26 6.93 2.35 5.26
3 9299 123G 37K N O 971 298 11.69 9.33 2.36 4.86 9.33 2.36 4.86
-------------------------------------------------------------------------------------------------
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 4329 38G 38G CA C 300 301 -155.19 -180.00 24.81 4.96 -180.00 24.81 4.96
-------------------------------------------------------------------------------------------------
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 4148 1S 2G C N 5 7 75.71 78.70 5.64 0.09 82.20 169.94 8.58
1 2G 2G N CA 7 8 -161.31 -166.10 8.50
2 4149 2G 3K C N 9 11 -70.98 -70.20 1.85 0.15 -62.90 179.71 22.91
2 3K 3K N CA 11 12 138.72 140.40 -40.80
3 4150 3K 4Y C N 18 20 -118.02 -124.30 6.78 0.41 -63.50 -175.52 26.73
3 4Y 4Y N CA 20 21 132.83 135.40 -43.40
4 4152 5I 6S C N 38 40 -70.93 -72.40 3.29 0.15 -64.10 175.67 13.14
4 6S 6S N CA 40 41 149.46 152.40 -35.00
5 4153 6S 7W C N 44 46 -125.93 -124.90 8.76 0.40 -63.00 175.38 26.14
5 7W 7W N CA 46 47 152.10 143.40 -44.20
6 4154 7W 8E C N 58 60 -70.49 -69.30 6.72 0.55 -63.60 176.32 23.14
6 8E 8E N CA 60 61 135.89 142.50 -40.30
7 4155 8E 9D C N 67 69 -121.65 -96.50 30.11 1.23 -63.30 149.50 15.96
7 9D 9D N CA 69 70 97.65 114.20 -40.00
8 4156 9D 10S C N 75 77 -134.55 -136.60 2.46 0.13 -64.10 -173.73 18.49
8 10S 10S N CA 77 78 152.56 151.20 -35.00
9 4158 11C 12S C N 87 89 165.19 -136.60 78.40 2.48 -64.10 178.30 22.23
9 12S 12S N CA 89 90 -156.28 151.20 -35.00
10 4159 12S 13Y C N 93 95 -71.65 -98.40 27.32 1.13 -63.50 177.54 27.75
10 13Y 13Y N CA 95 96 133.95 128.40 -43.40
11 4160 13Y 14L C N 105 107 -85.65 -108.50 34.51 1.57 -63.50 149.49 19.60
11 14L 14L N CA 107 108 106.64 132.50 -41.20
12 4161 14L 15Q C N 113 115 -171.71 -121.10 52.01 1.73 -63.80 -160.30 34.83
12 15Q 15Q N CA 115 116 151.67 139.70 -40.30
13 4162 15Q 16L C N 122 124 -76.66 -70.70 9.19 0.58 -63.50 170.71 24.48
13 16L 16L N CA 124 125 148.60 141.60 -41.20
14 4163 16L 17Q C N 130 132 -102.48 -121.10 29.67 1.01 -63.80 161.60 21.92
14 17Q 17Q N CA 132 133 116.60 139.70 -40.30
15 4183 36F 37K C N 288 290 65.55 -70.20 158.93 13.13 56.60 175.78 11.89
15 37K 37K N CA 290 291 -136.95 140.40 38.60
16 4184 37K 38G C N 297 299 -90.67 -62.40 38.62 5.50 82.20 174.44 12.48
16 38G 38G N CA 299 300 -14.88 -41.20 8.50
17 4198 51E 52S C N 414 416 -138.10 -64.10 79.09 8.74 -64.10 79.09 8.74
17 52S 52S N CA 416 417 -7.08 -35.00 -35.00
18 4209 62N 63P C N 497 499 -64.43 -64.50 58.69 4.38 -58.70 123.75 10.69
18 63P 63P N CA 499 500 -154.11 147.20 -30.50
19 4210 63P 64P C N 504 506 -56.38 -58.70 23.17 2.11 -64.50 154.85 11.13
19 64P 64P N CA 506 507 -7.44 -30.50 147.20
20 4265 118D 119P C N 942 944 -65.07 -64.50 32.07 2.42 -58.70 145.78 11.54
20 119P 119P N CA 944 945 115.14 147.20 -30.50
21 4266 119P 120N C N 949 951 151.59 -63.20 145.22 21.93 -63.20 145.22 21.93
21 120N 120N N CA 951 952 -39.45 -41.10 -41.10
22 4279 132C 133K C N 1054 1056 -51.71 -62.90 27.80 3.20 -70.20 154.46 11.62
22 133K 133K N CA 1056 1057 -66.25 -40.80 140.40
23 4280 133K 134G C N 1063 1065 -75.24 -62.40 15.51 2.31 82.20 162.69 12.13
23 134G 134G N CA 1065 1066 -32.50 -41.20 8.50
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 1 12 18 47 78 134 121 136 177 181 205
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 948.23181
seq_lig.B99990002.pdb 998.45715
In [28]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
Белок жабы имеет сигнальный пептид на С-конце, а белок форели - нет. Поэтому основная часть остатков хорошо соответствует друг другу, а выявить конформацию С-конца не получается точно.
Перемещение лиганда в другое место
In [31]:
os.remove("seq_lig.rsr")
In [46]:
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 [47]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C +N
atom indices : 1164 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 146
atom names : C CA +N O
atom indices : 1164 1159 0 1165
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: 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.
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: 14446 13410
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 : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13410 13410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2659
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 : 2332.3047
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 : 1197 3 6 0.013 0.013 64.862 1.000
2 Bond angle potential : 1618 4 16 2.936 2.936 266.61 1.000
3 Stereochemical cosine torsion poten: 814 0 34 48.385 48.385 297.73 1.000
4 Stereochemical improper torsion pot: 502 1 3 1.721 1.721 39.844 1.000
5 Soft-sphere overlap restraints : 2659 2 5 0.009 0.009 28.269 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 2 13 0.240 0.240 162.26 1.000
10 Distance restraints 2 (N-O) : 2564 6 25 0.321 0.321 308.31 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: 145 3 8 7.742 7.742 102.48 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 73.019 73.019 29.721 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 1 84.398 84.398 44.940 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 77.104 77.104 23.220 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 82.131 82.131 12.783 1.000
18 Disulfide distance restraints : 4 0 0 0.004 0.004 0.12681E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.498 2.498 1.1021 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.076 27.076 2.6525 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) : 1582 0 1 0.437 0.437 52.366 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 144 23 24 28.312 64.960 197.22 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 2 0.825 0.825 80.643 1.000
27 Distance restraints 5 (X-Y) : 1402 1 7 0.142 0.142 617.28 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: 19140.5645
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
1 997 123G 123G O C 974 973 1.38 1.23 0.15 6.79 1.23 0.15 6.79
2 998 123G 123G C CA 973 972 1.75 1.49 0.26 7.58 1.49 0.26 7.58
-------------------------------------------------------------------------------------------------
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 2556 123G 123G CA C 972 973 138.26 121.00 17.26 4.96 121.00 17.26 4.96
-------------------------------------------------------------------------------------------------
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 8128 67S 87P N O 530 712 8.64 6.49 2.15 4.73 6.49 2.15 4.73
2 9371 126V 123G N O 994 974 6.89 4.81 2.07 4.54 4.81 2.07 4.54
3 9446 130K 123G N O 1029 974 10.52 7.82 2.70 5.10 7.82 2.70 5.10
-------------------------------------------------------------------------------------------------
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 4414 123G 123G CA C 972 973 -123.15 -180.00 56.85 11.37 -180.00 56.85 11.37
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 1S 2G C N 5 7 71.80 78.70 7.14 0.39 82.20 176.76 9.10
1 2G 2G N CA 7 8 -167.95 -166.10 8.50
2 4149 2G 3K C N 9 11 -73.65 -70.20 9.27 0.74 -62.90 172.93 21.89
2 3K 3K N CA 11 12 131.80 140.40 -40.80
3 4150 3K 4Y C N 18 20 -133.26 -124.30 17.86 0.70 -63.50 179.83 32.00
3 4Y 4Y N CA 20 21 150.85 135.40 -43.40
4 4152 5I 6S C N 38 40 -141.83 -136.60 9.93 0.37 -64.10 -177.28 18.79
4 6S 6S N CA 40 41 159.64 151.20 -35.00
5 4153 6S 7W C N 44 46 -125.22 -124.90 17.81 0.86 -63.00 166.65 25.01
5 7W 7W N CA 46 47 161.20 143.40 -44.20
6 4154 7W 8E C N 58 60 -86.37 -69.30 54.15 4.66 -63.60 133.37 16.63
6 8E 8E N CA 60 61 91.11 142.50 -40.30
7 4155 8E 9D C N 67 69 -134.83 -96.50 43.10 1.78 -63.30 -171.96 20.11
7 9D 9D N CA 69 70 133.91 114.20 -40.00
8 4156 9D 10S C N 75 77 -69.32 -72.40 5.03 0.39 -64.10 168.70 12.54
8 10S 10S N CA 77 78 156.38 152.40 -35.00
9 4158 11C 12S C N 87 89 -177.74 -136.60 50.16 1.53 -64.10 -175.71 21.55
9 12S 12S N CA 89 90 179.91 151.20 -35.00
10 4159 12S 13Y C N 93 95 -100.62 -98.40 3.06 0.25 -63.50 177.82 26.41
10 13Y 13Y N CA 95 96 130.51 128.40 -43.40
11 4160 13Y 14L C N 105 107 -76.64 -70.70 50.22 4.04 -63.50 133.58 17.83
11 14L 14L N CA 107 108 91.73 141.60 -41.20
12 4161 14L 15Q C N 113 115 -146.95 -121.10 38.09 1.26 -63.80 173.28 29.77
12 15Q 15Q N CA 115 116 167.67 139.70 -40.30
13 4162 15Q 16L C N 122 124 -125.64 -108.50 17.14 0.82 -63.50 -175.70 22.89
13 16L 16L N CA 124 125 132.31 132.50 -41.20
14 4163 16L 17Q C N 130 132 -116.62 -121.10 30.66 1.38 -63.80 158.72 20.98
14 17Q 17Q N CA 132 133 109.37 139.70 -40.30
15 4198 51E 52S C N 414 416 -137.89 -64.10 82.51 8.56 -64.10 82.51 8.56
15 52S 52S N CA 416 417 1.91 -35.00 -35.00
16 4209 62N 63P C N 497 499 -55.07 -64.50 21.75 1.27 -58.70 158.14 13.36
16 63P 63P N CA 499 500 127.60 147.20 -30.50
17 4233 86T 87P C N 704 706 -43.61 -58.70 63.50 4.16 -64.50 122.41 10.27
17 87P 87P N CA 706 707 -92.18 -30.50 147.20
18 4234 87P 88R C N 711 713 -98.94 -125.20 64.20 2.43 57.30 162.32 16.54
18 88R 88R N CA 713 714 82.01 140.60 38.00
19 4260 113K 114R C N 903 905 -127.54 -63.00 84.46 10.31 -63.00 84.46 10.31
19 114R 114R N CA 905 906 13.38 -41.10 -41.10
20 4269 122M 123G C N 969 971 -65.43 -62.40 67.79 10.27 -62.40 67.79 10.27
20 123G 123G N CA 971 972 -108.93 -41.20 -41.20
21 4270 123G 124A C N 973 975 33.14 -62.50 98.00 19.57 -62.50 98.00 19.57
21 124A 124A N CA 975 976 -19.53 -40.90 -40.90
22 4288 141T 142Q C N 1128 1130 16.25 -63.80 116.90 15.17 -73.00 129.48 10.03
22 142Q 142Q N CA 1130 1131 -125.50 -40.30 140.70
23 4289 142Q 143G C N 1137 1139 -59.75 -62.40 29.76 4.58 82.20 143.37 10.28
23 143G 143G N CA 1139 1140 -11.56 -41.20 8.50
-------------------------------------------------------------------------------------------------
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 13410 123G 114R O CA 974 906 7.28 3.00 4.28 42.82 3.00 4.28 42.82
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 7 22 68 90 131 121 135 156 201 214
<< 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 : 149
Number of all, selected real atoms : 1209 1209
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13410 13410
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2597
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 : 2160.4841
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 : 1197 3 6 0.013 0.013 62.886 1.000
2 Bond angle potential : 1618 4 13 2.845 2.845 249.37 1.000
3 Stereochemical cosine torsion poten: 814 0 27 47.156 47.156 283.50 1.000
4 Stereochemical improper torsion pot: 502 1 3 1.706 1.706 38.967 1.000
5 Soft-sphere overlap restraints : 2597 1 4 0.009 0.009 26.666 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 2 16 0.235 0.235 160.19 1.000
10 Distance restraints 2 (N-O) : 2564 6 20 0.306 0.306 280.15 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: 145 3 4 7.561 7.561 97.751 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 1 72.180 72.180 28.728 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 73.482 73.482 34.150 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 77.993 77.993 20.850 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 71.625 71.625 11.441 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.37977E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.500 1.500 0.39765 1.000
20 Disulfide dihedral angle restraints: 4 0 0 30.177 30.177 3.4794 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) : 1582 0 0 0.396 0.396 37.669 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: 144 21 17 25.302 64.189 176.16 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.655 0.655 46.877 1.000
27 Distance restraints 5 (X-Y) : 1402 1 7 0.139 0.139 601.22 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: 17800.8184
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
1 997 123G 123G O C 974 973 1.37 1.23 0.14 6.63 1.23 0.14 6.63
2 998 123G 123G C CA 973 972 1.75 1.49 0.26 7.44 1.49 0.26 7.44
-------------------------------------------------------------------------------------------------
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 2556 123G 123G CA C 972 973 137.43 121.00 16.43 4.72 121.00 16.43 4.72
-------------------------------------------------------------------------------------------------
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 8128 67S 87P N O 530 712 8.58 6.49 2.08 4.59 6.49 2.08 4.59
2 9371 126V 123G N O 994 974 6.91 4.81 2.09 4.58 4.81 2.09 4.58
3 9446 130K 123G N O 1029 974 10.57 7.82 2.75 5.19 7.82 2.75 5.19
-------------------------------------------------------------------------------------------------
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 4414 123G 123G CA C 972 973 -121.17 -180.00 58.83 11.76 -180.00 58.83 11.76
-------------------------------------------------------------------------------------------------
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 4148 1S 2G C N 5 7 -83.59 -80.20 6.01 0.15 82.20 -122.14 7.33
1 2G 2G N CA 7 8 179.06 174.10 8.50
2 4149 2G 3K C N 9 11 -72.71 -70.20 7.54 0.49 -62.90 171.97 22.88
2 3K 3K N CA 11 12 147.51 140.40 -40.80
3 4150 3K 4Y C N 18 20 -118.55 -124.30 10.43 0.79 -63.50 -178.93 31.52
3 4Y 4Y N CA 20 21 144.10 135.40 -43.40
4 4152 5I 6S C N 38 40 -57.82 -72.40 19.83 0.96 -64.10 174.08 13.00
4 6S 6S N CA 40 41 138.97 152.40 -35.00
5 4153 6S 7W C N 44 46 -71.14 -71.30 3.20 0.25 -63.00 173.79 22.23
5 7W 7W N CA 46 47 142.20 139.00 -44.20
6 4154 7W 8E C N 58 60 -122.48 -117.80 6.24 0.19 -63.60 -171.79 28.42
6 8E 8E N CA 60 61 140.94 136.80 -40.30
7 4155 8E 9D C N 67 69 -73.84 -96.50 22.70 0.93 -63.30 156.02 18.64
7 9D 9D N CA 69 70 115.67 114.20 -40.00
8 4156 9D 10S C N 75 77 -141.59 -136.60 9.85 0.37 -64.10 -177.42 18.77
8 10S 10S N CA 77 78 159.68 151.20 -35.00
9 4159 12S 13Y C N 93 95 -124.02 -124.30 15.75 0.85 -63.50 176.17 31.00
9 13Y 13Y N CA 95 96 151.15 135.40 -43.40
10 4160 13Y 14L C N 105 107 -65.43 -70.70 10.37 0.64 -63.50 173.88 24.03
10 14L 14L N CA 107 108 132.67 141.60 -41.20
11 4161 14L 15Q C N 113 115 -138.78 -121.10 23.01 1.16 -63.80 -178.53 23.58
11 15Q 15Q N CA 115 116 124.96 139.70 -40.30
12 4162 15Q 16L C N 122 124 -131.51 -108.50 43.64 2.06 -63.50 163.98 26.98
12 16L 16L N CA 124 125 169.58 132.50 -41.20
13 4163 16L 17Q C N 130 132 -80.20 -73.00 19.61 1.43 -63.80 163.59 23.22
13 17Q 17Q N CA 132 133 122.47 140.70 -40.30
14 4198 51E 52S C N 414 416 -136.55 -64.10 77.14 8.58 -64.10 77.14 8.58
14 52S 52S N CA 416 417 -8.52 -35.00 -35.00
15 4209 62N 63P C N 497 499 -66.61 -64.50 58.21 4.23 -58.70 124.38 10.93
15 63P 63P N CA 499 500 -154.63 147.20 -30.50
16 4210 63P 64P C N 504 506 -57.37 -58.70 24.59 2.14 -64.50 153.31 11.07
16 64P 64P N CA 506 507 -5.95 -30.50 147.20
17 4233 86T 87P C N 704 706 -46.11 -58.70 67.49 4.63 -64.50 117.45 9.76
17 87P 87P N CA 706 707 -96.80 -30.50 147.20
18 4234 87P 88R C N 711 713 -101.34 -125.20 55.31 2.06 57.30 167.17 16.53
18 88R 88R N CA 713 714 90.71 140.60 38.00
19 4260 113K 114R C N 903 905 -133.56 -63.00 95.69 11.50 -63.00 95.69 11.50
19 114R 114R N CA 905 906 23.53 -41.10 -41.10
20 4269 122M 123G C N 969 971 -65.22 -62.40 68.92 10.43 -62.40 68.92 10.43
20 123G 123G N CA 971 972 -110.06 -41.20 -41.20
21 4270 123G 124A C N 973 975 30.44 -62.50 95.78 19.18 -62.50 95.78 19.18
21 124A 124A N CA 975 976 -17.73 -40.90 -40.90
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 13410 123G 114R O CA 974 906 7.24 3.00 4.24 42.37 3.00 4.24 42.37
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 8 13 69 79 142 112 146 178 200 211
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_lig.B99990001.pdb 2332.30469
seq_lig.B99990002.pdb 2160.48413
In [48]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
Опять же, модели получились похожими в области вторичных структур, но не имеют единообразия в петлях и на С-конце. В таблице ниже представлено изменение скоров.
| Было | Стало |
|---|---|
| 948.23181 | 2332.30469 |
| 998.45715 | 2160.48413 |
Теперь создадим белок полностью из аланина и проведем с ним эти манипуляции
In [49]:
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 [50]:
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
>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 [51]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_ala pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
55 1 55 65 A A 16.730
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C +N
atom indices : 599 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 120
atom names : C CA +N O
atom indices : 599 597 0 600
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 8748 8155
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 644 644
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 8155 8155
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1146
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1067.4041
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 10.994 1.000
2 Bond angle potential : 839 0 2 2.054 2.054 72.134 1.000
3 Stereochemical cosine torsion poten: 244 0 32 74.058 74.058 220.85 1.000
4 Stereochemical improper torsion pot: 240 0 0 1.001 1.001 6.2266 1.000
5 Soft-sphere overlap restraints : 1146 1 2 0.011 0.011 16.562 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 1968 7 27 0.789 0.789 273.82 1.000
10 Distance restraints 2 (N-O) : 2093 7 32 0.767 0.767 343.83 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 4.814 4.814 32.520 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 0.326 0.326 7.2722 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 20 16 31.944 65.352 64.085 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 1.239 1.239 5.5988 1.000
27 Distance restraints 5 (X-Y) : 1216 0 0 0.035 0.035 13.511 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: 11376.6885
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 13.24 7.04 6.20 5.85 7.04 6.20 5.85
2 3584 56A 64A CA CA 277 317 13.96 7.69 6.27 4.88 7.69 6.27 4.88
3 3585 56A 65A CA CA 277 322 11.67 5.45 6.22 7.16 5.45 6.22 7.16
4 3588 56A 68A CA CA 277 337 12.14 7.46 4.67 4.54 7.46 4.67 4.54
5 3589 56A 69A CA CA 277 342 9.89 6.07 3.81 5.36 6.07 3.81 5.36
6 3590 56A 70A CA CA 277 347 9.22 4.69 4.53 6.47 4.69 4.53 6.47
-------------------------------------------------------------------------------------------------
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 8.27 5.51 2.76 4.71 5.51 2.76 4.71
2 5216 56A 63A N O 276 315 14.58 7.89 6.69 5.43 7.89 6.69 5.43
3 5218 56A 65A N O 276 325 11.15 6.37 4.79 4.53 6.37 4.79 4.53
4 5221 56A 68A N O 276 340 12.60 7.02 5.58 5.21 7.02 5.58 5.21
5 5222 56A 69A N O 276 345 8.56 2.70 5.87 11.46 2.70 5.87 11.46
6 5389 71A 56A N O 351 280 5.77 2.97 2.80 5.91 2.97 2.80 5.91
7 5427 73A 70A N O 361 350 6.00 3.17 2.83 4.60 3.17 2.83 4.60
-------------------------------------------------------------------------------------------------
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 78.39 55.40 26.89 1.94 -62.50 155.22 31.53
1 16A 16A N CA 76 77 24.24 38.20 -40.90
2 1941 18A 19A C N 89 91 65.31 55.40 23.01 0.83 -62.50 140.49 28.54
2 19A 19A N CA 91 92 17.43 38.20 -40.90
3 1943 20A 21A C N 99 101 54.00 55.40 4.32 0.37 -62.50 138.56 28.15
3 21A 21A N CA 101 102 34.11 38.20 -40.90
4 1944 21A 22A C N 104 106 62.94 55.40 11.19 0.55 -62.50 144.05 29.30
4 22A 22A N CA 106 107 29.93 38.20 -40.90
5 1959 36A 37A C N 179 181 66.08 55.40 14.49 0.81 -62.50 146.07 29.71
5 37A 37A N CA 181 182 28.41 38.20 -40.90
6 1960 37A 38A C N 184 186 60.61 55.40 8.37 0.37 -62.50 142.90 29.06
6 38A 38A N CA 186 187 31.66 38.20 -40.90
7 1971 48A 49A C N 239 241 83.94 55.40 37.23 2.22 -62.50 156.49 31.68
7 49A 49A N CA 241 242 14.29 38.20 -40.90
8 1979 56A 57A C N 279 281 -136.34 -134.00 40.40 2.24 -62.50 151.05 28.70
8 57A 57A N CA 281 282 -172.67 147.00 -40.90
9 1980 57A 58A C N 284 286 -73.69 -68.20 26.56 1.95 -62.50 148.24 24.86
9 58A 58A N CA 286 287 171.29 145.30 -40.90
10 1984 61A 62A C N 304 306 64.53 55.40 24.85 0.91 -62.50 138.82 28.18
10 62A 62A N CA 306 307 15.09 38.20 -40.90
11 1986 63A 64A C N 314 316 -77.80 -68.20 14.12 0.89 -62.50 164.16 27.68
11 64A 64A N CA 316 317 155.66 145.30 -40.90
12 1988 65A 66A C N 324 326 75.03 -62.50 161.86 26.58 -62.50 161.86 26.58
12 66A 66A N CA 326 327 -126.24 -40.90 -40.90
13 1989 66A 67A C N 329 331 -60.67 -68.20 27.93 1.99 -62.50 159.31 26.20
13 67A 67A N CA 331 332 118.41 145.30 -40.90
14 1990 67A 68A C N 334 336 -77.92 -68.20 45.90 4.03 -62.50 142.18 22.59
14 68A 68A N CA 336 337 100.45 145.30 -40.90
15 1992 69A 70A C N 344 346 -66.01 -62.50 19.51 3.38 -134.00 167.35 10.33
15 70A 70A N CA 346 347 -60.08 -40.90 147.00
16 1993 70A 71A C N 349 351 -179.25 -62.50 117.08 22.12 -62.50 117.08 22.12
16 71A 71A N CA 351 352 -32.25 -40.90 -40.90
17 2017 94A 95A C N 469 471 81.00 -134.00 159.77 3.63 -62.50 177.83 28.56
17 95A 95A N CA 471 472 -145.93 147.00 -40.90
18 2030 107A 108A C N 534 536 50.40 55.40 10.33 0.38 -62.50 143.23 28.96
18 108A 108A N CA 536 537 47.24 38.20 -40.90
19 2038 115A 116A C N 574 576 59.28 -68.20 140.25 13.48 -68.20 140.25 13.48
19 116A 116A N CA 576 577 -156.21 145.30 145.30
20 2041 118A 119A C N 589 591 49.51 55.40 17.46 0.66 -62.50 147.21 29.66
20 119A 119A N CA 591 592 54.64 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 39 42 63 65 76 96 100 68
<< 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): 1127
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 : 1215.1989
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 0.009 0.009 15.690 1.000
2 Bond angle potential : 839 0 5 2.269 2.269 91.107 1.000
3 Stereochemical cosine torsion poten: 244 0 34 75.045 75.045 225.67 1.000
4 Stereochemical improper torsion pot: 240 0 0 1.039 1.039 6.7613 1.000
5 Soft-sphere overlap restraints : 1127 1 2 0.011 0.011 16.127 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 9 26 0.785 0.785 282.17 1.000
10 Distance restraints 2 (N-O) : 2093 9 38 0.794 0.794 417.28 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 4.976 4.976 34.754 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 7.8035 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 118 22 18 41.067 73.742 85.620 1.000
26 Distance restraints 4 (SDCH-SDCH) : 50 0 1 0.988 0.988 3.6341 1.000
27 Distance restraints 5 (X-Y) : 1216 0 1 0.053 0.053 28.580 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: 12488.5635
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 3252 38A 55A CA CA 187 272 7.84 5.53 2.32 5.02 5.53 2.32 5.02
2 3583 56A 63A CA CA 277 312 13.43 7.04 6.39 6.03 7.04 6.39 6.03
3 3584 56A 64A CA CA 277 317 13.94 7.69 6.25 4.86 7.69 6.25 4.86
4 3585 56A 65A CA CA 277 322 10.88 5.45 5.43 6.24 5.45 5.43 6.24
5 3588 56A 68A CA CA 277 337 12.44 7.46 4.98 4.83 7.46 4.98 4.83
6 3589 56A 69A CA CA 277 342 10.17 6.07 4.10 5.76 6.07 4.10 5.76
7 3590 56A 70A CA CA 277 347 9.96 4.69 5.27 7.52 4.69 5.27 7.52
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4905 38A 55A N O 186 275 9.15 5.51 3.65 6.22 5.51 3.65 6.22
2 5033 44A 52A N O 216 260 5.77 3.15 2.62 4.59 3.15 2.62 4.59
3 5216 56A 63A N O 276 315 14.58 7.89 6.69 5.43 7.89 6.69 5.43
4 5217 56A 64A N O 276 320 13.61 7.21 6.40 4.86 7.21 6.40 4.86
5 5218 56A 65A N O 276 325 12.90 6.37 6.53 6.17 6.37 6.53 6.17
6 5221 56A 68A N O 276 340 12.74 7.02 5.71 5.33 7.02 5.71 5.33
7 5222 56A 69A N O 276 345 9.05 2.70 6.35 12.41 2.70 6.35 12.41
8 5389 71A 56A N O 351 280 6.04 2.97 3.07 6.48 2.97 3.07 6.48
9 5667 86A 53A N O 426 265 12.60 8.88 3.71 4.85 8.88 3.71 4.85
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1938 15A 16A C N 74 76 79.64 55.40 27.95 2.08 -62.50 156.37 31.76
1 16A 16A N CA 76 77 24.28 38.20 -40.90
2 1941 18A 19A C N 89 91 139.06 -134.00 149.11 5.41 -62.50 166.44 33.56
2 19A 19A N CA 91 92 -91.86 147.00 -40.90
3 1942 19A 20A C N 94 96 58.15 -68.20 134.22 12.68 -68.20 134.22 12.68
3 20A 20A N CA 96 97 -169.42 145.30 145.30
4 1943 20A 21A C N 99 101 -78.74 -68.20 57.68 5.01 -62.50 130.51 20.65
4 21A 21A N CA 101 102 88.59 145.30 -40.90
5 1944 21A 22A C N 104 106 58.34 55.40 14.28 0.64 -62.50 137.28 27.92
5 22A 22A N CA 106 107 24.23 38.20 -40.90
6 1959 36A 37A C N 179 181 78.11 55.40 151.53 11.01 -62.50 -167.77 29.95
6 37A 37A N CA 181 182 -171.98 38.20 -40.90
7 1971 48A 49A C N 239 241 167.54 -134.00 59.42 1.60 -62.50 -152.75 40.74
7 49A 49A N CA 241 242 157.66 147.00 -40.90
8 1972 49A 50A C N 244 246 93.92 -134.00 134.28 3.60 -68.20 164.18 14.74
8 50A 50A N CA 246 247 171.20 147.00 145.30
9 1974 51A 52A C N 254 256 -64.93 -62.50 7.50 1.36 -134.00 178.88 11.03
9 52A 52A N CA 256 257 -47.99 -40.90 147.00
10 1976 53A 54A C N 264 266 -150.08 -134.00 99.69 5.25 -62.50 114.48 23.08
10 54A 54A N CA 266 267 -114.61 147.00 -40.90
11 1979 56A 57A C N 279 281 152.86 -134.00 78.80 1.81 -62.50 -156.76 40.63
11 57A 57A N CA 281 282 176.32 147.00 -40.90
12 1980 57A 58A C N 284 286 47.45 55.40 37.94 1.68 -62.50 159.98 31.84
12 58A 58A N CA 286 287 75.30 38.20 -40.90
13 1984 61A 62A C N 304 306 65.86 55.40 28.33 1.04 -62.50 138.79 28.14
13 62A 62A N CA 306 307 11.87 38.20 -40.90
14 1986 63A 64A C N 314 316 -92.42 -68.20 30.41 3.00 -62.50 170.46 26.63
14 64A 64A N CA 316 317 126.92 145.30 -40.90
15 1987 64A 65A C N 319 321 -79.28 -68.20 41.77 3.74 -62.50 146.89 23.30
15 65A 65A N CA 321 322 105.03 145.30 -40.90
16 1988 65A 66A C N 324 326 -63.95 -68.20 12.44 1.14 -62.50 162.12 26.64
16 66A 66A N CA 326 327 156.99 145.30 -40.90
17 1989 66A 67A C N 329 331 53.65 -68.20 136.25 9.39 -62.50 170.80 33.95
17 67A 67A N CA 331 332 84.33 145.30 -40.90
18 1990 67A 68A C N 334 336 -61.43 -68.20 41.00 3.06 -62.50 145.77 23.94
18 68A 68A N CA 336 337 104.86 145.30 -40.90
19 2017 94A 95A C N 469 471 80.25 -134.00 160.34 3.64 -62.50 177.37 28.46
19 95A 95A N CA 471 472 -146.16 147.00 -40.90
20 2030 107A 108A C N 534 536 51.03 55.40 8.29 0.32 -62.50 142.51 28.84
20 108A 108A N CA 536 537 45.24 38.20 -40.90
21 2039 116A 117A C N 579 581 68.63 55.40 32.95 1.19 -62.50 139.95 28.32
21 117A 117A N CA 581 582 8.02 38.20 -40.90
22 2041 118A 119A C N 589 591 61.28 55.40 8.87 0.43 -62.50 143.42 29.17
22 119A 119A N CA 591 592 31.56 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 8 4 44 48 67 53 80 90 88 67
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq_ala.B99990001.pdb 1067.40405
seq_ala.B99990002.pdb 1215.19885
In [52]:
pdb2img('seq_ala.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_ala.B99990002.pdb', '1lmp.pdb')
Моделирование завершилось со скорами, сравнимыми со случаем истинного гомологичного моделирования. Полиаланин принял практически ту же конфигурацию, за исключением беталистов. Это демонстрирует, что подбирать пару белков для моделирования надо очень тщательно и обязательно следить за биологической адекватностью и гомологией.