Гомологичное моделирование комплекса белка с лигандом¶
In [2]:
import sys
import modeller
import _modeller
import modeller.automodel
import requests
In [13]:
env=modeller.environ()
env.io.hetatm=True
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-10-13 03:09:25-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2020-10-13 03:09:26-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. ERROR: The certificate of `www.rcsb.org' is not trusted. ERROR: The certificate of `www.rcsb.org' hasn't got a known issuer.
In [12]:
url = 'http://www.pdb.org/pdb/files/1lmp.pdb'
r = requests.get(url)
with open('1lmp.pdb', 'wb') as f:
f.write(r.content)
In [3]:
! wget http://www.uniprot.org/uniprot/LYS_BUFAN.fasta
--2020-10-13 03:08:30-- http://www.uniprot.org/uniprot/LYS_BUFAN.fasta Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.193.81 Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/LYS_BUFAN.fasta [following] --2020-10-13 03:08:31-- https://www.uniprot.org/uniprot/LYS_BUFAN.fasta Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected. HTTP request sent, awaiting response... 302 Location: /uniprot/P85045.fasta [following] --2020-10-13 03:08:32-- https://www.uniprot.org/uniprot/P85045.fasta Reusing existing connection to www.uniprot.org:443. HTTP request sent, awaiting response... 200 Length: 240 [text/plain] Saving to: `LYS_BUFAN.fasta' 100%[======================================>] 240 --.-K/s in 0s 2020-10-13 03:08:33 (131 MB/s) - `LYS_BUFAN.fasta' saved [240/240]
In [14]:
alignm=modeller.alignment(env)
In [15]:
alignm.append(file='LYS_BUFAN.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')
# а также присвоим им идентификаторы
alignm[0].code = 'seq'
alignm[1].code = 'mod'
read_pd_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.
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.
In [16]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [7]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq mod
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): 2336
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 : 878.3400
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 12.519 1.000
2 Bond angle potential : 1618 0 4 2.231 2.231 158.64 1.000
3 Stereochemical cosine torsion poten: 814 0 27 47.331 47.331 280.14 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.349 1.349 20.337 1.000
5 Soft-sphere overlap restraints : 2336 0 0 0.002 0.002 1.0259 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 0.135 0.135 41.774 1.000
10 Distance restraints 2 (N-O) : 2564 0 2 0.198 0.198 83.769 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 4.519 4.519 34.913 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 64.604 64.604 23.943 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 69.103 69.103 31.002 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 74.948 74.948 24.160 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 81.740 81.740 14.579 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.39093E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.768 1.768 0.55200 1.000
20 Disulfide dihedral angle restraints: 4 0 0 32.809 32.809 3.6785 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 0.409 0.409 44.158 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 14 23.130 61.806 48.665 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.665 0.665 54.444 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: 15111.6699
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 -92.72 -80.20 57.03 1.65 82.20 -136.72 17.38
1 2G 2G N CA 7 8 -130.26 174.10 8.50
2 4149 2G 3K C N 9 11 -100.98 -118.00 17.28 0.61 -62.90 -179.05 21.71
2 3K 3K N CA 11 12 136.10 139.10 -40.80
3 4150 3K 4Y C N 18 20 -131.69 -124.30 19.16 0.77 -63.50 177.17 31.50
3 4Y 4Y N CA 20 21 153.08 135.40 -43.40
4 4152 5I 6S C N 38 40 -70.73 -72.40 4.08 0.30 -64.10 169.01 12.65
4 6S 6S N CA 40 41 156.12 152.40 -35.00
5 4153 6S 7W C N 44 46 -135.70 -124.90 33.32 1.34 -63.00 158.53 24.71
5 7W 7W N CA 46 47 174.92 143.40 -44.20
6 4154 7W 8E C N 58 60 -68.29 -69.30 3.90 0.33 -63.60 173.50 23.39
6 8E 8E N CA 60 61 146.27 142.50 -40.30
7 4155 8E 9D C N 67 69 -68.78 -70.90 14.41 0.61 -63.30 176.13 21.41
7 9D 9D N CA 69 70 136.05 150.30 -40.00
8 4156 9D 10S C N 75 77 -128.20 -136.60 19.98 0.80 -64.10 179.88 11.11
8 10S 10S N CA 77 78 133.06 151.20 -35.00
9 4158 11C 12S C N 87 89 -79.98 -72.40 11.27 0.89 -64.10 179.77 12.17
9 12S 12S N CA 89 90 144.06 152.40 -35.00
10 4159 12S 13Y C N 93 95 -127.81 -124.30 8.86 0.35 -63.50 -175.37 32.52
10 13Y 13Y N CA 95 96 143.53 135.40 -43.40
11 4160 13Y 14L C N 105 107 -87.72 -108.50 22.37 0.99 -63.50 167.20 21.94
11 14L 14L N CA 107 108 124.24 132.50 -41.20
12 4161 14L 15Q C N 113 115 -154.04 -121.10 108.16 4.50 -63.80 118.62 21.48
12 15Q 15Q N CA 115 116 -117.28 139.70 -40.30
13 4162 15Q 16L C N 122 124 -59.78 -70.70 11.07 1.06 -63.50 175.39 24.14
13 16L 16L N CA 124 125 143.45 141.60 -41.20
14 4163 16L 17Q C N 130 132 -113.81 -121.10 20.34 0.82 -63.80 168.60 22.50
14 17Q 17Q N CA 132 133 120.71 139.70 -40.30
15 4198 51E 52S C N 414 416 -138.18 -64.10 82.00 8.62 -64.10 82.00 8.62
15 52S 52S N CA 416 417 0.16 -35.00 -35.00
16 4210 63P 64P C N 504 506 -60.67 -58.70 24.80 2.21 -64.50 157.62 11.97
16 64P 64P N CA 506 507 -55.23 -30.50 147.20
17 4288 141T 142Q C N 1128 1130 -1.28 -63.80 98.26 12.65 -73.00 125.66 9.56
17 142Q 142Q N CA 1130 1131 -116.11 -40.30 140.70
18 4289 142Q 143G C N 1137 1139 -55.77 -62.40 23.83 3.91 82.20 140.56 10.27
18 143G 143G N CA 1139 1140 -18.31 -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 5 7 38 69 128 117 116 154 192 172
<< 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 : 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): 2401
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 : 769.9892
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 11.459 1.000
2 Bond angle potential : 1618 0 5 2.121 2.121 142.79 1.000
3 Stereochemical cosine torsion poten: 814 0 33 47.656 47.656 279.95 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.258 1.258 18.276 1.000
5 Soft-sphere overlap restraints : 2401 0 0 0.002 0.002 0.72514 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 0.128 0.128 34.322 1.000
10 Distance restraints 2 (N-O) : 2564 0 0 0.165 0.165 70.749 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 4.123 4.123 29.068 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 64.505 64.505 17.517 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 73.445 73.445 33.073 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 62.115 62.115 22.693 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 90.665 90.665 15.219 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.45074E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.903 1.903 0.63973 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.977 27.977 3.0637 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 0.375 0.375 26.630 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 15 13 21.498 58.307 32.415 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.544 0.544 31.357 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: 14472.9033
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 -156.16 -167.20 26.98 0.85 82.20 -173.42 14.08
1 2G 2G N CA 7 8 149.98 174.60 8.50
2 4149 2G 3K C N 9 11 -110.33 -118.00 10.45 0.52 -62.90 179.39 26.10
2 3K 3K N CA 11 12 146.20 139.10 -40.80
3 4150 3K 4Y C N 18 20 -68.90 -98.40 30.68 1.36 -63.50 179.86 28.82
3 4Y 4Y N CA 20 21 136.82 128.40 -43.40
4 4152 5I 6S C N 38 40 -139.11 -136.60 3.20 0.10 -64.10 -172.52 18.92
4 6S 6S N CA 40 41 153.17 151.20 -35.00
5 4153 6S 7W C N 44 46 -134.97 -124.90 22.80 0.85 -63.00 168.13 25.86
5 7W 7W N CA 46 47 163.86 143.40 -44.20
6 4154 7W 8E C N 58 60 -111.05 -117.80 7.09 0.31 -63.60 -174.57 22.46
6 8E 8E N CA 60 61 138.95 136.80 -40.30
7 4155 8E 9D C N 67 69 -113.51 -96.50 28.00 1.18 -63.30 -176.56 20.14
7 9D 9D N CA 69 70 136.44 114.20 -40.00
8 4158 11C 12S C N 87 89 -170.21 -136.60 36.35 1.15 -64.10 -168.06 21.57
8 12S 12S N CA 89 90 165.06 151.20 -35.00
9 4159 12S 13Y C N 93 95 -110.43 -98.40 16.86 1.29 -63.50 166.74 24.25
9 13Y 13Y N CA 95 96 116.59 128.40 -43.40
10 4160 13Y 14L C N 105 107 -103.93 -108.50 25.78 1.43 -63.50 165.93 25.52
10 14L 14L N CA 107 108 157.87 132.50 -41.20
11 4161 14L 15Q C N 113 115 -109.63 -121.10 12.11 0.54 -63.80 -178.02 29.21
11 15Q 15Q N CA 115 116 143.59 139.70 -40.30
12 4162 15Q 16L C N 122 124 -97.47 -70.70 62.69 3.94 -63.50 125.21 19.47
12 16L 16L N CA 124 125 -161.71 141.60 -41.20
13 4163 16L 17Q C N 130 132 -78.18 -73.00 46.77 3.16 -63.80 135.29 19.16
13 17Q 17Q N CA 132 133 94.22 140.70 -40.30
14 4198 51E 52S C N 414 416 -138.44 -64.10 82.56 8.64 -64.10 82.56 8.64
14 52S 52S N CA 416 417 0.92 -35.00 -35.00
15 4210 63P 64P C N 504 506 -73.72 -58.70 15.24 1.80 -64.50 175.37 13.58
15 64P 64P N CA 506 507 -27.93 -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 4 12 48 67 110 114 125 169 186 182
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
seq.B99990001.pdb 878.34003
seq.B99990002.pdb 769.98920
In [9]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('seq.B99990001.pdb')
w1
In [10]:
w2 = nglview.show_structure_file('seq.B99990002.pdb')
w2
Полученные модели и исходный референс были совмещены для сравнения в Pymol
In [22]:
from IPython.display import Image
Image(filename='overlay1.png')
Out[22]:
Зеленым обозначена структура 1lmp, голубым - модели без ограничений, розовым с дополнительными ограничением.
В целом, структуры очень похожи. Видно, что есть отличия по N-концевому участку
Добавим лиганд к последовательности LYS_BUFAN из 1lmp и посроим модель
In [17]:
seq_liganded = ''
for res in alignm[0].residues:
seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'lys_lig'
del alignm[0]
In [18]:
#добавим в выравнивание
alignm.salign()
alignm.write(file='all_in_one_lig.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [19]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one_lig.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
lys_lig mod
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
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.
>> 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): 2678
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 : 1018.6566
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 0.007 0.007 14.806 1.000
2 Bond angle potential : 1618 0 6 2.278 2.278 165.48 1.000
3 Stereochemical cosine torsion poten: 814 0 29 47.023 47.023 280.47 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.357 1.357 20.886 1.000
5 Soft-sphere overlap restraints : 2678 1 2 0.008 0.008 17.900 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 0.119 0.119 37.112 1.000
10 Distance restraints 2 (N-O) : 2564 1 11 0.233 0.233 129.30 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 0 3 4.762 4.762 38.772 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 0 72.352 72.352 27.646 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 2 81.355 81.355 44.959 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 76.353 76.353 26.050 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 86.997 86.997 16.447 1.000
18 Disulfide distance restraints : 4 0 0 0.007 0.007 0.35324E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.841 2.841 1.4259 1.000
20 Disulfide dihedral angle restraints: 4 0 0 28.794 28.794 2.7176 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 0.404 0.404 44.086 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 22 14 23.505 66.455 64.995 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 1 0.778 0.778 71.077 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 14.496 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: lys_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: 16793.7031
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 8128 67S 87P N O 530 712 8.73 6.49 2.23 4.92 6.49 2.23 4.92
-------------------------------------------------------------------------------------------------
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 7 127.20 78.70 48.99 2.29 82.20 -175.94 11.12
1 2G 2G N CA 7 8 -173.02 -166.10 8.50
2 4149 2G 3K C N 9 11 -65.92 -70.20 8.67 0.53 -62.90 173.68 22.39
2 3K 3K N CA 11 12 132.86 140.40 -40.80
3 4150 3K 4Y C N 18 20 -126.28 -124.30 3.38 0.14 -63.50 -170.82 33.18
3 4Y 4Y N CA 20 21 138.14 135.40 -43.40
4 4152 5I 6S C N 38 40 -130.11 -136.60 10.88 0.38 -64.10 -170.66 11.68
4 6S 6S N CA 40 41 142.46 151.20 -35.00
5 4153 6S 7W C N 44 46 -76.43 -71.30 19.33 1.32 -63.00 158.74 20.69
5 7W 7W N CA 46 47 157.63 139.00 -44.20
6 4154 7W 8E C N 58 60 -59.01 -69.30 13.44 0.75 -63.60 174.21 23.48
6 8E 8E N CA 60 61 133.85 142.50 -40.30
7 4155 8E 9D C N 67 69 -93.87 -96.50 7.18 0.30 -63.30 150.66 16.97
7 9D 9D N CA 69 70 107.52 114.20 -40.00
8 4156 9D 10S C N 75 77 -84.09 -72.40 19.29 0.88 -64.10 158.51 12.78
8 10S 10S N CA 77 78 167.75 152.40 -35.00
9 4157 10S 11C C N 81 83 -63.43 -63.00 8.27 1.04 -117.90 178.08 7.68
9 11C 11C N CA 83 84 -49.36 -41.10 141.10
10 4158 11C 12S C N 87 89 -75.76 -72.40 7.75 0.36 -64.10 166.02 12.76
10 12S 12S N CA 89 90 159.38 152.40 -35.00
11 4159 12S 13Y C N 93 95 -77.40 -98.40 22.02 1.01 -63.50 178.95 27.69
11 13Y 13Y N CA 95 96 135.01 128.40 -43.40
12 4160 13Y 14L C N 105 107 -62.10 -70.70 27.90 1.82 -63.50 156.27 21.78
12 14L 14L N CA 107 108 115.06 141.60 -41.20
13 4161 14L 15Q C N 113 115 -141.76 -121.10 21.00 0.87 -63.80 -167.28 25.08
13 15Q 15Q N CA 115 116 135.95 139.70 -40.30
14 4162 15Q 16L C N 122 124 -136.67 -108.50 29.70 1.53 -63.50 179.85 22.11
14 16L 16L N CA 124 125 123.09 132.50 -41.20
15 4163 16L 17Q C N 130 132 -133.47 -121.10 15.35 0.76 -63.80 -175.43 24.15
15 17Q 17Q N CA 132 133 130.61 139.70 -40.30
16 4198 51E 52S C N 414 416 -136.99 -64.10 81.18 8.47 -64.10 81.18 8.47
16 52S 52S N CA 416 417 0.74 -35.00 -35.00
17 4209 62N 63P C N 497 499 -64.45 -64.50 56.36 4.21 -58.70 126.08 10.89
17 63P 63P N CA 499 500 -156.44 147.20 -30.50
18 4210 63P 64P C N 504 506 -57.25 -58.70 24.36 2.13 -64.50 153.56 11.08
18 64P 64P N CA 506 507 -6.19 -30.50 147.20
19 4233 86T 87P C N 704 706 -46.01 -58.70 63.98 4.34 -64.50 121.01 10.03
19 87P 87P N CA 706 707 -93.21 -30.50 147.20
20 4234 87P 88R C N 711 713 -97.75 -125.20 60.46 2.21 57.30 162.53 16.24
20 88R 88R N CA 713 714 86.74 140.60 38.00
21 4288 141T 142Q C N 1128 1130 17.83 -63.80 120.51 15.62 -73.00 128.11 9.94
21 142Q 142Q N CA 1130 1131 -128.96 -40.30 140.70
22 4289 142Q 143G C N 1137 1139 -61.13 -62.40 30.61 4.63 82.20 144.60 10.33
22 143G 143G N CA 1139 1140 -10.62 -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 7 15 54 95 124 128 156 188 183 230
<< end of ENERGY.
>> 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): 2603
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 : 886.5428
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 12.115 1.000
2 Bond angle potential : 1618 0 5 2.179 2.179 151.61 1.000
3 Stereochemical cosine torsion poten: 814 0 26 46.358 46.358 275.25 1.000
4 Stereochemical improper torsion pot: 502 0 0 1.336 1.336 20.365 1.000
5 Soft-sphere overlap restraints : 2603 1 2 0.008 0.008 17.710 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 0.103 0.103 29.134 1.000
10 Distance restraints 2 (N-O) : 2564 1 7 0.210 0.210 107.41 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 4.239 4.239 30.723 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 2 72.880 72.880 26.808 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 75.174 75.174 32.369 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 69.467 69.467 25.136 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 84.720 84.720 13.165 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.40860E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.815 1.815 0.58187 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.338 29.338 3.2852 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 0.357 0.357 30.671 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 15 21.458 61.540 45.602 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 1 0.686 0.686 52.607 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.030 0.030 11.966 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: lys_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: 15709.1064
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 8128 67S 87P N O 530 712 8.63 6.49 2.14 4.71 6.49 2.14 4.71
-------------------------------------------------------------------------------------------------
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 86.45 78.70 8.87 0.30 82.20 178.98 8.47
1 2G 2G N CA 7 8 -170.43 -166.10 8.50
2 4149 2G 3K C N 9 11 -71.43 -70.20 3.39 0.22 -62.90 175.84 23.31
2 3K 3K N CA 11 12 143.56 140.40 -40.80
3 4150 3K 4Y C N 18 20 -125.86 -124.30 6.66 0.29 -63.50 -174.48 32.58
3 4Y 4Y N CA 20 21 141.87 135.40 -43.40
4 4152 5I 6S C N 38 40 -71.74 -72.40 7.27 0.40 -64.10 180.00 13.51
4 6S 6S N CA 40 41 145.16 152.40 -35.00
5 4153 6S 7W C N 44 46 -137.82 -124.90 13.27 0.51 -63.00 -174.83 28.18
5 7W 7W N CA 46 47 146.42 143.40 -44.20
6 4154 7W 8E C N 58 60 -76.48 -69.30 8.48 0.77 -63.60 178.75 23.15
6 8E 8E N CA 60 61 137.99 142.50 -40.30
7 4155 8E 9D C N 67 69 -81.06 -96.50 15.77 0.65 -63.30 152.02 17.76
7 9D 9D N CA 69 70 110.98 114.20 -40.00
8 4156 9D 10S C N 75 77 -157.32 -136.60 33.77 1.17 -64.10 174.18 19.35
8 10S 10S N CA 77 78 177.86 151.20 -35.00
9 4159 12S 13Y C N 93 95 -117.15 -124.30 10.39 0.45 -63.50 179.47 25.98
9 13Y 13Y N CA 95 96 127.87 135.40 -43.40
10 4160 13Y 14L C N 105 107 -64.82 -70.70 14.68 0.93 -63.50 169.35 23.44
10 14L 14L N CA 107 108 128.15 141.60 -41.20
11 4161 14L 15Q C N 113 115 -129.38 -121.10 18.63 0.72 -63.80 175.99 29.34
11 15Q 15Q N CA 115 116 156.39 139.70 -40.30
12 4162 15Q 16L C N 122 124 -108.81 -108.50 11.20 0.60 -63.50 -179.14 27.89
12 16L 16L N CA 124 125 143.70 132.50 -41.20
13 4163 16L 17Q C N 130 132 -91.74 -73.00 29.89 2.30 -63.80 160.17 22.18
13 17Q 17Q N CA 132 133 117.41 140.70 -40.30
14 4198 51E 52S C N 414 416 -135.59 -64.10 75.62 8.49 -64.10 75.62 8.49
14 52S 52S N CA 416 417 -10.35 -35.00 -35.00
15 4209 62N 63P C N 497 499 -66.85 -64.50 58.86 4.27 -58.70 123.76 10.89
15 63P 63P N CA 499 500 -153.99 147.20 -30.50
16 4210 63P 64P C N 504 506 -59.05 -58.70 27.48 2.24 -64.50 150.32 10.93
16 64P 64P N CA 506 507 -3.02 -30.50 147.20
17 4233 86T 87P C N 704 706 -46.38 -58.70 65.21 4.47 -64.50 119.65 9.91
17 87P 87P N CA 706 707 -94.53 -30.50 147.20
18 4234 87P 88R C N 711 713 -99.04 -125.20 58.20 2.14 57.30 164.33 16.33
18 88R 88R N CA 713 714 88.61 140.60 38.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 11 60 79 140 133 143 186 186 197
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
lys_lig.B99990001.pdb 1018.65662
lys_lig.B99990002.pdb 886.54285
In [20]:
import nglview
import ipywidgets
w3 = nglview.show_structure_file('lys_lig.B99990001.pdb')
w3.clear_representations()
w3.add_cartoon('protein', color_scheme='residueindex')
w3.add_ball_and_stick('ligand', opacity=0.5)
w3
In [21]:
w0 = nglview.show_structure_file('1lmp.pdb')
w0.clear_representations()
w0.add_cartoon('protein', color_scheme='residueindex')
w0.add_ball_and_stick('ligand', opacity=0.5)
w0
У получившихся моделей метостоположение лиганда совпадает с координатами в рефенсном лизоциме.
Структурно модель почти полностью совпадает с 1lmp, хотя на уровне последовательностей различий много.
In [24]:
from IPython.display import Image
Image(filename='overlay2.png')
Out[24]:
Зеленым обозначена референсная структура, голубым - модель выданной последовательности.
Переместим лиганд (добавим случайный шум к его местоположению)
In [26]:
#удаляем файл с автоматическими ограничениями
! rm lys_lig.rsr
In [43]:
env.libs.topology.clear()
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('CG2:92','O6:147'),('N:78','OD2:118')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=1.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one_lig.ali', knowns=pdb.code, sequence=s.code)
In [44]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
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: 14447 13411
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 : 13411 13411
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2672
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 : 4289.7935
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 7 15 0.040 0.040 448.44 1.000
2 Bond angle potential : 1618 18 36 3.986 3.986 468.92 1.000
3 Stereochemical cosine torsion poten: 814 0 32 48.048 48.048 288.89 1.000
4 Stereochemical improper torsion pot: 502 2 4 2.398 2.398 57.506 1.000
5 Soft-sphere overlap restraints : 2672 2 7 0.012 0.012 47.433 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 9 27 0.311 0.311 291.98 1.000
10 Distance restraints 2 (N-O) : 2564 3 25 0.290 0.290 270.60 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 2 4 5.688 5.688 55.328 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 2 68.992 68.992 36.374 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 0 82.848 82.848 33.529 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 78.329 78.329 19.530 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 80.211 80.211 11.504 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.42737E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.241 2.241 0.88715 1.000
20 Disulfide dihedral angle restraints: 4 0 0 33.249 33.249 3.9746 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 0.531 0.531 73.326 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 19 22.899 57.780 78.729 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 1 0.761 0.761 65.089 1.000
27 Distance restraints 5 (X-Y) : 1403 8 38 0.268 0.268 2037.7 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: lys_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: 20074.9531
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
1 633 77S 78R C N 615 617 1.51 1.35 0.16 5.81 1.35 0.16 5.81
2 641 78R 78R N CA 617 618 1.59 1.43 0.16 5.19 1.43 0.16 5.19
3 770 92T 92T CB CA 749 748 2.17 1.50 0.67 18.46 1.50 0.67 18.46
4 772 92T 92T CG2 CB 751 749 2.22 1.54 0.68 18.74 1.54 0.68 18.74
5 960 118D 118D CB CA 938 937 2.09 1.54 0.55 15.17 1.54 0.55 15.17
6 961 118D 118D CG CB 939 938 2.11 1.52 0.59 15.37 1.52 0.59 15.37
7 963 118D 118D OD2 CG 941 939 1.50 1.26 0.24 10.09 1.26 0.24 10.09
-------------------------------------------------------------------------------------------------
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 2056 77S 77S CA C 612 615 133.85 116.50 17.35 4.99 116.50 17.35 4.99
2 2098 80W 80W N CA 642 643 129.86 107.00 22.86 6.57 107.00 22.86 6.57
3 2236 91N 91N N CA 739 740 123.25 107.00 16.25 4.67 107.00 16.25 4.67
4 2244 91N 92T C N 745 747 145.62 120.00 25.62 5.82 120.00 25.62 5.82
5 2246 92T 92T N CA 747 748 136.56 113.50 23.06 6.20 113.50 23.06 6.20
6 2249 92T 92T CA CB 748 749 161.23 108.50 52.73 12.37 108.50 52.73 12.37
7 2253 92T 92T C CA 752 748 137.79 108.00 29.78 6.90 108.00 29.78 6.90
8 2257 93C 93C N CA 754 755 128.62 107.00 21.62 6.22 107.00 21.62 6.22
9 2508 118D 118D CA CB 937 938 156.79 108.00 48.78 11.31 108.00 48.78 11.31
10 2512 118D 118D CB CG 938 939 150.64 118.00 32.64 6.63 118.00 32.64 6.63
11 2514 118D 118D C CA 942 937 127.59 108.00 19.59 4.54 108.00 19.59 4.54
-------------------------------------------------------------------------------------------------
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 4368 77S 77S CA C 612 615 -154.29 -180.00 25.71 5.14 -180.00 25.71 5.14
2 4409 118D 118D CA C 937 942 -156.86 -180.00 23.14 4.63 -180.00 23.14 4.63
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4148 1S 2G C N 5 7 -63.73 -62.40 2.04 0.37 82.20 154.67 11.78
1 2G 2G N CA 7 8 -42.75 -41.20 8.50
2 4149 2G 3K C N 9 11 -75.24 -70.20 8.37 0.70 -62.90 174.96 22.07
2 3K 3K N CA 11 12 133.72 140.40 -40.80
3 4150 3K 4Y C N 18 20 -133.28 -124.30 28.78 1.20 -63.50 168.94 30.25
3 4Y 4Y N CA 20 21 162.74 135.40 -43.40
4 4152 5I 6S C N 38 40 -60.71 -72.40 24.04 1.11 -64.10 166.43 12.26
4 6S 6S N CA 40 41 131.39 152.40 -35.00
5 4153 6S 7W C N 44 46 -140.86 -124.90 21.62 0.69 -63.00 175.98 27.24
5 7W 7W N CA 46 47 157.98 143.40 -44.20
6 4154 7W 8E C N 58 60 -73.85 -69.30 8.99 0.81 -63.60 175.35 22.83
6 8E 8E N CA 60 61 134.74 142.50 -40.30
7 4156 9D 10S C N 75 77 -66.92 -72.40 11.00 0.51 -64.10 177.89 12.72
7 10S 10S N CA 77 78 142.86 152.40 -35.00
8 4158 11C 12S C N 87 89 -162.94 -136.60 32.29 0.99 -64.10 -176.06 20.46
8 12S 12S N CA 89 90 169.87 151.20 -35.00
9 4159 12S 13Y C N 93 95 -114.91 -124.30 18.82 0.74 -63.50 170.43 24.65
9 13Y 13Y N CA 95 96 119.10 135.40 -43.40
10 4160 13Y 14L C N 105 107 -135.42 -108.50 42.39 1.95 -63.50 169.56 27.99
10 14L 14L N CA 107 108 165.25 132.50 -41.20
11 4161 14L 15Q C N 113 115 -126.65 -121.10 43.72 1.98 -63.80 150.40 25.40
11 15Q 15Q N CA 115 116 -176.94 139.70 -40.30
12 4162 15Q 16L C N 122 124 -65.46 -70.70 6.37 0.64 -63.50 173.57 24.21
12 16L 16L N CA 124 125 145.24 141.60 -41.20
13 4163 16L 17Q C N 130 132 -102.53 -121.10 29.47 1.00 -63.80 161.83 21.95
13 17Q 17Q N CA 132 133 116.82 139.70 -40.30
14 4198 51E 52S C N 414 416 -137.07 -64.10 81.25 8.48 -64.10 81.25 8.48
14 52S 52S N CA 416 417 0.74 -35.00 -35.00
15 4210 63P 64P C N 504 506 -81.49 -58.70 30.40 2.28 -64.50 158.49 12.74
15 64P 64P N CA 506 507 -10.38 -30.50 147.20
16 4224 77S 78R C N 615 617 -115.26 -63.00 53.42 8.23 -63.00 53.42 8.23
16 78R 78R N CA 617 618 -30.00 -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 13410 92T 147. CG2 O6 751 1178 6.99 1.00 5.99 59.85 1.00 5.99 59.85
2 13411 78R 118D N OD2 617 941 5.55 1.00 4.55 45.48 1.00 4.55 45.48
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 2 13 22 64 80 129 127 157 169 203 193
<< end of ENERGY.
>> 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 : 13411 13411
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2718
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 : 4438.9775
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 8 16 0.040 0.040 458.55 1.000
2 Bond angle potential : 1618 15 38 4.021 4.021 481.41 1.000
3 Stereochemical cosine torsion poten: 814 0 28 47.379 47.379 285.55 1.000
4 Stereochemical improper torsion pot: 502 2 5 2.412 2.412 58.352 1.000
5 Soft-sphere overlap restraints : 2718 2 6 0.012 0.012 46.161 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 9 26 0.311 0.311 293.11 1.000
10 Distance restraints 2 (N-O) : 2564 4 30 0.328 0.328 318.65 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 145 1 5 5.701 5.701 55.584 1.000
14 Sidechain Chi_1 dihedral restraints: 126 0 2 77.108 77.108 41.028 1.000
15 Sidechain Chi_2 dihedral restraints: 93 0 1 72.643 72.643 32.921 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 75.057 75.057 27.432 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 86.954 86.954 13.256 1.000
18 Disulfide distance restraints : 4 0 0 0.008 0.008 0.49403E-01 1.000
19 Disulfide angle restraints : 8 0 0 2.742 2.742 1.3278 1.000
20 Disulfide dihedral angle restraints: 4 0 0 35.384 35.384 4.2531 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 0.497 0.497 74.450 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 19 21 25.223 63.238 103.25 1.000
26 Distance restraints 4 (SDCH-SDCH) : 744 0 0 0.807 0.807 77.278 1.000
27 Distance restraints 5 (X-Y) : 1403 8 40 0.270 0.270 2066.4 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: lys_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: 21082.1699
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
1 633 77S 78R C N 615 617 1.51 1.35 0.17 6.02 1.35 0.17 6.02
2 641 78R 78R N CA 617 618 1.59 1.43 0.16 5.18 1.43 0.16 5.18
3 770 92T 92T CB CA 749 748 2.18 1.50 0.68 18.60 1.50 0.68 18.60
4 772 92T 92T CG2 CB 751 749 2.23 1.54 0.69 18.89 1.54 0.69 18.89
5 960 118D 118D CB CA 938 937 2.10 1.54 0.56 15.34 1.54 0.56 15.34
6 961 118D 118D CG CB 939 938 2.12 1.52 0.60 15.62 1.52 0.60 15.62
7 963 118D 118D OD2 CG 941 939 1.50 1.26 0.24 10.20 1.26 0.24 10.20
8 966 118D 118D C CA 942 937 1.65 1.49 0.16 4.53 1.49 0.16 4.53
-------------------------------------------------------------------------------------------------
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 2056 77S 77S CA C 612 615 134.60 116.50 18.10 5.20 116.50 18.10 5.20
2 2098 80W 80W N CA 642 643 128.17 107.00 21.17 6.09 107.00 21.17 6.09
3 2244 91N 92T C N 745 747 147.53 120.00 27.53 6.26 120.00 27.53 6.26
4 2246 92T 92T N CA 747 748 136.38 113.50 22.88 6.15 113.50 22.88 6.15
5 2249 92T 92T CA CB 748 749 159.89 108.50 51.38 12.05 108.50 51.38 12.05
6 2253 92T 92T C CA 752 748 136.76 108.00 28.75 6.66 108.00 28.75 6.66
7 2257 93C 93C N CA 754 755 128.15 107.00 21.15 6.08 107.00 21.15 6.08
8 2508 118D 118D CA CB 937 938 151.58 108.00 43.57 10.10 108.00 43.57 10.10
9 2512 118D 118D CB CG 938 939 151.24 118.00 33.24 6.75 118.00 33.24 6.75
-------------------------------------------------------------------------------------------------
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 4368 77S 77S CA C 612 615 -154.63 -180.00 25.37 5.07 -180.00 25.37 5.07
-------------------------------------------------------------------------------------------------
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 -79.43 -80.20 5.87 0.27 82.20 -124.40 7.14
1 2G 2G N CA 7 8 179.91 174.10 8.50
2 4149 2G 3K C N 9 11 -74.95 -70.20 11.31 0.71 -62.90 168.97 22.62
2 3K 3K N CA 11 12 150.66 140.40 -40.80
3 4150 3K 4Y C N 18 20 -76.13 -98.40 22.29 0.85 -63.50 173.08 26.82
3 4Y 4Y N CA 20 21 129.22 128.40 -43.40
4 4152 5I 6S C N 38 40 -159.47 -136.60 42.45 1.56 -64.10 167.78 19.04
4 6S 6S N CA 40 41 -173.04 151.20 -35.00
5 4153 6S 7W C N 44 46 -57.56 -71.30 27.18 1.68 -63.00 159.84 20.32
5 7W 7W N CA 46 47 115.55 139.00 -44.20
6 4154 7W 8E C N 58 60 -140.05 -117.80 44.14 1.67 -63.60 163.73 26.08
6 8E 8E N CA 60 61 174.92 136.80 -40.30
7 4156 9D 10S C N 75 77 -121.63 -136.60 16.93 0.52 -64.10 -172.65 11.54
7 10S 10S N CA 77 78 143.30 151.20 -35.00
8 4159 12S 13Y C N 93 95 -128.02 -124.30 17.40 1.08 -63.50 174.20 24.77
8 13Y 13Y N CA 95 96 118.41 135.40 -43.40
9 4160 13Y 14L C N 105 107 -147.03 -108.50 44.52 1.96 -63.50 -175.97 30.71
9 14L 14L N CA 107 108 154.81 132.50 -41.20
10 4161 14L 15Q C N 113 115 -129.34 -121.10 11.20 0.36 -63.80 -175.55 30.59
10 15Q 15Q N CA 115 116 147.28 139.70 -40.30
11 4162 15Q 16L C N 122 124 -127.07 -108.50 62.23 3.14 -63.50 141.94 23.64
11 16L 16L N CA 124 125 -168.11 132.50 -41.20
12 4163 16L 17Q C N 130 132 -73.76 -73.00 2.89 0.20 -63.80 178.49 25.73
12 17Q 17Q N CA 132 133 137.91 140.70 -40.30
13 4209 62N 63P C N 497 499 -63.40 -64.50 57.13 4.32 -58.70 125.27 10.73
13 63P 63P N CA 499 500 -155.68 147.20 -30.50
14 4210 63P 64P C N 504 506 -58.66 -58.70 27.87 2.31 -64.50 149.94 10.88
14 64P 64P N CA 506 507 -2.63 -30.50 147.20
15 4224 77S 78R C N 615 617 -112.48 -63.00 50.05 7.89 -63.00 50.05 7.89
15 78R 78R N CA 617 618 -33.51 -41.10 -41.10
16 4279 132C 133K C N 1054 1056 -51.99 -62.90 29.29 3.38 -70.20 152.72 11.48
16 133K 133K N CA 1056 1057 -67.98 -40.80 140.40
17 4280 133K 134G C N 1063 1065 -73.84 -62.40 13.42 2.03 82.20 161.77 12.11
17 134G 134G N CA 1065 1066 -34.17 -41.20 8.50
18 4288 141T 142Q C N 1128 1130 25.53 -63.80 129.91 16.87 -73.00 129.92 10.12
18 142Q 142Q N CA 1130 1131 -134.62 -40.30 140.70
19 4289 142Q 143G C N 1137 1139 -61.42 -62.40 29.51 4.45 82.20 145.03 10.40
19 143G 143G N CA 1139 1140 -11.71 -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 92T 147. CG2 O6 751 1178 7.06 1.00 6.06 60.61 1.00 6.06 60.61
2 13411 78R 118D N OD2 617 941 5.53 1.00 4.53 45.31 1.00 4.53 45.31
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 2 16 20 80 88 127 164 151 149 207 208
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
lys_lig.B99990001.pdb 4289.79346
lys_lig.B99990002.pdb 4438.97754
In [45]:
from IPython.display import Image
Image(filename='overlay3.png')
Out[45]:
Структуры моделей с (голубой) и без (зеленый) дополнительных ограничений
Построим структуру лизоцима с лигандом где все аминокислоты аланин и сравним скор функцию с "нативной" последовательностью.
In [51]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb')
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alanin = 'A' * 146 + '...'
alignm.append_sequence(alanin)
alignm[0].code = 'pdb'
alignm[1].code = 'alanin'
In [52]:
alignm.salign()
alignm.write(file='all_in_one_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [53]:
## 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_one_ala.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
alanin pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 146
atom names : C +N
atom indices : 729 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 146
atom names : C CA +N O
atom indices : 729 727 0 730
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: 10506 9783
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1491
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 : 900.8751
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 : 730 0 0 0.007 0.007 9.1025 1.000
2 Bond angle potential : 1021 1 6 2.325 2.325 114.12 1.000
3 Stereochemical cosine torsion poten: 296 0 37 76.908 76.908 287.10 1.000
4 Stereochemical improper torsion pot: 292 0 0 1.032 1.032 9.1105 1.000
5 Soft-sphere overlap restraints : 1491 1 2 0.012 0.012 23.802 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 7 0.333 0.333 102.02 1.000
10 Distance restraints 2 (N-O) : 2564 1 8 0.426 0.426 174.37 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 7 5.371 5.371 49.334 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.278 0.278 7.2790 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 36 23 35.947 85.484 101.70 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.740 0.740 3.5256 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.040 0.040 19.413 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: alanin.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: 15812.7422
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 6626 93A 80A N O 461 400 5.13 2.92 2.20 5.52 2.92 2.20 5.52
-------------------------------------------------------------------------------------------------
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 2354 15A 16A C N 74 76 78.92 55.40 27.44 1.99 -62.50 155.62 31.61
1 16A 16A N CA 76 77 24.06 38.20 -40.90
2 2357 18A 19A C N 89 91 139.41 -134.00 151.68 5.59 -62.50 165.10 33.24
2 19A 19A N CA 91 92 -88.48 147.00 -40.90
3 2358 19A 20A C N 94 96 57.92 -68.20 133.83 12.64 -68.20 133.83 12.64
3 20A 20A N CA 96 97 -169.92 145.30 145.30
4 2359 20A 21A C N 99 101 -78.31 -68.20 57.92 5.02 -62.50 130.14 20.61
4 21A 21A N CA 101 102 88.27 145.30 -40.90
5 2360 21A 22A C N 104 106 58.84 55.40 14.86 0.64 -62.50 137.48 27.96
5 22A 22A N CA 106 107 23.74 38.20 -40.90
6 2375 36A 37A C N 179 181 66.50 55.40 13.78 0.89 -62.50 147.21 29.94
6 37A 37A N CA 181 182 30.03 38.20 -40.90
7 2376 37A 38A C N 184 186 62.43 55.40 10.57 0.51 -62.50 143.80 29.24
7 38A 38A N CA 186 187 30.31 38.20 -40.90
8 2387 48A 49A C N 239 241 85.43 55.40 40.83 2.28 -62.50 156.62 31.65
8 49A 49A N CA 241 242 10.54 38.20 -40.90
9 2392 53A 54A C N 264 266 92.67 -134.00 138.40 3.39 -62.50 -154.35 32.30
9 54A 54A N CA 266 267 -175.86 147.00 -40.90
10 2395 56A 57A C N 279 281 60.36 55.40 14.47 1.28 -62.50 153.90 31.16
10 57A 57A N CA 281 282 51.79 38.20 -40.90
11 2401 62A 63A C N 309 311 -75.03 -68.20 12.84 0.82 -62.50 163.41 27.41
11 63A 63A N CA 311 312 156.18 145.30 -40.90
12 2402 63A 64A C N 314 316 -158.73 -134.00 26.03 0.62 -62.50 -169.85 36.29
12 64A 64A N CA 316 317 155.10 147.00 -40.90
13 2403 64A 65A C N 319 321 -83.17 -68.20 15.28 1.19 -62.50 172.02 29.25
13 65A 65A N CA 321 322 148.33 145.30 -40.90
14 2404 65A 66A C N 324 326 -70.62 -68.20 14.62 1.26 -62.50 171.98 27.80
14 66A 66A N CA 326 327 130.89 145.30 -40.90
15 2405 66A 67A C N 329 331 -79.41 -68.20 11.35 1.02 -62.50 176.44 29.77
15 67A 67A N CA 331 332 143.47 145.30 -40.90
16 2406 67A 68A C N 334 336 -74.05 -68.20 7.59 0.75 -62.50 179.00 29.92
16 68A 68A N CA 336 337 140.47 145.30 -40.90
17 2407 68A 69A C N 339 341 -157.97 -134.00 28.50 0.69 -62.50 -176.51 35.15
17 69A 69A N CA 341 342 162.41 147.00 -40.90
18 2408 69A 70A C N 344 346 -108.17 -134.00 32.42 0.84 -62.50 174.39 26.73
18 70A 70A N CA 346 347 127.40 147.00 -40.90
19 2409 70A 71A C N 349 351 159.11 -134.00 70.97 1.66 -62.50 -157.08 40.35
19 71A 71A N CA 351 352 170.70 147.00 -40.90
20 2410 71A 72A C N 354 356 -72.33 -68.20 5.64 0.56 -62.50 177.91 29.65
20 72A 72A N CA 356 357 141.46 145.30 -40.90
21 2411 72A 73A C N 359 361 -81.03 -68.20 13.36 1.00 -62.50 171.09 28.98
21 73A 73A N CA 361 362 149.02 145.30 -40.90
22 2412 73A 74A C N 364 366 -130.41 -134.00 15.36 0.77 -62.50 -174.18 28.03
22 74A 74A N CA 366 367 132.06 147.00 -40.90
23 2413 74A 75A C N 369 371 67.18 -68.20 135.39 11.42 -62.50 -141.89 32.91
23 75A 75A N CA 371 372 143.73 145.30 -40.90
24 2414 75A 76A C N 374 376 -112.70 -134.00 34.73 1.21 -62.50 168.14 25.61
24 76A 76A N CA 376 377 119.57 147.00 -40.90
25 2415 76A 77A C N 379 381 63.12 -68.20 131.48 11.36 -62.50 -150.83 31.59
25 77A 77A N CA 381 382 151.85 145.30 -40.90
26 2416 77A 78A C N 384 386 -159.93 -134.00 27.96 0.64 -62.50 -171.27 36.12
26 78A 78A N CA 386 387 157.47 147.00 -40.90
27 2417 78A 79A C N 389 391 175.73 -134.00 51.42 2.12 -62.50 -145.08 32.33
27 79A 79A N CA 391 392 136.20 147.00 -40.90
28 2422 83A 84A C N 414 416 74.98 55.40 52.19 1.91 -62.50 140.86 28.13
28 84A 84A N CA 416 417 -10.18 38.20 -40.90
29 2426 87A 88A C N 434 436 53.46 55.40 5.40 0.20 -62.50 143.27 29.04
29 88A 88A N CA 436 437 43.24 38.20 -40.90
30 2429 90A 91A C N 449 451 49.95 55.40 21.69 0.91 -62.50 150.54 30.27
30 91A 91A N CA 451 452 59.19 38.20 -40.90
31 2431 92A 93A C N 459 461 -76.25 -62.50 36.79 6.77 -62.50 36.79 6.77
31 93A 93A N CA 461 462 -75.02 -40.90 -40.90
32 2432 93A 94A C N 464 466 -94.62 -62.50 37.18 7.56 -62.50 37.18 7.56
32 94A 94A N CA 466 467 -59.61 -40.90 -40.90
33 2459 120A 121A C N 599 601 81.60 -134.00 158.33 3.60 -62.50 179.59 28.78
33 121A 121A N CA 601 602 -148.08 147.00 -40.90
34 2472 133A 134A C N 664 666 49.13 55.40 12.18 0.46 -62.50 143.10 28.91
34 134A 134A N CA 666 667 48.64 38.20 -40.90
35 2480 141A 142A C N 704 706 -53.77 -62.50 10.56 1.71 -68.20 168.47 14.09
35 142A 142A N CA 706 707 -46.85 -40.90 145.30
36 2483 144A 145A C N 719 721 57.74 55.40 4.84 0.48 -62.50 146.29 29.68
36 145A 145A N CA 721 722 42.43 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 1 8 11 60 57 81 68 104 126 114 108
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 149
Number of all, selected real atoms : 774 774
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9783 9783
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1450
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 : 826.4486
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 : 730 0 0 0.007 0.007 9.2107 1.000
2 Bond angle potential : 1021 0 5 2.322 2.322 111.17 1.000
3 Stereochemical cosine torsion poten: 296 0 42 79.299 79.299 304.42 1.000
4 Stereochemical improper torsion pot: 292 0 0 1.096 1.096 8.9672 1.000
5 Soft-sphere overlap restraints : 1450 1 2 0.012 0.012 23.407 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 2 0.281 0.281 73.149 1.000
10 Distance restraints 2 (N-O) : 2564 0 7 0.398 0.398 158.51 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 6 5.472 5.472 51.206 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.247 0.247 5.2027 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 37 19 30.984 86.828 58.438 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.506 0.506 1.4629 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.042 0.042 21.307 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: alanin.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: 16143.9502
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 2354 15A 16A C N 74 76 78.39 55.40 25.99 2.01 -62.50 156.00 31.70
1 16A 16A N CA 76 77 26.08 38.20 -40.90
2 2357 18A 19A C N 89 91 63.38 55.40 16.88 0.62 -62.50 141.31 28.73
2 19A 19A N CA 91 92 23.32 38.20 -40.90
3 2359 20A 21A C N 99 101 55.22 55.40 3.08 0.20 -62.50 140.14 28.47
3 21A 21A N CA 101 102 35.13 38.20 -40.90
4 2360 21A 22A C N 104 106 63.23 55.40 11.94 0.57 -62.50 143.94 29.27
4 22A 22A N CA 106 107 29.18 38.20 -40.90
5 2361 22A 23A C N 109 111 -69.22 -62.50 6.74 1.31 -134.00 -176.54 11.30
5 23A 23A N CA 111 112 -41.36 -40.90 147.00
6 2375 36A 37A C N 179 181 67.29 55.40 15.60 0.92 -62.50 146.99 29.89
6 37A 37A N CA 181 182 28.11 38.20 -40.90
7 2376 37A 38A C N 184 186 63.13 55.40 13.06 0.55 -62.50 143.12 29.11
7 38A 38A N CA 186 187 27.67 38.20 -40.90
8 2387 48A 49A C N 239 241 84.61 55.40 39.50 2.23 -62.50 156.20 31.58
8 49A 49A N CA 241 242 11.61 38.20 -40.90
9 2392 53A 54A C N 264 266 91.72 -134.00 139.06 3.44 -62.50 -154.40 32.24
9 54A 54A N CA 266 267 -176.87 147.00 -40.90
10 2395 56A 57A C N 279 281 58.86 55.40 14.06 1.13 -62.50 152.72 30.91
10 57A 57A N CA 281 282 51.83 38.20 -40.90
11 2401 62A 63A C N 309 311 -71.31 -68.20 68.26 5.62 -62.50 118.34 18.98
11 63A 63A N CA 311 312 77.11 145.30 -40.90
12 2402 63A 64A C N 314 316 173.07 -134.00 55.38 1.33 -62.50 -160.61 39.17
12 64A 64A N CA 316 317 163.30 147.00 -40.90
13 2403 64A 65A C N 319 321 -43.06 -68.20 32.68 2.09 -62.50 166.47 28.28
13 65A 65A N CA 321 322 124.43 145.30 -40.90
14 2404 65A 66A C N 324 326 163.53 -134.00 64.76 1.59 -62.50 -155.11 40.51
14 66A 66A N CA 326 327 164.08 147.00 -40.90
15 2405 66A 67A C N 329 331 -144.20 -134.00 12.13 0.65 -62.50 -163.54 36.57
15 67A 67A N CA 331 332 140.44 147.00 -40.90
16 2406 67A 68A C N 334 336 -164.14 -134.00 30.81 1.27 -62.50 -154.61 39.09
16 68A 68A N CA 336 337 140.63 147.00 -40.90
17 2407 68A 69A C N 339 341 59.78 -68.20 130.33 11.82 -62.50 -167.10 29.29
17 69A 69A N CA 341 342 169.92 145.30 -40.90
18 2408 69A 70A C N 344 346 -135.61 -134.00 2.20 0.06 -62.50 -174.38 34.34
18 70A 70A N CA 346 347 148.49 147.00 -40.90
19 2409 70A 71A C N 349 351 -152.61 -134.00 19.00 0.50 -62.50 -169.11 36.10
19 71A 71A N CA 351 352 150.83 147.00 -40.90
20 2410 71A 72A C N 354 356 -125.28 -134.00 24.93 1.15 -62.50 176.11 26.60
20 72A 72A N CA 356 357 123.64 147.00 -40.90
21 2411 72A 73A C N 359 361 -172.72 -134.00 43.42 0.99 -62.50 -171.87 36.64
21 73A 73A N CA 361 362 166.64 147.00 -40.90
22 2412 73A 74A C N 364 366 -117.25 -134.00 22.06 0.61 -62.50 -178.04 27.70
22 74A 74A N CA 366 367 132.63 147.00 -40.90
23 2413 74A 75A C N 369 371 161.97 -134.00 70.95 1.61 -62.50 -164.02 39.04
23 75A 75A N CA 371 372 177.54 147.00 -40.90
24 2414 75A 76A C N 374 376 -65.58 -68.20 2.67 0.24 -62.50 173.28 28.55
24 76A 76A N CA 376 377 145.85 145.30 -40.90
25 2415 76A 77A C N 379 381 -68.12 -68.20 2.04 0.17 -62.50 171.85 28.44
25 77A 77A N CA 381 382 147.34 145.30 -40.90
26 2416 77A 78A C N 384 386 -124.70 -134.00 34.18 1.68 -62.50 167.02 25.18
26 78A 78A N CA 386 387 114.11 147.00 -40.90
27 2417 78A 79A C N 389 391 -21.27 -68.20 84.36 8.17 -62.50 111.59 16.83
27 79A 79A N CA 391 392 -144.59 145.30 -40.90
28 2422 83A 84A C N 414 416 80.69 55.40 54.63 1.99 -62.50 146.44 29.21
28 84A 84A N CA 416 417 -10.22 38.20 -40.90
29 2426 87A 88A C N 434 436 44.95 55.40 37.70 1.52 -62.50 157.62 31.34
29 88A 88A N CA 436 437 74.42 38.20 -40.90
30 2429 90A 91A C N 449 451 62.25 55.40 12.34 1.28 -62.50 153.45 31.11
30 91A 91A N CA 451 452 48.46 38.20 -40.90
31 2432 93A 94A C N 464 466 64.98 55.40 9.83 1.14 -62.50 151.19 30.72
31 94A 94A N CA 466 467 40.39 38.20 -40.90
32 2459 120A 121A C N 599 601 81.13 -134.00 159.59 3.62 -62.50 178.01 28.59
32 121A 121A N CA 601 602 -146.05 147.00 -40.90
33 2471 132A 133A C N 659 661 -55.61 -62.50 14.04 2.10 -68.20 162.06 13.51
33 133A 133A N CA 661 662 -53.13 -40.90 145.30
34 2472 133A 134A C N 664 666 -111.90 -134.00 56.78 2.54 -62.50 144.31 21.83
34 134A 134A N CA 666 667 94.69 147.00 -40.90
35 2473 134A 135A C N 669 671 -167.13 -134.00 36.03 0.82 -68.20 100.19 7.93
35 135A 135A N CA 671 672 161.14 147.00 145.30
36 2481 142A 143A C N 709 711 71.88 55.40 42.07 1.53 -62.50 140.32 28.25
36 143A 143A N CA 711 712 -0.51 38.20 -40.90
37 2483 144A 145A C N 719 721 66.17 55.40 12.65 0.91 -62.50 147.68 30.03
37 145A 145A N CA 721 722 31.58 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 7 7 49 68 83 78 81 113 114 94
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
alanin.B99990001.pdb 900.87506
alanin.B99990002.pdb 826.44861
In [55]:
w4 = nglview.show_structure_file('alanin.B99990001.pdb')
w4.clear_representations()
w4.add_cartoon('protein', color_scheme='residueindex')
w4.add_ball_and_stick('ligand', opacity=0.5)
w4
Итоговая структура получилась очень похожей на лизоцим, что, разумеется, невозможно.
In [56]:
from IPython.display import Image
Image(filename='overlay4.png')
Out[56]:
Синим обозначена исходная структура 1lmp, розовым - получившаяся модель.
Очевидно, что использовать пакет Modeller подобным образом не стоит. Референсные структуры нужно подбирать с уверенностью в гомологии с изучаемой последовательностью.
Сравним скор-функции
In [59]:
import pandas as pd
data = [['Модель 1', 878.34003, 1018.65662, 4289.79346, 900.87506],['Модель 2', 769.98920, 886.54285, 4438.97754, 826.44861]]
pd.DataFrame(data, columns=["", "Без лиганда", "С лигандом", "С перемещенным лигандом", "Замещенный на аланины"])
Out[59]:
| Без лиганда | С лигандом | С перемещенным лигандом | Замещенный на аланины | ||
|---|---|---|---|---|---|
| 0 | Модель 1 | 878.34003 | 1018.65662 | 4289.79346 | 900.87506 |
| 1 | Модель 2 | 769.98920 | 886.54285 | 4438.97754 | 826.44861 |
У моделей со смещенным лигандом очень высокий показатель, поскольку введенные дополнительные ограничения не соответствуют изначальной структуре лизоцима 1lmp. Скор аланиновой последовательности сопоставим с моделями без лиганда, возможно по причине большой разницы первичных последовательностей 1lmp и выданного белка.