Гомологичное моделирование комплекса белка с лигандом
In [1]:
import sys
sys.path.append('/usr/lib/modeller9v7/modlib/')
sys.path.append('/usr/lib/modeller9v7/lib/x86_64-intel8/python2.5/')
import modeller
import _modeller
import modeller.automodel
In [3]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo.fbb.msu.ru 3.8-2-amd64 x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2018/05/09 23:53:52
Сегодня будем моделировать комплекс белка лизоцима с лигандом на основе структуры лизоцима радужной форели.
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2018-05-09 17:52:12-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 128.6.244.52
Connecting to 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]
--2018-05-09 17:52:13-- https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 128.6.244.65
Connecting to www.rcsb.org|128.6.244.65|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2018-05-09 17:52:13-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 128.6.244.231
Connecting to files.rcsb.org|128.6.244.231|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb'
[ <=> ] 130,410 324K/s in 0.4s
2018-05-09 17:52:14 (324 KB/s) - `1lmp.pdb' saved [130410]
для работы возьмем белок лизоцим LYS_HYACE из Hyalophora cecropia:
In [5]:
! wget http://www.uniprot.org/uniprot/P05105.fasta
--2018-05-09 17:53:13-- http://www.uniprot.org/uniprot/P05105.fasta Resolving www.uniprot.org... 128.175.240.211, 193.62.193.81 Connecting to www.uniprot.org|128.175.240.211|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 213 [text/plain] Saving to: `P05105.fasta' 100%[======================================>] 213 --.-K/s in 0s 2018-05-09 17:53:14 (27.7 MB/s) - `P05105.fasta' saved [213/213]
In [6]:
alignm=modeller.alignment(env)
alignm.append(file='P05105.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
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.
In [11]:
## есть смысл поправить идентификаторы
alignm[0].code = 'HYACE'
alignm[1].code = '1LMP'
In [13]:
alignm.salign()
alignm.write(file='hyase.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [15]:
! cat hyase.ali
>P1;HYACE sequence:: : : : :::-1.00:-1.00 MTKYVILLAVLAFALHCDAKRFTRCGLVQELRRLGFDETLMSNWVCLVENESGRFTDKIGKVNKNGSRDYGLFQI NDKYWCSKGTTPGKD--CNVTCNQLLTDDISVAATCAKKI-YKRHKFDAWYGWKNHCQHGLPDISDC-------* >P1;1LMP structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMD----------------GYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQI NSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
А где лиганд? Непорядок. Надо его добавить
In [16]:
with open('hyase.ali','r') as ali:
lines = ali.readlines()
with open('hyase.ali','w') as ali:
for c, line in enumerate(lines):
if c == 4:
line = line[:-5]+'...*'
ali.write(line)
In [17]:
! cat hyase.ali
>P1;HYACE sequence:: : : : :::-1.00:-1.00 MTKYVILLAVLAFALHCDAKRFTRCGLVQELRRLGFDETLMSNWVCLVENESGRFTDKIGKVNKNGSRDYGLFQI NDKYWCSKGTTPGKD--CNVTCNQLLTDDISVAATCAKKI-YKRHKFDAWYGWKNHCQHGLPDISDC----...* >P1;1LMP structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMD----------------GYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIFQI NSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Теперь всё в порядке! Можем строить модель.
In [20]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='hyase.ali', knowns= pdb.code, sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 5
a.make()
HYACE 1LMP
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C +N
atom indices : 1110 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C CA +N O
atom indices : 1110 1107 0 1111
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM 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: 13083 12116
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2582
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 : 1166.6425
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 : 1136 0 1 0.009 0.009 26.101 1.000
2 Bond angle potential : 1532 1 12 2.358 2.358 171.26 1.000
3 Stereochemical cosine torsion poten: 734 0 29 46.674 46.674 249.84 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.455 1.455 21.540 1.000
5 Soft-sphere overlap restraints : 2582 1 2 0.007 0.007 16.440 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) : 2217 0 5 0.370 0.370 114.74 1.000
10 Distance restraints 2 (N-O) : 2375 0 14 0.492 0.492 210.15 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: 138 0 2 5.037 5.037 41.291 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 74.927 74.927 41.494 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 2 65.225 65.225 37.688 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 77.785 77.785 18.116 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 90.820 90.820 12.417 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27912 1.000
19 Disulfide angle restraints : 6 0 0 3.765 3.765 1.8777 1.000
20 Disulfide dihedral angle restraints: 3 0 0 20.233 20.233 1.2433 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) : 1240 0 0 0.376 0.376 19.154 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: 137 23 29 35.932 71.419 122.16 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 1 0.751 0.751 27.533 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.055 0.055 33.315 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: HYACE.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: 16913.0332
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2119 90D 90D N CA 713 714 124.71 107.00 17.72 5.09 107.00 17.72 5.09
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -69.08 -68.20 11.93 0.93 -62.50 162.03 26.88
1 19A 19A N CA 141 142 157.20 145.30 -40.90
2 3911 19A 20K C N 144 146 -73.06 -70.20 5.91 0.36 -62.90 173.93 23.16
2 20K 20K N CA 146 147 145.57 140.40 -40.80
3 3912 20K 21R C N 153 155 -63.67 -72.10 12.24 1.06 -63.00 168.14 22.76
3 21R 21R N CA 155 156 150.76 141.90 -41.10
4 3913 21R 22F C N 164 166 -66.50 -71.40 11.91 0.80 -63.20 174.18 23.96
4 22F 22F N CA 166 167 129.85 140.70 -44.30
5 3914 22F 23T C N 175 177 -126.41 -124.80 50.56 2.12 -63.20 139.06 21.93
5 23T 23T N CA 177 178 -165.96 143.50 -42.10
6 3915 23T 24R C N 182 184 -59.22 -72.10 13.98 0.95 -63.00 177.60 24.25
6 24R 24R N CA 184 185 136.46 141.90 -41.10
7 3917 25C 26G C N 199 201 -95.87 -80.20 59.25 1.61 82.20 -135.17 17.52
7 26G 26G N CA 201 202 -128.76 174.10 8.50
8 3918 26G 27L C N 203 205 -64.01 -70.70 7.16 0.55 -63.50 179.76 24.99
8 27L 27L N CA 205 206 139.04 141.60 -41.20
9 3920 28V 29Q C N 218 220 -64.57 -73.00 30.22 1.82 -63.80 151.98 22.31
9 29Q 29Q N CA 220 221 111.68 140.70 -40.30
10 3922 30E 31L C N 236 238 -122.90 -108.50 39.61 1.96 -63.50 160.77 26.00
10 31L 31L N CA 238 239 169.40 132.50 -41.20
11 3923 31L 32R C N 244 246 -131.77 -125.20 8.27 0.44 -63.00 -170.42 21.94
11 32R 32R N CA 246 247 135.57 140.60 -41.10
12 3925 33R 34L C N 266 268 70.89 -70.70 148.15 11.86 -63.50 -166.51 34.75
12 34L 34L N CA 268 269 98.00 141.60 -41.20
13 3926 34L 35G C N 274 276 89.37 78.70 53.76 1.11 82.20 132.90 6.81
13 35G 35G N CA 276 277 141.21 -166.10 8.50
14 3928 36F 37D C N 289 291 48.70 -70.90 134.74 11.31 54.50 171.57 12.15
14 37D 37D N CA 291 292 -147.63 150.30 40.90
15 3929 37D 38E C N 297 299 -114.93 -117.80 84.23 4.18 -63.60 106.16 12.28
15 38E 38E N CA 299 300 52.62 136.80 -40.30
16 3956 64K 65N C N 512 514 -82.11 -119.90 54.80 2.97 -63.20 143.47 19.00
16 65N 65N N CA 514 515 176.69 137.00 -41.10
17 3957 65N 66G C N 520 522 -62.71 -62.40 20.43 3.04 82.20 147.84 10.83
17 66G 66G N CA 522 523 -20.78 -41.20 8.50
18 3978 86T 87P C N 691 693 -55.13 -58.70 46.24 3.54 -64.50 136.53 10.69
18 87P 87P N CA 693 694 -76.60 -30.50 147.20
19 3979 87P 88G C N 698 700 -65.69 -62.40 11.33 1.87 82.20 159.81 12.29
19 88G 88G N CA 700 701 -52.04 -41.20 8.50
20 3980 88G 89K C N 702 704 60.17 -70.20 130.47 9.64 -70.20 130.47 9.64
20 89K 89K N CA 704 705 145.35 140.40 140.40
21 3981 89K 90D C N 711 713 -152.18 -63.30 94.27 15.98 -63.30 94.27 15.98
21 90D 90D N CA 713 714 -71.43 -40.00 -40.00
22 4005 113I 114Y C N 884 886 -54.27 -98.40 49.97 3.18 -63.50 148.65 24.06
22 114Y 114Y N CA 886 887 104.96 128.40 -43.40
23 4029 137S 138D C N 1096 1098 -95.49 -70.90 72.17 2.54 -63.30 106.82 15.26
23 138D 138D N CA 1098 1099 -141.85 150.30 -40.00
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 11 12 81 108 121 122 153 170 183 205
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2446
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 : 1100.8982
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 : 1136 0 1 0.008 0.008 23.307 1.000
2 Bond angle potential : 1532 3 10 3.037 3.037 186.60 1.000
3 Stereochemical cosine torsion poten: 734 0 31 48.563 48.563 266.94 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.293 1.293 17.735 1.000
5 Soft-sphere overlap restraints : 2446 1 2 0.007 0.007 16.176 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) : 2217 0 2 0.330 0.330 95.315 1.000
10 Distance restraints 2 (N-O) : 2375 0 7 0.388 0.388 146.22 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: 138 0 2 4.808 4.808 37.617 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 76.086 76.086 36.961 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 76.633 76.633 41.569 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 91.689 91.689 22.779 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 84.121 84.121 13.236 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32193 1.000
19 Disulfide angle restraints : 6 0 0 2.614 2.614 0.90503 1.000
20 Disulfide dihedral angle restraints: 3 0 0 24.182 24.182 1.8126 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) : 1240 0 0 0.446 0.446 31.741 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: 137 22 19 30.941 72.235 94.477 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.807 0.807 34.396 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.054 0.054 32.791 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: HYACE.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: 17260.0801
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2119 90D 90D N CA 713 714 125.57 107.00 18.57 5.34 107.00 18.57 5.34
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3910 18D 19A C N 139 141 178.81 -134.00 53.26 1.22 -62.50 -170.74 37.21
1 19A 19A N CA 141 142 171.69 147.00 -40.90
2 3911 19A 20K C N 144 146 -111.89 -118.00 19.48 0.85 -62.90 168.67 19.79
2 20K 20K N CA 146 147 120.60 139.10 -40.80
3 3912 20K 21R C N 153 155 -150.36 -125.20 25.70 1.17 -63.00 -163.08 22.40
3 21R 21R N CA 155 156 135.38 140.60 -41.10
4 3913 21R 22F C N 164 166 -147.80 -124.20 23.87 1.04 -63.20 -164.73 32.57
4 22F 22F N CA 166 167 139.71 143.30 -44.30
5 3914 22F 23T C N 175 177 -100.68 -78.10 23.13 1.26 -63.20 167.33 23.96
5 23T 23T N CA 177 178 154.83 149.80 -42.10
6 3915 23T 24R C N 182 184 -123.75 -125.20 23.79 1.12 -63.00 169.23 19.61
6 24R 24R N CA 184 185 116.86 140.60 -41.10
7 3917 25C 26G C N 199 201 -75.73 -80.20 5.94 0.43 82.20 -128.33 6.98
7 26G 26G N CA 201 202 178.00 174.10 8.50
8 3918 26G 27L C N 203 205 -68.40 -70.70 7.73 0.67 -63.50 169.89 23.87
8 27L 27L N CA 205 206 148.98 141.60 -41.20
9 3919 27L 28V C N 211 213 -62.56 -62.40 1.75 0.23 -125.40 -176.36 10.30
9 28V 28V N CA 213 214 -44.14 -42.40 143.30
10 3921 29Q 30E C N 227 229 95.12 -117.80 148.59 5.98 -63.60 -137.50 37.75
10 30E 30E N CA 229 230 115.63 136.80 -40.30
11 3923 31L 32R C N 244 246 -18.71 -72.10 55.89 3.91 -63.00 172.26 26.33
11 32R 32R N CA 246 247 125.37 141.90 -41.10
12 3924 32R 33R C N 255 257 -150.41 -125.20 25.26 0.97 -63.00 -162.91 32.57
12 33R 33R N CA 257 258 142.25 140.60 -41.10
13 3925 33R 34L C N 266 268 -119.61 -108.50 20.30 0.95 -63.50 178.36 28.23
13 34L 34L N CA 268 269 149.49 132.50 -41.20
14 3926 34L 35G C N 274 276 100.02 78.70 37.42 0.62 82.20 155.67 8.44
14 35G 35G N CA 276 277 163.15 -166.10 8.50
15 3929 37D 38E C N 297 299 57.44 54.60 4.03 0.25 -63.60 145.00 24.94
15 38E 38E N CA 299 300 39.54 42.40 -40.30
16 3952 60G 61K C N 479 481 -106.29 -118.00 81.68 3.79 -70.20 89.71 7.25
16 61K 61K N CA 481 482 58.27 139.10 140.40
17 3981 89K 90D C N 711 713 -143.80 -63.30 87.85 14.97 -63.30 87.85 14.97
17 90D 90D N CA 713 714 -75.16 -40.00 -40.00
18 4005 113I 114Y C N 884 886 -48.58 -98.40 54.65 3.24 -63.50 150.08 24.58
18 114Y 114Y N CA 886 887 105.93 128.40 -43.40
19 4008 116R 117H C N 916 918 -97.82 -125.60 50.67 1.36 -63.20 142.98 16.02
19 117H 117H N CA 918 919 96.42 138.80 -42.30
20 4009 117H 118K C N 926 928 -55.06 -62.90 70.41 8.74 -118.00 126.84 6.57
20 118K 118K N CA 928 929 -110.78 -40.80 139.10
21 4019 127N 128H C N 1020 1022 -121.22 -63.20 74.38 8.76 -63.20 74.38 8.76
21 128H 128H N CA 1022 1023 4.24 -42.30 -42.30
22 4020 128H 129C C N 1030 1032 -126.56 -63.00 65.20 10.00 -63.00 65.20 10.00
22 129C 129C N CA 1032 1033 -26.57 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 19 65 77 131 134 139 167 164 179
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2462
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 : 1108.3013
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 : 1136 0 1 0.008 0.008 22.171 1.000
2 Bond angle potential : 1532 5 13 3.658 3.658 227.86 1.000
3 Stereochemical cosine torsion poten: 734 0 31 48.533 48.533 267.27 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.333 1.333 18.229 1.000
5 Soft-sphere overlap restraints : 2462 1 2 0.007 0.007 16.119 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) : 2217 0 3 0.325 0.325 92.523 1.000
10 Distance restraints 2 (N-O) : 2375 0 7 0.398 0.398 142.54 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 138 0 1 4.449 4.449 32.205 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 68.836 68.836 34.730 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 64.017 64.017 32.832 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 75.323 75.323 18.803 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 102.641 102.641 11.819 1.000
18 Disulfide distance restraints : 3 0 0 0.024 0.024 0.30332 1.000
19 Disulfide angle restraints : 6 0 0 2.652 2.652 0.93163 1.000
20 Disulfide dihedral angle restraints: 3 0 0 14.614 14.614 0.73469 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) : 1240 0 0 0.449 0.449 25.513 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: 137 23 19 31.460 71.405 97.228 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.715 0.715 36.707 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.052 0.052 29.787 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: HYACE.V99990003
# 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: 16012.6475
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2119 90D 90D N CA 713 714 126.51 107.00 19.51 5.61 107.00 19.51 5.61
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -80.72 -68.20 12.58 1.02 -62.50 173.51 29.36
1 19A 19A N CA 141 142 146.55 145.30 -40.90
2 3911 19A 20K C N 144 146 -130.50 -118.00 33.00 1.71 -62.90 163.95 18.87
2 20K 20K N CA 146 147 108.56 139.10 -40.80
3 3912 20K 21R C N 153 155 -127.12 -63.00 99.38 11.47 -63.00 99.38 11.47
3 21R 21R N CA 155 156 34.83 -41.10 -41.10
4 3914 22F 23T C N 175 177 -123.12 -124.80 9.13 0.44 -63.20 175.94 26.53
4 23T 23T N CA 177 178 152.47 143.50 -42.10
5 3915 23T 24R C N 182 184 -136.98 -125.20 18.52 0.59 -63.00 179.92 29.36
5 24R 24R N CA 184 185 154.90 140.60 -41.10
6 3917 25C 26G C N 199 201 -79.11 -80.20 6.06 0.29 82.20 -124.52 7.13
6 26G 26G N CA 201 202 -179.94 174.10 8.50
7 3918 26G 27L C N 203 205 -85.30 -108.50 42.21 1.98 -63.50 140.15 18.32
7 27L 27L N CA 205 206 97.24 132.50 -41.20
8 3920 28V 29Q C N 218 220 -81.01 -73.00 18.16 1.35 -63.80 165.60 23.48
8 29Q 29Q N CA 220 221 124.40 140.70 -40.30
9 3921 29Q 30E C N 227 229 -133.64 -117.80 41.86 1.74 -63.60 160.27 25.28
9 30E 30E N CA 229 230 175.54 136.80 -40.30
10 3922 30E 31L C N 236 238 -62.13 -70.70 22.95 1.47 -63.50 161.51 22.50
10 31L 31L N CA 238 239 120.30 141.60 -41.20
11 3923 31L 32R C N 244 246 -106.00 -125.20 20.04 0.66 -63.00 -178.87 21.90
11 32R 32R N CA 246 247 134.86 140.60 -41.10
12 3924 32R 33R C N 255 257 -76.03 -72.10 5.48 0.48 -63.00 179.65 23.42
12 33R 33R N CA 257 258 138.08 141.90 -41.10
13 3925 33R 34L C N 266 268 -102.78 -108.50 6.75 0.30 -63.50 174.59 22.31
13 34L 34L N CA 268 269 128.92 132.50 -41.20
14 3926 34L 35G C N 274 276 77.45 78.70 10.54 0.35 82.20 175.00 8.26
14 35G 35G N CA 276 277 -176.57 -166.10 8.50
15 3929 37D 38E C N 297 299 54.64 54.60 0.78 0.06 -63.60 144.74 24.88
15 38E 38E N CA 299 300 43.17 42.40 -40.30
16 3943 51E 52S C N 411 413 -134.36 -64.10 75.28 8.29 -64.10 75.28 8.29
16 52S 52S N CA 413 414 -7.97 -35.00 -35.00
17 3952 60G 61K C N 479 481 -104.68 -118.00 86.18 3.99 -70.20 93.07 7.47
17 61K 61K N CA 481 482 53.95 139.10 140.40
18 3953 61K 62V C N 488 490 -66.68 -62.40 19.51 2.25 -125.40 176.71 7.08
18 62V 62V N CA 490 491 -23.37 -42.40 143.30
19 3956 64K 65N C N 512 514 -73.35 -119.90 54.78 2.87 -63.20 153.36 19.74
19 65N 65N N CA 514 515 165.88 137.00 -41.10
20 3957 65N 66G C N 520 522 -61.10 -62.40 19.77 3.02 82.20 146.41 10.75
20 66G 66G N CA 522 523 -21.47 -41.20 8.50
21 3981 89K 90D C N 711 713 177.25 -96.50 91.96 3.74 -63.30 170.95 19.22
21 90D 90D N CA 713 714 82.30 114.20 -40.00
22 4005 113I 114Y C N 884 886 -48.78 -98.40 55.96 3.54 -63.50 146.68 24.03
22 114Y 114Y N CA 886 887 102.53 128.40 -43.40
23 4020 128H 129C C N 1030 1032 -124.33 -63.00 72.24 9.32 -63.00 72.24 9.32
23 129C 129C N CA 1032 1033 -2.92 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 12 14 71 88 134 111 127 170 176 191
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2689
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 : 1077.7384
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 : 1136 0 1 0.009 0.009 24.328 1.000
2 Bond angle potential : 1532 1 7 2.184 2.184 147.02 1.000
3 Stereochemical cosine torsion poten: 734 0 30 47.793 47.793 259.31 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.425 1.425 20.852 1.000
5 Soft-sphere overlap restraints : 2689 1 2 0.007 0.007 17.164 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) : 2217 0 4 0.367 0.367 107.61 1.000
10 Distance restraints 2 (N-O) : 2375 0 8 0.423 0.423 158.82 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: 138 0 1 4.351 4.351 30.804 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 85.798 85.798 57.149 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 81.799 81.799 46.345 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 91.489 91.489 24.479 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 108.534 108.534 12.585 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32342 1.000
19 Disulfide angle restraints : 6 0 0 2.441 2.441 0.78966 1.000
20 Disulfide dihedral angle restraints: 3 0 0 27.893 27.893 2.2465 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) : 1240 0 0 0.478 0.478 32.637 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: 137 18 19 25.336 60.666 74.883 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.701 0.701 28.367 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.054 0.054 32.019 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: HYACE.V99990004
# 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: 17558.4863
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2119 90D 90D N CA 713 714 124.35 107.00 17.35 4.99 107.00 17.35 4.99
-------------------------------------------------------------------------------------------------
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 3911 19A 20K C N 144 146 57.16 56.60 9.74 0.65 -62.90 138.81 24.24
1 20K 20K N CA 146 147 28.87 38.60 -40.80
2 3912 20K 21R C N 153 155 -137.40 -125.20 12.73 0.42 -63.00 -170.17 30.74
2 21R 21R N CA 155 156 144.26 140.60 -41.10
3 3913 21R 22F C N 164 166 -116.40 -124.20 17.63 0.60 -63.20 179.84 21.73
3 22F 22F N CA 166 167 127.49 143.30 -44.30
4 3914 22F 23T C N 175 177 -134.40 -124.80 30.28 1.04 -63.20 162.15 25.43
4 23T 23T N CA 177 178 172.21 143.50 -42.10
5 3915 23T 24R C N 182 184 -89.49 -72.10 44.80 3.78 -63.00 144.16 17.84
5 24R 24R N CA 184 185 100.61 141.90 -41.10
6 3917 25C 26G C N 199 201 70.66 78.70 8.08 0.42 82.20 175.74 9.11
6 26G 26G N CA 201 202 -166.85 -166.10 8.50
7 3918 26G 27L C N 203 205 -119.69 -108.50 40.55 2.06 -63.50 157.67 25.37
7 27L 27L N CA 205 206 171.48 132.50 -41.20
8 3920 28V 29Q C N 218 220 -129.67 -121.10 30.02 1.26 -63.80 164.95 27.72
8 29Q 29Q N CA 220 221 168.47 139.70 -40.30
9 3922 30E 31L C N 236 238 -70.03 -70.70 8.47 0.67 -63.50 168.88 23.83
9 31L 31L N CA 238 239 150.05 141.60 -41.20
10 3923 31L 32R C N 244 246 -77.52 -72.10 5.67 0.40 -63.00 175.94 24.76
10 32R 32R N CA 246 247 143.57 141.90 -41.10
11 3925 33R 34L C N 266 268 -58.44 -70.70 12.53 1.21 -63.50 174.64 23.96
11 34L 34L N CA 268 269 144.23 141.60 -41.20
12 3926 34L 35G C N 274 276 101.74 78.70 40.33 0.67 82.20 153.54 8.42
12 35G 35G N CA 276 277 160.79 -166.10 8.50
13 3929 37D 38E C N 297 299 62.42 54.60 9.87 0.70 -63.60 147.52 25.39
13 38E 38E N CA 299 300 36.38 42.40 -40.30
14 3943 51E 52S C N 411 413 -138.52 -64.10 83.15 8.64 -64.10 83.15 8.64
14 52S 52S N CA 413 414 2.09 -35.00 -35.00
15 3981 89K 90D C N 711 713 -143.69 -63.30 89.02 15.19 -63.30 89.02 15.19
15 90D 90D N CA 713 714 -78.24 -40.00 -40.00
16 4005 113I 114Y C N 884 886 -50.71 -98.40 52.08 3.05 -63.50 151.41 24.68
16 114Y 114Y N CA 886 887 107.47 128.40 -43.40
17 4008 116R 117H C N 916 918 -93.80 -125.60 51.39 1.32 -63.20 144.02 16.32
17 117H 117H N CA 918 919 98.43 138.80 -42.30
18 4029 137S 138D C N 1096 1098 -111.59 -63.30 71.02 7.91 -63.30 71.02 7.91
18 138D 138D N CA 1098 1099 12.08 -40.00 -40.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 16 16 95 94 151 122 142 176 205 230
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12116 12116
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2450
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 : 1191.8379
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 : 1136 0 1 0.009 0.009 24.572 1.000
2 Bond angle potential : 1532 4 11 3.012 3.012 194.74 1.000
3 Stereochemical cosine torsion poten: 734 0 26 47.122 47.122 252.79 1.000
4 Stereochemical improper torsion pot: 478 0 0 1.288 1.288 17.080 1.000
5 Soft-sphere overlap restraints : 2450 1 2 0.007 0.007 16.041 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) : 2217 0 3 0.372 0.372 116.24 1.000
10 Distance restraints 2 (N-O) : 2375 0 12 0.412 0.412 179.72 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: 138 0 2 5.063 5.063 41.719 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 77.352 77.352 38.479 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 0 71.952 71.952 37.626 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 76.098 76.098 20.951 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 91.997 91.997 14.182 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.37169 1.000
19 Disulfide angle restraints : 6 0 0 2.568 2.568 0.87365 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.362 25.362 1.9255 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) : 1240 0 0 0.465 0.465 31.467 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: 137 27 19 30.436 76.948 133.25 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 0 0.852 0.852 40.477 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.052 0.052 29.337 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: HYACE.V99990005
# 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: 17388.0352
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1826 63N 63N ND2 CG 502 500 139.32 122.50 16.83 4.68 122.50 16.83 4.68
2 2119 90D 90D N CA 713 714 124.87 107.00 17.87 5.14 107.00 17.87 5.14
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -162.53 -134.00 29.56 1.28 -62.50 -154.21 39.07
1 19A 19A N CA 141 142 139.26 147.00 -40.90
2 3911 19A 20K C N 144 146 167.88 -118.00 74.22 2.87 -62.90 -141.52 25.48
2 20K 20K N CA 146 147 135.37 139.10 -40.80
3 3912 20K 21R C N 153 155 -106.99 -125.20 18.37 0.80 -63.00 -178.71 27.53
3 21R 21R N CA 155 156 143.03 140.60 -41.10
4 3913 21R 22F C N 164 166 -86.97 -71.40 37.18 3.29 -63.20 153.10 19.71
4 22F 22F N CA 166 167 106.94 140.70 -44.30
5 3914 22F 23T C N 175 177 -138.20 -124.80 52.10 1.86 -63.20 144.97 23.37
5 23T 23T N CA 177 178 -166.16 143.50 -42.10
6 3915 23T 24R C N 182 184 -61.71 -72.10 15.53 1.35 -63.00 165.47 22.27
6 24R 24R N CA 184 185 153.44 141.90 -41.10
7 3917 25C 26G C N 199 201 -99.47 -80.20 27.86 0.86 82.20 -110.65 7.90
7 26G 26G N CA 201 202 -165.79 174.10 8.50
8 3918 26G 27L C N 203 205 -77.55 -70.70 9.00 0.59 -63.50 171.93 24.70
8 27L 27L N CA 205 206 147.44 141.60 -41.20
9 3919 27L 28V C N 211 213 -67.24 -62.40 4.95 0.73 -125.40 -175.25 10.30
9 28V 28V N CA 213 214 -41.34 -42.40 143.30
10 3921 29Q 30E C N 227 229 -79.40 -69.30 12.42 1.13 -63.60 176.29 22.67
10 30E 30E N CA 229 230 135.28 142.50 -40.30
11 3922 30E 31L C N 236 238 -104.46 -108.50 6.83 0.32 -63.50 173.11 22.04
11 31L 31L N CA 238 239 126.99 132.50 -41.20
12 3923 31L 32R C N 244 246 -76.35 -72.10 6.50 0.56 -63.00 178.57 23.25
12 32R 32R N CA 246 247 136.98 141.90 -41.10
13 3924 32R 33R C N 255 257 -71.87 -72.10 18.93 1.45 -63.00 164.31 21.61
13 33R 33R N CA 257 258 122.97 141.90 -41.10
14 3925 33R 34L C N 266 268 -99.15 -108.50 18.59 1.06 -63.50 173.93 26.32
14 34L 34L N CA 268 269 148.57 132.50 -41.20
15 3926 34L 35G C N 274 276 101.28 78.70 38.93 0.66 82.20 154.86 8.47
15 35G 35G N CA 276 277 162.19 -166.10 8.50
16 3929 37D 38E C N 297 299 52.68 54.60 7.38 0.43 -63.60 146.94 25.20
16 38E 38E N CA 299 300 49.53 42.40 -40.30
17 3943 51E 52S C N 411 413 -137.94 -64.10 82.79 8.56 -64.10 82.79 8.56
17 52S 52S N CA 413 414 2.45 -35.00 -35.00
18 3974 82S 83K C N 664 666 -74.58 -62.90 89.67 12.31 -62.90 89.67 12.31
18 83K 83K N CA 666 667 -129.70 -40.80 -40.80
19 3975 83K 84G C N 673 675 -103.35 -62.40 41.26 7.55 82.20 -177.16 9.86
19 84G 84G N CA 675 676 -46.26 -41.20 8.50
20 3981 89K 90D C N 711 713 -143.05 -63.30 88.58 15.12 -63.30 88.58 15.12
20 90D 90D N CA 713 714 -78.54 -40.00 -40.00
21 4005 113I 114Y C N 884 886 -48.85 -98.40 55.31 3.42 -63.50 147.95 24.23
21 114Y 114Y N CA 886 887 103.82 128.40 -43.40
22 4019 127N 128H C N 1020 1022 -123.75 -63.20 76.08 9.07 -63.20 76.08 9.07
22 128H 128H N CA 1022 1023 3.75 -42.30 -42.30
23 4020 128H 129C C N 1030 1032 -126.88 -63.00 66.96 9.89 -63.00 66.96 9.89
23 129C 129C N CA 1032 1033 -20.99 -41.10 -41.10
24 4021 129C 130Q C N 1036 1038 -63.43 -63.80 2.71 0.42 -121.10 -173.54 7.75
24 130Q 130Q N CA 1038 1039 -37.61 -40.30 139.70
25 4022 130Q 131H C N 1045 1047 -58.85 -63.20 7.88 0.84 56.30 145.94 23.14
25 131H 131H N CA 1047 1048 -48.87 -42.30 40.80
26 4023 131H 132G C N 1055 1057 143.52 -167.20 55.97 0.89 -80.20 138.93 8.31
26 132G 132G N CA 1057 1058 -158.85 174.60 174.10
27 4024 132G 133L C N 1059 1061 52.20 60.20 28.95 1.12 -108.50 177.38 7.84
27 133L 133L N CA 1061 1062 57.42 29.60 132.50
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 13 18 76 89 137 127 124 183 162 193
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
HYACE.B99990001.pdb 1166.64246
HYACE.B99990002.pdb 1100.89819
HYACE.B99990003.pdb 1108.30127
HYACE.B99990004.pdb 1077.73840
HYACE.B99990005.pdb 1191.83789
отлично! теперь посмотрим что у нас получилось
 |
 |
Получилось вполне неплохо! Во всех структурах лиганд на месте, а в структуре 5 на месте даже все спирали.
Теперь попробуем передвинуть лиганд в другое место:
In [ ]:
! rm HYASE.rsr
In [30]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O6:140', 'CG:83')]:
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='hyase.ali', knowns= pdb.code , sequence = s.code )
a.make()
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 target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
90 1 73 76 D C 8.895
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C +N
atom indices : 1110 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 139
atom names : C CA +N O
atom indices : 1110 1107 0 1111
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM 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: 13084 12117
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
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 : 142
Number of all, selected real atoms : 1155 1155
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12117 12117
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2588
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 : 3121.6934
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 : 1136 2 5 0.020 0.020 104.52 1.000
2 Bond angle potential : 1532 15 30 4.631 4.631 387.12 1.000
3 Stereochemical cosine torsion poten: 734 0 30 47.019 47.019 254.64 1.000
4 Stereochemical improper torsion pot: 478 1 1 3.039 3.039 79.596 1.000
5 Soft-sphere overlap restraints : 2588 1 3 0.011 0.011 37.076 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) : 2217 8 30 0.489 0.489 327.46 1.000
10 Distance restraints 2 (N-O) : 2375 6 29 0.509 0.509 330.42 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: 138 0 1 4.553 4.553 33.743 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 68.312 68.312 37.976 1.000
15 Sidechain Chi_2 dihedral restraints: 89 0 1 75.876 75.876 41.528 1.000
16 Sidechain Chi_3 dihedral restraints: 32 0 0 90.988 90.988 27.204 1.000
17 Sidechain Chi_4 dihedral restraints: 20 0 0 97.953 97.953 12.175 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.40411 1.000
19 Disulfide angle restraints : 6 0 0 3.888 3.888 2.0024 1.000
20 Disulfide dihedral angle restraints: 3 0 0 36.957 36.957 2.9652 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) : 1240 0 0 0.407 0.407 30.914 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: 137 24 24 35.177 71.729 170.37 1.000
26 Distance restraints 4 (SDCH-SDCH) : 466 0 5 0.864 0.864 61.138 1.000
27 Distance restraints 5 (X-Y) : 1390 25 36 0.225 0.225 1180.4 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: HYACE.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: 19694.2910
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
1 679 83K 83K CB CA 668 667 1.90 1.54 0.37 10.07 1.54 0.37 10.07
2 680 83K 83K CG CB 669 668 1.93 1.53 0.40 11.02 1.53 0.40 11.02
-------------------------------------------------------------------------------------------------
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 1691 50N 50N ND2 CG 401 399 138.96 122.50 16.46 4.58 122.50 16.46 4.58
2 1848 65N 65N ND2 CG 519 517 139.71 122.50 17.22 4.79 122.50 17.22 4.79
3 1997 79Y 79Y N CA 628 629 130.77 107.00 23.77 6.84 107.00 23.77 6.84
4 2056 83K 83K CA CB 667 668 146.36 113.50 32.87 8.07 113.50 32.87 8.07
5 2060 83K 83K CG CD 669 670 132.09 113.60 18.49 4.54 113.60 18.49 4.54
6 2062 83K 83K C CA 673 667 133.86 108.00 25.86 5.99 108.00 25.86 5.99
7 2119 90D 90D N CA 713 714 127.61 107.00 20.61 5.93 107.00 20.61 5.93
-------------------------------------------------------------------------------------------------
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 6217 83K 96N CA CA 667 756 10.01 7.27 2.74 4.76 7.27 2.74 4.76
-------------------------------------------------------------------------------------------------
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 3910 18D 19A C N 139 141 -70.16 -68.20 5.62 0.52 -62.50 179.23 29.75
1 19A 19A N CA 141 142 140.04 145.30 -40.90
2 3911 19A 20K C N 144 146 -159.31 -118.00 42.45 1.78 -62.90 -164.45 22.48
2 20K 20K N CA 146 147 129.33 139.10 -40.80
3 3912 20K 21R C N 153 155 -129.88 -125.20 5.61 0.17 -63.00 -172.45 29.94
3 21R 21R N CA 155 156 143.68 140.60 -41.10
4 3913 21R 22F C N 164 166 -66.69 -71.40 6.06 0.34 -63.20 178.85 25.07
4 22F 22F N CA 166 167 136.88 140.70 -44.30
5 3914 22F 23T C N 175 177 -84.83 -78.10 22.30 0.77 -63.20 148.42 20.48
5 23T 23T N CA 177 178 171.06 149.80 -42.10
6 3915 23T 24R C N 182 184 -100.64 -125.20 27.02 1.36 -63.00 171.22 25.73
6 24R 24R N CA 184 185 151.87 140.60 -41.10
7 3917 25C 26G C N 199 201 78.90 78.70 11.79 0.34 82.20 162.85 8.07
7 26G 26G N CA 201 202 -154.32 -166.10 8.50
8 3918 26G 27L C N 203 205 -64.31 -70.70 7.05 0.53 -63.50 179.80 24.92
8 27L 27L N CA 205 206 138.60 141.60 -41.20
9 3920 28V 29Q C N 218 220 -81.86 -73.00 49.11 3.04 -63.80 131.93 20.36
9 29Q 29Q N CA 220 221 -170.99 140.70 -40.30
10 3921 29Q 30E C N 227 229 -64.42 -69.30 5.16 0.44 -63.60 175.53 23.45
10 30E 30E N CA 229 230 144.17 142.50 -40.30
11 3922 30E 31L C N 236 238 -79.34 -70.70 13.45 0.84 -63.50 167.65 24.22
11 31L 31L N CA 238 239 151.90 141.60 -41.20
12 3923 31L 32R C N 244 246 -90.22 -72.10 18.73 1.33 -63.00 174.41 25.43
12 32R 32R N CA 246 247 146.63 141.90 -41.10
13 3924 32R 33R C N 255 257 -66.38 -72.10 11.37 0.97 -63.00 167.22 22.82
13 33R 33R N CA 257 258 151.72 141.90 -41.10
14 3925 33R 34L C N 266 268 -105.35 -108.50 29.37 1.62 -63.50 162.57 25.14
14 34L 34L N CA 268 269 161.71 132.50 -41.20
15 3926 34L 35G C N 274 276 103.61 78.70 58.60 0.87 82.20 134.07 7.57
15 35G 35G N CA 276 277 140.85 -166.10 8.50
16 3929 37D 38E C N 297 299 56.54 54.60 1.96 0.24 -63.60 145.97 25.10
16 38E 38E N CA 299 300 42.60 42.40 -40.30
17 3953 61K 62V C N 488 490 -56.37 -62.40 20.80 3.00 -125.40 179.59 6.89
17 62V 62V N CA 490 491 -22.49 -42.40 143.30
18 3970 78K 79Y C N 626 628 -108.08 -63.50 45.65 7.38 -63.50 45.65 7.38
18 79Y 79Y N CA 628 629 -33.57 -43.40 -43.40
19 3981 89K 90D C N 711 713 -155.88 -63.30 101.97 17.39 -63.30 101.97 17.39
19 90D 90D N CA 713 714 -82.74 -40.00 -40.00
20 4005 113I 114Y C N 884 886 -56.75 -98.40 47.00 2.97 -63.50 150.18 24.18
20 114Y 114Y N CA 886 887 106.63 128.40 -43.40
21 4007 115K 116R C N 905 907 -81.26 -125.20 76.06 2.53 -63.00 121.00 15.20
21 116R 116R N CA 907 908 78.52 140.60 -41.10
22 4008 116R 117H C N 916 918 -165.62 -63.20 102.71 15.90 -63.20 102.71 15.90
22 117H 117H N CA 918 919 -34.67 -42.30 -42.30
23 4020 128H 129C C N 1030 1032 -126.10 -63.00 73.82 9.59 -63.00 73.82 9.59
23 129C 129C N CA 1032 1033 -2.79 -41.10 -41.10
24 4025 133L 134P C N 1067 1069 -173.95 -58.70 122.17 12.93 -58.70 122.17 12.93
24 134P 134P N CA 1069 1070 10.04 -30.50 -30.50
-------------------------------------------------------------------------------------------------
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 11056 113I 140. CA O6 879 1125 7.31 6.37 0.95 4.74 6.37 0.95 4.74
2 11068 114Y 140. CA O6 887 1125 9.12 8.22 0.90 4.51 8.22 0.90 4.51
3 11078 115K 140. CA O6 899 1125 7.13 5.07 2.06 10.30 5.07 2.06 10.30
4 11094 116R 140. CA O6 908 1125 8.99 6.81 2.17 10.86 6.81 2.17 10.86
5 11110 117H 140. CA O6 919 1125 8.78 6.72 2.06 10.30 6.72 2.06 10.30
6 11121 118K 140. CA O6 929 1125 10.32 8.23 2.09 10.47 8.23 2.09 10.47
7 11139 120D 140. CA O6 949 1125 11.43 9.75 1.67 8.35 9.75 1.67 8.35
8 11169 121A 140. CA O6 957 1125 8.27 6.94 1.33 6.63 6.94 1.33 6.63
9 11632 140. 140. C7 O6 1119 1125 6.69 6.44 0.25 5.02 6.44 0.25 5.02
10 11671 140. 140. O3 O6 1122 1125 5.20 4.85 0.35 7.03 4.85 0.35 7.03
11 11705 140. 140. O6 C7 1125 1119 6.69 6.44 0.25 5.02 6.44 0.25 5.02
12 11708 140. 140. O6 O3 1125 1122 5.20 4.85 0.35 7.03 4.85 0.35 7.03
13 11711 140. 140. O6 O7 1125 1126 7.08 6.45 0.63 12.53 6.45 0.63 12.53
14 11724 140. 140. O7 O6 1126 1125 7.08 6.45 0.63 12.53 6.45 0.63 12.53
15 12117 140. 83K O6 CG 1125 669 7.30 3.00 4.30 43.03 3.00 4.30 43.03
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 17 22 84 85 119 135 133 193 172 204
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
HYACE.B99990001.pdb 3121.69336
Отлично! Теперь мы умеем моделировать структуру белка используя известную, а также модифицировать результат. Теперь попробуем построить структуру лизоцима с лигандом где все аминокислоты аланин:
In [50]:
with open('P05105.fasta', 'r') as f:
lines = f.readlines()
prot = "".join([lines[1].strip('\n'), lines[2].strip('\n'), lines[3].strip('\n')])
polyala = "". join(["A" for i in range(1, len(prot))])
with open ('polyala.fasta', 'w') as f:
f.write(lines[0])
f.write(polyala + '\n')
In [4]:
alignm=modeller.alignment(env)
alignm.append(file='polyala.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
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.
In [6]:
alignm[0].code = 'NE_HYASE'
alignm[1].code = '1LMP'
In [8]:
alignm.salign()
alignm.write(file='nehyase.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [9]:
! cat nehyase.ali
>P1;NE_HYASE sequence:: : : : :::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA* >P1;1LMP structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------WCDDGRT PGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Добавим в выравнивание лиганд...
In [10]:
! cat nehyase.ali
>P1;NE_HYASE sequence:: : : : :::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...* >P1;1LMP structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY------WCDDGRT PGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV---...*
In [11]:
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='nehyase.ali', knowns= pdb.code, sequence = s.code )
a.name='alamod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
NE_HYASE 1LMP
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 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: 1 138
atom names : C +N
atom indices : 689 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 1 138
atom names : C CA +N O
atom indices : 689 687 0 690
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 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: 10322 9639
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 141
Number of all, selected real atoms : 734 734
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9639 9639
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1480
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 : 853.3341
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 : 690 0 0 0.010 0.010 18.009 1.000
2 Bond angle potential : 965 4 12 2.757 2.757 150.18 1.000
3 Stereochemical cosine torsion poten: 280 0 34 76.400 76.400 266.31 1.000
4 Stereochemical improper torsion pot: 276 0 2 1.648 1.648 15.522 1.000
5 Soft-sphere overlap restraints : 1480 1 2 0.012 0.012 23.405 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 3 0.321 0.321 86.224 1.000
10 Distance restraints 2 (N-O) : 2564 0 4 0.383 0.383 124.19 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: 137 0 6 5.384 5.384 46.836 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 0.249 0.249 4.9908 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: 136 24 22 33.665 67.863 93.248 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.837 0.837 3.8312 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.042 0.042 20.587 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: NE_HYASE.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: 12971.1133
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1126 63A 63A N CA 311 312 125.23 107.00 18.23 5.24 107.00 18.23 5.24
2 1130 63A 64A C N 314 316 140.81 120.00 20.81 4.73 120.00 20.81 4.73
3 1133 64A 64A N CA 316 317 125.18 107.00 18.18 5.23 107.00 18.18 5.23
4 1168 69A 69A N CA 341 342 127.90 107.00 20.90 6.01 107.00 20.90 6.01
-------------------------------------------------------------------------------------------------
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 2226 15A 16A C N 74 76 78.66 55.40 27.05 1.98 -62.50 155.53 31.59
1 16A 16A N CA 76 77 24.40 38.20 -40.90
2 2229 18A 19A C N 89 91 65.61 55.40 24.25 0.88 -62.50 140.26 28.48
2 19A 19A N CA 91 92 16.20 38.20 -40.90
3 2231 20A 21A C N 99 101 54.72 55.40 6.23 0.43 -62.50 138.04 28.06
3 21A 21A N CA 101 102 32.01 38.20 -40.90
4 2232 21A 22A C N 104 106 64.13 55.40 13.45 0.63 -62.50 144.14 29.32
4 22A 22A N CA 106 107 27.97 38.20 -40.90
5 2247 36A 37A C N 179 181 66.87 55.40 13.40 0.97 -62.50 148.13 30.13
5 37A 37A N CA 181 182 31.26 38.20 -40.90
6 2248 37A 38A C N 184 186 62.40 55.40 10.60 0.51 -62.50 143.73 29.23
6 38A 38A N CA 186 187 30.23 38.20 -40.90
7 2259 48A 49A C N 239 241 84.53 55.40 39.24 2.23 -62.50 156.23 31.59
7 49A 49A N CA 241 242 11.91 38.20 -40.90
8 2264 53A 54A C N 264 266 91.70 -134.00 139.45 3.42 -62.50 -155.34 32.13
8 54A 54A N CA 266 267 -175.47 147.00 -40.90
9 2267 56A 57A C N 279 281 59.80 55.40 13.37 1.16 -62.50 152.87 30.95
9 57A 57A N CA 281 282 50.82 38.20 -40.90
10 2273 62A 63A C N 309 311 84.17 -134.00 148.21 3.57 -62.50 -164.62 30.65
10 63A 63A N CA 311 312 -169.98 147.00 -40.90
11 2275 64A 65A C N 319 321 -128.66 -134.00 96.60 5.60 -62.50 100.50 19.89
11 65A 65A N CA 321 322 -116.55 147.00 -40.90
12 2276 65A 66A C N 324 326 -69.06 -68.20 12.56 1.04 -62.50 173.79 28.17
12 66A 66A N CA 326 327 132.77 145.30 -40.90
13 2277 66A 67A C N 329 331 5.37 -68.20 78.37 5.68 -62.50 173.04 31.99
13 67A 67A N CA 331 332 118.28 145.30 -40.90
14 2278 67A 68A C N 334 336 127.57 -134.00 131.60 3.70 -62.50 -170.11 38.60
14 68A 68A N CA 336 337 -125.64 147.00 -40.90
15 2279 68A 69A C N 339 341 -68.16 -62.50 59.12 9.98 -62.50 59.12 9.98
15 69A 69A N CA 341 342 -99.75 -40.90 -40.90
16 2283 72A 73A C N 359 361 80.11 55.40 56.14 2.03 -62.50 145.47 28.97
16 73A 73A N CA 361 362 -12.21 38.20 -40.90
17 2287 76A 77A C N 379 381 60.44 55.40 7.66 0.37 -62.50 143.15 29.11
17 77A 77A N CA 381 382 32.43 38.20 -40.90
18 2290 79A 80A C N 394 396 66.29 55.40 20.39 2.08 -62.50 160.83 32.57
18 80A 80A N CA 396 397 55.43 38.20 -40.90
19 2293 82A 83A C N 409 411 77.49 55.40 23.60 2.05 -62.50 156.88 31.90
19 83A 83A N CA 411 412 29.91 38.20 -40.90
20 2320 109A 110A C N 544 546 81.49 -134.00 159.16 3.61 -62.50 178.44 28.66
20 110A 110A N CA 546 547 -146.30 147.00 -40.90
21 2332 121A 122A C N 604 606 38.20 -68.20 119.39 11.55 -68.20 119.39 11.55
21 122A 122A N CA 606 607 -160.55 145.30 145.30
22 2333 122A 123A C N 609 611 -83.60 -68.20 48.07 4.38 -62.50 142.24 22.37
22 123A 123A N CA 611 612 99.77 145.30 -40.90
23 2342 131A 132A C N 654 656 63.46 55.40 8.79 0.73 -62.50 146.89 29.87
23 132A 132A N CA 656 657 34.68 38.20 -40.90
24 2347 136A 137A C N 679 681 -71.67 -68.20 7.71 0.51 -62.50 167.17 27.85
24 137A 137A N CA 681 682 152.18 145.30 -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 11 10 58 60 84 73 93 121 121 115
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 141
Number of all, selected real atoms : 734 734
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9639 9639
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1432
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 : 824.9315
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 : 690 0 1 0.009 0.009 15.835 1.000
2 Bond angle potential : 965 2 9 2.648 2.648 142.22 1.000
3 Stereochemical cosine torsion poten: 280 0 37 77.628 77.628 273.56 1.000
4 Stereochemical improper torsion pot: 276 0 0 1.288 1.288 11.542 1.000
5 Soft-sphere overlap restraints : 1432 1 2 0.012 0.012 22.563 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 0.247 0.247 59.651 1.000
10 Distance restraints 2 (N-O) : 2564 0 9 0.383 0.383 139.56 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: 137 1 6 5.683 5.683 52.171 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 0.246 0.246 5.1380 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: 136 24 23 31.478 70.567 68.379 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.431 0.431 1.0705 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.055 0.055 33.240 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: NE_HYASE.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: 13173.6553
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1119 62A 62A N CA 306 307 131.67 107.00 24.67 7.09 107.00 24.67 7.09
-------------------------------------------------------------------------------------------------
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 2383 36A 36A CA C 177 179 -154.99 -180.00 25.01 5.00 -180.00 25.01 5.00
-------------------------------------------------------------------------------------------------
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 2226 15A 16A C N 74 76 78.99 55.40 27.75 1.99 -62.50 155.49 31.58
1 16A 16A N CA 76 77 23.59 38.20 -40.90
2 2229 18A 19A C N 89 91 65.38 55.40 23.68 0.86 -62.50 140.26 28.48
2 19A 19A N CA 91 92 16.72 38.20 -40.90
3 2231 20A 21A C N 99 101 54.08 55.40 5.14 0.42 -62.50 138.15 28.07
3 21A 21A N CA 101 102 33.23 38.20 -40.90
4 2232 21A 22A C N 104 106 62.15 55.40 8.93 0.52 -62.50 144.57 29.40
4 22A 22A N CA 106 107 32.34 38.20 -40.90
5 2247 36A 37A C N 179 181 78.07 55.40 151.45 11.00 -62.50 -167.74 29.95
5 37A 37A N CA 181 182 -172.06 38.20 -40.90
6 2259 48A 49A C N 239 241 84.69 55.40 39.84 2.23 -62.50 156.14 31.56
6 49A 49A N CA 241 242 11.20 38.20 -40.90
7 2264 53A 54A C N 264 266 92.40 -134.00 139.20 3.38 -62.50 -155.80 32.12
7 54A 54A N CA 266 267 -173.95 147.00 -40.90
8 2267 56A 57A C N 279 281 61.17 55.40 12.33 1.20 -62.50 152.95 31.00
8 57A 57A N CA 281 282 49.09 38.20 -40.90
9 2272 61A 62A C N 304 306 -97.36 -62.50 41.12 8.36 -62.50 41.12 8.36
9 62A 62A N CA 306 307 -62.72 -40.90 -40.90
10 2273 62A 63A C N 309 311 -178.37 -134.00 46.76 1.10 -62.50 -164.57 38.12
10 63A 63A N CA 311 312 161.73 147.00 -40.90
11 2274 63A 64A C N 314 316 -166.21 -134.00 70.57 4.35 -62.50 162.50 24.70
11 64A 64A N CA 316 317 84.21 147.00 -40.90
12 2275 64A 65A C N 319 321 -0.17 -68.20 74.32 5.23 -62.50 168.25 30.91
12 65A 65A N CA 321 322 115.38 145.30 -40.90
13 2276 65A 66A C N 324 326 134.70 -134.00 113.84 2.91 -62.50 -166.76 39.26
13 66A 66A N CA 326 327 -145.00 147.00 -40.90
14 2278 67A 68A C N 334 336 -160.84 -134.00 31.69 1.68 -62.50 -162.68 29.56
14 68A 68A N CA 336 337 130.16 147.00 -40.90
15 2283 72A 73A C N 359 361 78.82 55.40 58.63 2.13 -62.50 143.57 28.50
15 73A 73A N CA 361 362 -15.55 38.20 -40.90
16 2287 76A 77A C N 379 381 51.13 55.40 13.47 0.52 -62.50 146.12 29.51
16 77A 77A N CA 381 382 50.97 38.20 -40.90
17 2290 79A 80A C N 394 396 57.88 55.40 33.63 2.23 -62.50 164.86 33.06
17 80A 80A N CA 396 397 71.74 38.20 -40.90
18 2293 82A 83A C N 409 411 71.33 55.40 16.28 1.89 -62.50 157.19 31.95
18 83A 83A N CA 411 412 41.55 38.20 -40.90
19 2320 109A 110A C N 544 546 80.71 -134.00 159.90 3.63 -62.50 177.78 28.54
19 110A 110A N CA 546 547 -146.25 147.00 -40.90
20 2333 122A 123A C N 609 611 50.11 55.40 9.62 0.38 -62.50 142.38 28.80
20 123A 123A N CA 611 612 46.23 38.20 -40.90
21 2342 131A 132A C N 654 656 70.66 55.40 39.82 1.45 -62.50 139.72 28.17
21 132A 132A N CA 656 657 1.41 38.20 -40.90
22 2344 133A 134A C N 664 666 62.06 55.40 9.67 0.49 -62.50 143.91 29.27
22 134A 134A N CA 666 667 31.18 38.20 -40.90
23 2346 135A 136A C N 674 676 -74.43 -68.20 10.00 0.63 -62.50 166.41 27.87
23 136A 136A N CA 676 677 153.12 145.30 -40.90
24 2347 136A 137A C N 679 681 -74.17 -68.20 8.50 0.54 -62.50 168.16 28.15
24 137A 137A N CA 681 682 151.35 145.30 -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 9 7 54 58 78 75 90 117 107 104
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
NE_HYASE.B99990001.pdb 853.33411
NE_HYASE.B99990002.pdb 824.93146
Значение скор функции заметно уменьшилось: 853 в лучшем случае против ~1100 в случае "нативной" последовательности. Посмотрим как же это выглядит:
