In [2]:
import numpy as np
from IPython.display import display,Image
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): 2017/05/26 13:06:11
В этом практикуме будем моделировать лизоцим тутового шелкопряда по известной структуре лизоцим радужной форели
In [4]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
! wget http://www.uniprot.org/uniprot/P48816.fasta # LYS_BOMMO
--2017-05-26 13:11:40-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 132.249.231.77
Connecting to www.pdb.org|132.249.231.77|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-05-26 13:11:40-- http://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 132.249.231.10
Connecting to www.rcsb.org|132.249.231.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-05-26 13:11:41-- 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'
[ <=> ] 131,301 251K/s in 0.5s
2017-05-26 13:11:41 (251 KB/s) - `1lmp.pdb' saved [131301]
--2017-05-26 13:11:41-- http://www.uniprot.org/uniprot/P48816.fasta
Resolving www.uniprot.org... 193.62.193.81, 128.175.240.211
Connecting to www.uniprot.org|193.62.193.81|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 195 [text/plain]
Saving to: `P48816.fasta'
100%[======================================>] 195 --.-K/s in 0s
2017-05-26 13:11:42 (16.1 MB/s) - `P48816.fasta' saved [195/195]
In [5]:
alignm=modeller.alignment(env)
alignm.append(file='P48816.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 = 'QUERY'
alignm[1].code = 'TARGET'
In [7]:
alignm.salign()
alignm.write(file='bommo.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [8]:
%cat bommo.ali
>P1;QUERY sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC-------* >P1;TARGET 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 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
В QUERY нет лиганда! Добавим его
In [9]:
with open('bommo.ali','r') as bommo:
lines = bommo.readlines()
with open('bommo.ali','w') as bommo:
for c, line in enumerate(lines):
if c == 4:
line = line[:-5]+'...*'
bommo.write(line)
%cat bommo.ali
>P1;QUERY sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC----...* >P1;TARGET 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 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Теперь все в порядке, можно моделировать
In [10]:
query = alignm[0]
target = alignm[1]
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='bommo.ali', knowns = target.code, sequence = query.code )
a.name='mod'+query.code
a.starting_model = 1
a.ending_model = 10
a.make()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
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: 2 137
atom names : C +N
atom indices : 1094 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 2 137
atom names : C CA +N O
atom indices : 1094 1091 0 1095
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: 13094 12134
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2349
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 : 1038.5112
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 : 1119 0 6 0.010 0.010 31.274 1.000
2 Bond angle potential : 1504 1 10 2.309 2.309 160.69 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.457 47.457 251.10 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.259 1.259 16.344 1.000
5 Soft-sphere overlap restraints : 2349 1 2 0.008 0.008 17.080 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) : 2215 0 3 0.290 0.290 98.473 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.343 0.343 140.84 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: 136 0 4 4.800 4.800 36.946 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 81.276 81.276 39.084 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 68.860 68.860 37.505 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 75.377 75.377 23.887 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 92.762 92.762 14.219 1.000
18 Disulfide distance restraints : 3 0 0 0.030 0.030 0.46541 1.000
19 Disulfide angle restraints : 6 0 0 5.185 5.185 3.5616 1.000
20 Disulfide dihedral angle restraints: 3 0 0 38.498 38.498 2.8015 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) : 1316 0 0 0.390 0.390 33.777 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: 135 15 16 26.079 56.345 78.077 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.591 0.591 28.608 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.045 0.045 23.785 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: QUERY.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: 15816.2100
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 2080 88D 88D N CA 697 698 128.39 107.00 21.39 6.15 107.00 21.39 6.15
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -113.96 -121.10 23.82 1.22 -63.80 165.08 26.94
1 2Q 2Q N CA 9 10 162.42 139.70 -40.30
2 3811 2Q 3K C N 16 18 -69.81 -70.20 52.59 3.82 -62.90 126.40 16.80
2 3K 3K N CA 18 19 -167.01 140.40 -40.80
3 3812 3K 4L C N 25 27 -57.83 -70.70 13.76 1.07 -63.50 178.01 25.05
3 4L 4L N CA 27 28 136.72 141.60 -41.20
4 3815 6I 7F C N 49 51 -93.62 -71.40 25.65 1.44 -63.20 165.02 24.96
4 7F 7F N CA 51 52 153.51 140.70 -44.30
5 3816 7F 8A C N 60 62 -65.09 -68.20 25.68 1.96 -62.50 160.73 26.22
5 8A 8A N CA 62 63 119.81 145.30 -40.90
6 3820 11V 12L C N 87 89 -58.64 -70.70 21.22 1.31 -63.50 165.41 23.25
6 12L 12L N CA 89 90 124.14 141.60 -41.20
7 3823 14V 15G C N 108 110 -84.44 -80.20 33.95 1.13 82.20 -128.49 17.81
7 15G 15G N CA 110 111 -152.21 174.10 8.50
8 3824 15G 16S C N 112 114 -64.10 -72.40 34.23 1.75 -64.10 154.20 11.17
8 16S 16S N CA 114 115 119.20 152.40 -35.00
9 3844 35F 36E C N 274 276 56.44 54.60 10.85 0.69 -63.60 139.98 24.09
9 36E 36E N CA 276 277 31.71 42.40 -40.30
10 3860 51S 52S C N 411 413 64.99 56.90 10.63 0.70 -64.10 144.31 19.17
10 52S 52S N CA 413 414 29.50 36.40 -35.00
11 3896 87K 88D C N 695 697 -144.25 -63.30 85.60 14.50 -63.30 85.60 14.50
11 88D 88D N CA 697 698 -67.81 -40.00 -40.00
12 3920 111I 112Y C N 872 874 -33.91 -98.40 68.53 3.71 -63.50 151.53 25.56
12 112Y 112Y N CA 874 875 105.21 128.40 -43.40
13 3923 114R 115H C N 904 906 -89.18 -125.60 51.83 1.28 -63.20 146.55 16.85
13 115H 115H N CA 906 907 101.92 138.80 -42.30
14 3924 115H 116R C N 914 916 -58.70 -63.00 71.32 9.35 -125.20 126.08 6.98
14 116R 116R N CA 916 917 -112.29 -41.10 140.60
15 3935 126H 127C C N 1020 1022 -115.80 -63.00 54.08 8.32 -63.00 54.08 8.32
15 127C 127C N CA 1022 1023 -29.40 -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 11 10 61 70 123 125 129 161 180 171
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2465
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 : 1175.5990
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 : 1119 0 3 0.010 0.010 30.784 1.000
2 Bond angle potential : 1504 3 13 3.173 3.173 210.17 1.000
3 Stereochemical cosine torsion poten: 713 0 32 48.300 48.300 266.86 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.457 1.457 20.444 1.000
5 Soft-sphere overlap restraints : 2465 1 2 0.008 0.008 16.974 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) : 2215 0 7 0.327 0.327 126.20 1.000
10 Distance restraints 2 (N-O) : 2371 0 10 0.352 0.352 162.41 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.856 4.856 37.822 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 77.620 77.620 41.398 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 74.150 74.150 38.510 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.183 80.183 27.542 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 77.127 77.127 14.873 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.41158 1.000
19 Disulfide angle restraints : 6 0 0 3.953 3.953 2.0703 1.000
20 Disulfide dihedral angle restraints: 3 0 0 10.414 10.414 0.38689 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) : 1316 0 0 0.347 0.347 26.762 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: 135 21 23 29.896 69.257 92.121 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.669 0.669 36.469 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.046 0.046 23.387 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: QUERY.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: 16628.3516
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 2080 88D 88D N CA 697 698 126.39 107.00 19.39 5.58 107.00 19.39 5.58
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -64.45 -73.00 10.01 0.78 -63.80 173.79 25.59
1 2Q 2Q N CA 9 10 145.91 140.70 -40.30
2 3811 2Q 3K C N 16 18 -63.46 -70.20 6.93 0.47 -62.90 179.58 23.29
2 3K 3K N CA 18 19 138.78 140.40 -40.80
3 3812 3K 4L C N 25 27 -112.92 -108.50 14.84 0.75 -63.50 179.08 27.91
3 4L 4L N CA 27 28 146.67 132.50 -41.20
4 3815 6I 7F C N 49 51 -156.83 -124.20 36.14 1.82 -63.20 -164.10 22.33
4 7F 7F N CA 51 52 127.77 143.30 -44.30
5 3816 7F 8A C N 60 62 -168.80 -134.00 42.47 1.06 -62.50 -177.98 35.43
5 8A 8A N CA 62 63 171.35 147.00 -40.90
6 3817 8A 9L C N 65 67 -126.72 -108.50 26.56 1.20 -63.50 178.54 28.70
6 9L 9L N CA 67 68 151.82 132.50 -41.20
7 3819 10V 11V C N 80 82 -56.60 -62.40 5.91 0.88 -125.40 -173.67 10.51
7 11V 11V N CA 82 83 -43.53 -42.40 143.30
8 3820 11V 12L C N 87 89 -107.77 -108.50 32.39 1.74 -63.50 148.09 18.55
8 12L 12L N CA 89 90 100.12 132.50 -41.20
9 3823 14V 15G C N 108 110 -97.99 -80.20 43.40 1.02 82.20 -122.73 8.10
9 15G 15G N CA 110 111 -146.31 174.10 8.50
10 3824 15G 16S C N 112 114 -85.58 -72.40 45.38 3.12 -64.10 145.57 9.48
10 16S 16S N CA 114 115 108.98 152.40 -35.00
11 3844 35F 36E C N 274 276 55.42 54.60 9.35 0.66 -63.60 139.82 24.06
11 36E 36E N CA 276 277 33.08 42.40 -40.30
12 3860 51S 52S C N 411 413 63.54 56.90 8.00 0.61 -64.10 144.13 19.10
12 52S 52S N CA 413 414 31.95 36.40 -35.00
13 3896 87K 88D C N 695 697 -141.25 -63.30 84.14 14.32 -63.30 84.14 14.32
13 88D 88D N CA 697 698 -71.67 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -45.32 -98.40 57.12 3.22 -63.50 151.78 25.02
14 112Y 112Y N CA 874 875 107.29 128.40 -43.40
15 3934 125N 126H C N 1010 1012 -131.40 -63.20 91.05 10.50 -63.20 91.05 10.50
15 126H 126H N CA 1012 1013 18.03 -42.30 -42.30
16 3935 126H 127C C N 1020 1022 -134.13 -63.00 74.04 11.06 -63.00 74.04 11.06
16 127C 127C N CA 1022 1023 -20.53 -41.10 -41.10
17 3936 127C 128Q C N 1026 1028 -63.57 -63.80 7.94 1.18 -121.10 -178.57 7.51
17 128Q 128Q N CA 1028 1029 -32.36 -40.30 139.70
18 3937 128Q 129G C N 1035 1037 -59.72 -62.40 12.73 2.04 82.20 146.73 10.95
18 129G 129G N CA 1037 1038 -28.76 -41.20 8.50
19 3938 129G 130S C N 1039 1041 79.78 56.90 27.15 2.12 -72.40 -159.46 9.81
19 130S 130S N CA 1041 1042 21.79 36.40 152.40
20 3939 130S 131L C N 1045 1047 -66.29 -63.50 4.19 0.53 -108.50 175.72 9.00
20 131L 131L N CA 1047 1048 -38.08 -41.20 132.50
21 3940 131L 132P C N 1053 1055 -41.99 -64.50 77.44 4.77 -58.70 104.94 10.05
21 132P 132P N CA 1055 1056 73.10 147.20 -30.50
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 9 13 74 70 127 127 157 166 173 184
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2436
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 : 1160.8132
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 : 1119 0 3 0.010 0.010 29.587 1.000
2 Bond angle potential : 1504 1 14 2.323 2.323 164.10 1.000
3 Stereochemical cosine torsion poten: 713 0 30 48.073 48.073 255.46 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.429 1.429 21.312 1.000
5 Soft-sphere overlap restraints : 2436 1 2 0.008 0.008 17.467 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) : 2215 0 5 0.296 0.296 107.22 1.000
10 Distance restraints 2 (N-O) : 2371 3 21 0.393 0.393 221.57 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: 136 0 3 4.933 4.933 39.028 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 78.376 78.376 44.378 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 80.155 80.155 42.224 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 1 73.497 73.497 24.664 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 75.565 75.565 14.609 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.27425 1.000
19 Disulfide angle restraints : 6 0 0 2.493 2.493 0.82362 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.659 21.659 1.3853 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) : 1316 0 0 0.334 0.334 25.828 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: 135 19 22 25.604 68.119 88.472 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.627 0.627 34.536 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.050 0.050 27.880 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: QUERY.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: 16680.0664
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 2080 88D 88D N CA 697 698 129.35 107.00 22.35 6.43 107.00 22.35 6.43
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8023 86G 63N N O 684 508 10.66 7.27 3.39 4.79 7.27 3.39 4.79
2 8033 87K 63N N O 688 508 12.08 8.66 3.42 5.72 8.66 3.42 5.72
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -83.93 -73.00 33.41 1.99 -63.80 148.79 22.95
1 2Q 2Q N CA 9 10 172.28 140.70 -40.30
2 3811 2Q 3K C N 16 18 -65.36 -70.20 11.56 0.94 -62.90 168.33 21.99
2 3K 3K N CA 18 19 150.89 140.40 -40.80
3 3812 3K 4L C N 25 27 -83.50 -70.70 30.20 2.77 -63.50 156.73 20.70
3 4L 4L N CA 27 28 114.25 141.60 -41.20
4 3815 6I 7F C N 49 51 -154.71 -124.20 33.25 0.94 -63.20 -176.38 31.28
4 7F 7F N CA 51 52 156.51 143.30 -44.30
5 3816 7F 8A C N 60 62 -130.88 -134.00 6.10 0.24 -62.50 -169.93 34.81
5 8A 8A N CA 62 63 141.75 147.00 -40.90
6 3817 8A 9L C N 65 67 -71.02 -70.70 0.50 0.03 -63.50 176.98 25.01
6 9L 9L N CA 67 68 141.98 141.60 -41.20
7 3820 11V 12L C N 87 89 -99.05 -108.50 9.98 0.52 -63.50 -179.55 23.26
7 12L 12L N CA 89 90 135.71 132.50 -41.20
8 3824 15G 16S C N 112 114 -64.40 -72.40 38.36 1.99 -64.10 149.89 10.84
8 16S 16S N CA 114 115 114.88 152.40 -35.00
9 3841 32K 33H C N 249 251 -55.53 -63.20 8.93 1.12 -125.60 -172.12 8.22
9 33H 33H N CA 251 252 -46.87 -42.30 138.80
10 3842 33H 34G C N 259 261 -88.45 -62.40 30.43 4.61 82.20 174.00 12.74
10 34G 34G N CA 261 262 -25.46 -41.20 8.50
11 3844 35F 36E C N 274 276 51.99 54.60 6.64 0.71 -63.60 138.67 23.85
11 36E 36E N CA 276 277 36.29 42.40 -40.30
12 3859 50E 51S C N 405 407 -137.00 -64.10 83.39 8.41 -64.10 83.39 8.41
12 51S 51S N CA 407 408 5.49 -35.00 -35.00
13 3860 51S 52S C N 411 413 55.53 56.90 2.33 0.26 -64.10 138.36 18.22
13 52S 52S N CA 413 414 34.52 36.40 -35.00
14 3871 62R 63N C N 499 501 -69.91 -119.90 67.37 3.64 -63.20 136.90 17.49
14 63N 63N N CA 501 502 -177.83 137.00 -41.10
15 3872 63N 64G C N 507 509 -64.47 -62.40 23.46 3.41 82.20 149.02 10.84
15 64G 64G N CA 509 510 -17.84 -41.20 8.50
16 3896 87K 88D C N 695 697 171.77 -96.50 95.45 3.88 -63.30 178.75 20.10
16 88D 88D N CA 697 698 87.85 114.20 -40.00
17 3920 111I 112Y C N 872 874 -33.86 -98.40 66.87 3.29 -63.50 157.11 26.45
17 112Y 112Y N CA 874 875 110.89 128.40 -43.40
18 3923 114R 115H C N 904 906 -89.82 -125.60 53.18 1.33 -63.20 144.24 16.54
18 115H 115H N CA 906 907 99.46 138.80 -42.30
19 3924 115H 116R C N 914 916 -58.25 -63.00 69.93 9.14 -125.20 127.53 7.06
19 116R 116R N CA 916 917 -110.87 -41.10 140.60
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 15 64 81 125 115 121 169 195 203
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2340
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 : 1106.0771
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 : 1119 0 6 0.009 0.009 29.015 1.000
2 Bond angle potential : 1504 6 16 3.745 3.745 240.38 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.763 47.763 257.79 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.284 1.284 16.483 1.000
5 Soft-sphere overlap restraints : 2340 1 2 0.008 0.008 16.083 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) : 2215 0 2 0.306 0.306 100.70 1.000
10 Distance restraints 2 (N-O) : 2371 0 7 0.342 0.342 137.20 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: 136 0 1 4.217 4.217 28.527 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 76.593 76.593 38.746 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 70.364 70.364 31.623 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 82.666 82.666 22.747 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 95.433 95.433 13.616 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.39218 1.000
19 Disulfide angle restraints : 6 0 0 3.190 3.190 1.3482 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.944 21.944 1.4004 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) : 1316 0 0 0.401 0.401 39.298 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: 135 16 13 27.304 59.813 61.719 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.716 0.716 43.084 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 25.931 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: QUERY.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: 15853.2061
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 1814 63N 63N ND2 CG 506 504 138.73 122.50 16.23 4.52 122.50 16.23 4.52
2 2080 88D 88D N CA 697 698 128.10 107.00 21.10 6.07 107.00 21.10 6.07
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -92.01 -73.00 22.04 1.71 -63.80 172.17 23.92
1 2Q 2Q N CA 9 10 129.54 140.70 -40.30
2 3811 2Q 3K C N 16 18 -124.34 -118.00 12.71 0.50 -62.90 179.89 27.03
2 3K 3K N CA 18 19 150.12 139.10 -40.80
3 3812 3K 4L C N 25 27 -70.15 -70.70 9.53 0.74 -63.50 167.82 23.69
3 4L 4L N CA 27 28 151.11 141.60 -41.20
4 3815 6I 7F C N 49 51 -70.75 -71.40 3.87 0.33 -63.20 171.35 24.30
4 7F 7F N CA 51 52 144.51 140.70 -44.30
5 3816 7F 8A C N 60 62 -169.22 -134.00 56.39 1.93 -62.50 166.71 32.87
5 8A 8A N CA 62 63 -168.97 147.00 -40.90
6 3817 8A 9L C N 65 67 -60.11 -70.70 10.68 0.92 -63.50 178.65 24.61
6 9L 9L N CA 67 68 140.18 141.60 -41.20
7 3820 11V 12L C N 87 89 -78.95 -70.70 23.15 2.07 -63.50 161.91 21.64
7 12L 12L N CA 89 90 119.97 141.60 -41.20
8 3821 12L 13C C N 95 97 -65.55 -63.00 2.83 0.51 -117.90 -175.85 7.90
8 13C 13C N CA 97 98 -42.34 -41.10 141.10
9 3823 14V 15G C N 108 110 177.52 -167.20 16.85 0.51 82.20 -174.64 13.22
9 15G 15G N CA 110 111 167.48 174.60 8.50
10 3824 15G 16S C N 112 114 -141.92 -136.60 18.07 1.00 -64.10 -174.00 11.69
10 16S 16S N CA 114 115 133.93 151.20 -35.00
11 3844 35F 36E C N 274 276 49.63 54.60 5.18 0.67 -63.60 139.35 23.94
11 36E 36E N CA 276 277 40.93 42.40 -40.30
12 3859 50E 51S C N 405 407 -135.80 -64.10 81.21 8.29 -64.10 81.21 8.29
12 51S 51S N CA 407 408 3.14 -35.00 -35.00
13 3860 51S 52S C N 411 413 58.11 56.90 2.35 0.10 -64.10 140.53 18.54
13 52S 52S N CA 413 414 34.39 36.40 -35.00
14 3896 87K 88D C N 695 697 -142.27 -63.30 82.52 13.93 -63.30 82.52 13.93
14 88D 88D N CA 697 698 -63.94 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -40.79 -98.40 63.74 3.86 -63.50 146.30 24.38
15 112Y 112Y N CA 874 875 101.13 128.40 -43.40
16 3935 126H 127C C N 1020 1022 -121.14 -63.00 64.37 8.85 -63.00 64.37 8.85
16 127C 127C N CA 1022 1023 -13.47 -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 9 18 59 75 110 107 144 143 170 171
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2406
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 : 1049.3771
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 : 1119 0 4 0.010 0.010 29.477 1.000
2 Bond angle potential : 1504 1 12 2.284 2.284 161.18 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.715 47.715 254.24 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.250 1.250 16.306 1.000
5 Soft-sphere overlap restraints : 2406 1 2 0.008 0.008 16.093 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) : 2215 0 3 0.308 0.308 103.11 1.000
10 Distance restraints 2 (N-O) : 2371 2 11 0.371 0.371 172.76 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: 136 0 5 4.512 4.512 32.658 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 78.608 78.608 39.360 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 79.356 79.356 34.531 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 66.208 66.208 18.259 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 75.990 75.990 11.459 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.43446 1.000
19 Disulfide angle restraints : 6 0 0 4.119 4.119 2.2474 1.000
20 Disulfide dihedral angle restraints: 3 0 0 11.479 11.479 0.46403 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) : 1316 0 0 0.294 0.294 20.901 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: 135 18 19 28.173 63.206 74.528 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.662 0.662 36.666 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 24.691 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: QUERY.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: 15811.9824
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 2080 88D 88D N CA 697 698 128.85 107.00 21.85 6.28 107.00 21.85 6.28
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8023 86G 63N N O 684 508 10.75 7.27 3.48 4.91 7.27 3.48 4.91
2 8033 87K 63N N O 688 508 12.17 8.66 3.51 5.87 8.66 3.51 5.87
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -65.59 -73.00 14.86 1.12 -63.80 166.13 24.52
1 2Q 2Q N CA 9 10 153.58 140.70 -40.30
2 3811 2Q 3K C N 16 18 -69.37 -70.20 13.16 0.97 -62.90 165.79 21.89
2 3K 3K N CA 18 19 153.54 140.40 -40.80
3 3812 3K 4L C N 25 27 -67.86 -70.70 3.02 0.30 -63.50 176.23 24.72
3 4L 4L N CA 27 28 142.62 141.60 -41.20
4 3815 6I 7F C N 49 51 -65.79 -71.40 37.81 2.89 -63.20 147.64 20.33
4 7F 7F N CA 51 52 103.31 140.70 -44.30
5 3816 7F 8A C N 60 62 -173.76 -134.00 56.38 1.70 -62.50 172.74 34.08
5 8A 8A N CA 62 63 -173.04 147.00 -40.90
6 3817 8A 9L C N 65 67 -62.43 -70.70 18.37 1.15 -63.50 166.40 23.16
6 9L 9L N CA 67 68 125.19 141.60 -41.20
7 3818 9L 10V C N 73 75 -59.92 -62.40 8.46 0.95 -125.40 178.65 10.07
7 10V 10V N CA 75 76 -50.49 -42.40 143.30
8 3820 11V 12L C N 87 89 -86.56 -70.70 23.21 1.47 -63.50 161.91 23.87
8 12L 12L N CA 89 90 158.54 141.60 -41.20
9 3821 12L 13C C N 95 97 -60.06 -63.00 5.12 0.54 -117.90 -177.01 7.91
9 13C 13C N CA 97 98 -45.29 -41.10 141.10
10 3824 15G 16S C N 112 114 -60.92 -72.40 32.25 1.55 -64.10 157.30 11.59
10 16S 16S N CA 114 115 122.27 152.40 -35.00
11 3844 35F 36E C N 274 276 52.14 54.60 4.87 0.56 -63.60 139.85 24.05
11 36E 36E N CA 276 277 38.20 42.40 -40.30
12 3859 50E 51S C N 405 407 -139.98 -64.10 87.54 8.73 -64.10 87.54 8.73
12 51S 51S N CA 407 408 8.65 -35.00 -35.00
13 3860 51S 52S C N 411 413 58.49 56.90 3.28 0.14 -64.10 140.44 18.54
13 52S 52S N CA 413 414 33.53 36.40 -35.00
14 3871 62R 63N C N 499 501 -71.47 -119.90 72.28 3.92 -63.20 128.50 16.53
14 63N 63N N CA 501 502 -169.33 137.00 -41.10
15 3872 63N 64G C N 507 509 -68.80 -62.40 21.30 2.94 82.20 153.84 11.25
15 64G 64G N CA 509 510 -20.89 -41.20 8.50
16 3896 87K 88D C N 695 697 -141.12 -63.30 79.97 13.38 -63.30 79.97 13.38
16 88D 88D N CA 697 698 -58.42 -40.00 -40.00
17 3920 111I 112Y C N 872 874 -47.73 -98.40 53.78 2.90 -63.50 154.59 25.34
17 112Y 112Y N CA 874 875 110.38 128.40 -43.40
18 3935 126H 127C C N 1020 1022 -125.59 -63.00 73.87 9.52 -63.00 73.87 9.52
18 127C 127C N CA 1022 1023 -1.87 -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 7 9 61 77 120 118 139 153 194 176
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2439
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 : 1017.0812
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 : 1119 0 2 0.009 0.009 27.064 1.000
2 Bond angle potential : 1504 1 11 2.303 2.303 160.28 1.000
3 Stereochemical cosine torsion poten: 713 0 32 48.429 48.429 261.95 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.418 1.418 19.653 1.000
5 Soft-sphere overlap restraints : 2439 1 2 0.007 0.007 16.189 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) : 2215 0 4 0.295 0.295 98.217 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.329 0.329 132.88 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: 136 0 2 4.384 4.384 30.829 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 74.488 74.488 36.822 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 68.394 68.394 33.832 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 79.885 79.885 21.858 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 91.323 91.323 14.015 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.44983 1.000
19 Disulfide angle restraints : 6 0 0 2.576 2.576 0.87913 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.135 21.135 1.4325 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) : 1316 0 0 0.325 0.325 24.106 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: 135 15 17 32.965 59.892 82.161 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.618 0.618 30.613 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.046 0.046 23.846 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: QUERY.V99990006
# 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: 15340.9385
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 2080 88D 88D N CA 697 698 128.24 107.00 21.24 6.11 107.00 21.24 6.11
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -118.47 -121.10 18.73 0.93 -63.80 170.46 27.97
1 2Q 2Q N CA 9 10 158.24 139.70 -40.30
2 3811 2Q 3K C N 16 18 -72.26 -70.20 14.07 0.97 -62.90 165.15 21.97
2 3K 3K N CA 18 19 154.32 140.40 -40.80
3 3812 3K 4L C N 25 27 -65.52 -70.70 5.64 0.43 -63.50 179.45 25.03
3 4L 4L N CA 27 28 139.36 141.60 -41.20
4 3815 6I 7F C N 49 51 -151.66 -124.20 32.48 0.85 -63.20 178.52 30.38
4 7F 7F N CA 51 52 160.64 143.30 -44.30
5 3816 7F 8A C N 60 62 79.12 -134.00 153.39 3.70 -62.50 -169.17 29.84
5 8A 8A N CA 62 63 -168.81 147.00 -40.90
6 3820 11V 12L C N 87 89 -113.25 -108.50 39.23 2.07 -63.50 155.53 24.67
6 12L 12L N CA 89 90 171.44 132.50 -41.20
7 3821 12L 13C C N 95 97 -57.11 -63.00 8.19 0.94 -117.90 -177.47 7.91
7 13C 13C N CA 97 98 -46.78 -41.10 141.10
8 3823 14V 15G C N 108 110 -95.19 -80.20 51.31 1.35 82.20 -130.68 17.83
8 15G 15G N CA 110 111 -136.82 174.10 8.50
9 3824 15G 16S C N 112 114 -61.91 -72.40 37.60 1.88 -64.10 151.31 11.09
9 16S 16S N CA 114 115 116.29 152.40 -35.00
10 3844 35F 36E C N 274 276 58.84 54.60 15.00 0.85 -63.60 140.20 24.12
10 36E 36E N CA 276 277 28.01 42.40 -40.30
11 3859 50E 51S C N 405 407 -140.03 -64.10 84.48 8.82 -64.10 84.48 8.82
11 51S 51S N CA 407 408 2.05 -35.00 -35.00
12 3860 51S 52S C N 411 413 60.36 56.90 6.72 0.29 -64.10 140.71 18.64
12 52S 52S N CA 413 414 30.64 36.40 -35.00
13 3896 87K 88D C N 695 697 -145.29 -63.30 86.45 14.63 -63.30 86.45 14.63
13 88D 88D N CA 697 698 -67.41 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -45.91 -98.40 56.72 3.23 -63.50 151.32 24.92
14 112Y 112Y N CA 874 875 106.89 128.40 -43.40
15 3935 126H 127C C N 1020 1022 -126.63 -63.00 75.84 9.68 -63.00 75.84 9.68
15 127C 127C N CA 1022 1023 0.17 -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 11 63 79 109 120 141 151 186 197
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2501
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 : 1054.9854
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 : 1119 0 5 0.009 0.009 28.590 1.000
2 Bond angle potential : 1504 3 13 3.062 3.062 192.03 1.000
3 Stereochemical cosine torsion poten: 713 0 26 47.478 47.478 252.08 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.282 1.282 16.723 1.000
5 Soft-sphere overlap restraints : 2501 1 2 0.008 0.008 16.621 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) : 2215 0 2 0.303 0.303 96.547 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.354 0.354 140.30 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 2 4.402 4.402 31.072 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 75.903 75.903 39.560 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 77.394 77.394 39.490 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 74.123 74.123 22.356 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 102.279 102.279 17.041 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.42815 1.000
19 Disulfide angle restraints : 6 0 0 3.300 3.300 1.4425 1.000
20 Disulfide dihedral angle restraints: 3 0 0 19.721 19.721 1.1930 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) : 1316 0 0 0.355 0.355 31.157 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: 135 18 15 23.870 61.489 66.430 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.669 0.669 36.522 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 25.403 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: QUERY.V99990007
# 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: 16165.1309
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 2080 88D 88D N CA 697 698 127.90 107.00 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 3810 1M 2Q C N 7 9 -113.00 -121.10 12.35 0.64 -63.80 177.63 28.74
1 2Q 2Q N CA 9 10 149.02 139.70 -40.30
2 3811 2Q 3K C N 16 18 -85.40 -70.20 37.79 2.39 -62.90 145.95 20.25
2 3K 3K N CA 18 19 175.00 140.40 -40.80
3 3812 3K 4L C N 25 27 -60.00 -70.70 10.85 0.92 -63.50 179.06 24.66
3 4L 4L N CA 27 28 139.77 141.60 -41.20
4 3813 4L 5I C N 33 35 -60.74 -63.40 2.66 0.47 -120.60 -175.92 8.36
4 5I 5I N CA 35 36 -43.77 -43.60 130.30
5 3815 6I 7F C N 49 51 -128.07 -124.20 4.10 0.20 -63.20 -174.55 30.03
5 7F 7F N CA 51 52 141.97 143.30 -44.30
6 3816 7F 8A C N 60 62 -104.44 -134.00 35.82 0.88 -62.50 172.83 26.60
6 8A 8A N CA 62 63 126.76 147.00 -40.90
7 3817 8A 9L C N 65 67 -69.28 -70.70 6.85 0.47 -63.50 176.19 24.14
7 9L 9L N CA 67 68 134.90 141.60 -41.20
8 3820 11V 12L C N 87 89 -73.72 -70.70 3.80 0.26 -63.50 175.20 24.92
8 12L 12L N CA 89 90 143.90 141.60 -41.20
9 3823 14V 15G C N 108 110 -87.75 -80.20 21.47 0.53 82.20 -116.55 18.63
9 15G 15G N CA 110 111 -165.80 174.10 8.50
10 3824 15G 16S C N 112 114 -59.65 -72.40 37.79 1.83 -64.10 151.89 11.28
10 16S 16S N CA 114 115 116.82 152.40 -35.00
11 3844 35F 36E C N 274 276 52.03 54.60 5.61 0.63 -63.60 139.32 23.96
11 36E 36E N CA 276 277 37.41 42.40 -40.30
12 3859 50E 51S C N 405 407 -137.91 -64.10 81.25 8.61 -64.10 81.25 8.61
12 51S 51S N CA 407 408 -1.02 -35.00 -35.00
13 3860 51S 52S C N 411 413 60.84 56.90 5.59 0.33 -64.10 141.98 18.79
13 52S 52S N CA 413 414 32.43 36.40 -35.00
14 3896 87K 88D C N 695 697 -146.31 -63.30 86.27 14.52 -63.30 86.27 14.52
14 88D 88D N CA 697 698 -63.52 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -49.26 -98.40 53.14 3.04 -63.50 152.23 24.89
15 112Y 112Y N CA 874 875 108.16 128.40 -43.40
16 3923 114R 115H C N 904 906 -90.10 -125.60 52.08 1.30 -63.20 145.51 16.68
16 115H 115H N CA 906 907 100.70 138.80 -42.30
17 3924 115H 116R C N 914 916 -59.39 -63.00 68.82 9.06 -125.20 127.82 7.07
17 116R 116R N CA 916 917 -109.82 -41.10 140.60
18 3935 126H 127C C N 1020 1022 -119.54 -63.00 60.05 8.70 -63.00 60.05 8.70
18 127C 127C N CA 1022 1023 -20.86 -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 8 14 78 89 113 111 132 169 186 174
<< 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_484W> Dihedral still outside +-90: -91.6070
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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2440
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 : 1229.9495
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 : 1119 0 4 0.010 0.010 29.609 1.000
2 Bond angle potential : 1504 8 24 4.307 4.307 290.13 1.000
3 Stereochemical cosine torsion poten: 713 0 32 48.112 48.112 257.94 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.351 1.351 18.395 1.000
5 Soft-sphere overlap restraints : 2440 1 2 0.008 0.008 16.911 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) : 2215 0 5 0.289 0.289 96.059 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.343 0.343 153.50 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 5 5.014 5.014 40.327 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 77.251 77.251 42.108 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 68.539 68.539 32.844 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.738 80.738 23.371 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 80.952 80.952 12.304 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.44287 1.000
19 Disulfide angle restraints : 6 0 0 4.181 4.181 2.3162 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.719 22.719 1.4950 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) : 1316 0 0 0.374 0.374 32.553 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: 135 16 16 28.849 59.052 122.35 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.631 0.631 32.782 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 24.514 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: QUERY.V99990008
# 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: 15719.2910
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 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 1933 74N 74N ND2 CG 593 591 138.67 122.50 16.17 4.50 122.50 16.17 4.50
2 2080 88D 88D N CA 697 698 128.19 107.00 21.19 6.09 107.00 21.19 6.09
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -78.38 -73.00 24.82 1.52 -63.80 155.45 23.63
1 2Q 2Q N CA 9 10 164.93 140.70 -40.30
2 3811 2Q 3K C N 16 18 -62.03 -70.20 8.90 0.72 -62.90 175.27 22.71
2 3K 3K N CA 18 19 143.93 140.40 -40.80
3 3812 3K 4L C N 25 27 -111.33 -108.50 26.16 1.38 -63.50 167.27 26.17
3 4L 4L N CA 27 28 158.51 132.50 -41.20
4 3815 6I 7F C N 49 51 -133.89 -124.20 17.45 0.54 -63.20 172.98 28.61
4 7F 7F N CA 51 52 157.82 143.30 -44.30
5 3816 7F 8A C N 60 62 -67.40 -68.20 10.54 0.88 -62.50 163.37 27.02
5 8A 8A N CA 62 63 155.81 145.30 -40.90
6 3817 8A 9L C N 65 67 -81.35 -108.50 40.92 1.86 -63.50 144.20 19.07
6 9L 9L N CA 67 68 101.89 132.50 -41.20
7 3820 11V 12L C N 87 89 -67.15 -70.70 26.02 1.84 -63.50 157.06 21.60
7 12L 12L N CA 89 90 115.82 141.60 -41.20
8 3823 14V 15G C N 108 110 163.62 -167.20 29.34 0.49 82.20 -172.23 12.84
8 15G 15G N CA 110 111 177.70 174.60 8.50
9 3824 15G 16S C N 112 114 -121.22 -136.60 15.87 0.73 -64.10 179.22 16.98
9 16S 16S N CA 114 115 155.12 151.20 -35.00
10 3844 35F 36E C N 274 276 49.97 54.60 4.87 0.63 -63.60 139.60 23.99
10 36E 36E N CA 276 277 40.88 42.40 -40.30
11 3859 50E 51S C N 405 407 -140.31 -64.10 86.41 8.81 -64.10 86.41 8.81
11 51S 51S N CA 407 408 5.72 -35.00 -35.00
12 3860 51S 52S C N 411 413 60.50 56.90 5.01 0.31 -64.10 141.91 18.77
12 52S 52S N CA 413 414 32.92 36.40 -35.00
13 3889 80S 81K C N 651 653 -73.43 -62.90 96.41 13.12 -62.90 96.41 13.12
13 81K 81K N CA 653 654 -136.64 -40.80 -40.80
14 3890 81K 82G C N 660 662 -103.05 -62.40 40.72 7.36 82.20 -177.67 9.96
14 82G 82G N CA 662 663 -43.53 -41.20 8.50
15 3896 87K 88D C N 695 697 -139.54 -63.30 81.80 13.90 -63.30 81.80 13.90
15 88D 88D N CA 697 698 -69.62 -40.00 -40.00
16 3920 111I 112Y C N 872 874 -27.49 -98.40 74.27 3.82 -63.50 153.99 26.28
16 112Y 112Y N CA 874 875 106.32 128.40 -43.40
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 15 67 74 120 105 140 165 185 190
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2388
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 : 1205.6426
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 : 1119 0 4 0.010 0.010 30.712 1.000
2 Bond angle potential : 1504 1 12 2.401 2.401 174.60 1.000
3 Stereochemical cosine torsion poten: 713 0 33 47.750 47.750 260.49 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.482 1.482 21.230 1.000
5 Soft-sphere overlap restraints : 2388 1 2 0.008 0.008 16.177 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) : 2215 0 4 0.291 0.291 104.59 1.000
10 Distance restraints 2 (N-O) : 2371 1 18 0.388 0.388 210.44 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: 136 0 3 4.765 4.765 36.414 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 5 75.561 75.561 48.596 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 73.803 73.803 37.614 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 77.270 77.270 22.923 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 97.288 97.288 16.091 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.41470 1.000
19 Disulfide angle restraints : 6 0 0 3.219 3.219 1.3727 1.000
20 Disulfide dihedral angle restraints: 3 0 0 20.996 20.996 1.3210 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) : 1316 0 0 0.406 0.406 35.926 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: 135 22 22 33.843 66.047 130.93 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.676 0.676 34.490 1.000
27 Distance restraints 5 (X-Y) : 1389 0 0 0.043 0.043 21.317 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: QUERY.V99990009
# 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: 16579.9629
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 2080 88D 88D N CA 697 698 126.98 107.00 19.98 5.75 107.00 19.98 5.75
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8033 87K 63N N O 688 508 11.54 8.66 2.88 4.80 8.66 2.88 4.80
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -84.18 -73.00 13.14 0.80 -63.80 173.30 26.57
1 2Q 2Q N CA 9 10 147.61 140.70 -40.30
2 3811 2Q 3K C N 16 18 -99.53 -118.00 34.79 1.35 -62.90 154.82 18.43
2 3K 3K N CA 18 19 109.62 139.10 -40.80
3 3812 3K 4L C N 25 27 -82.78 -70.70 18.98 1.19 -63.50 163.69 23.88
3 4L 4L N CA 27 28 156.24 141.60 -41.20
4 3815 6I 7F C N 49 51 -74.11 -71.40 28.47 2.36 -63.20 157.04 21.08
4 7F 7F N CA 51 52 112.36 140.70 -44.30
5 3816 7F 8A C N 60 62 -89.40 -68.20 30.32 1.91 -62.50 154.49 26.72
5 8A 8A N CA 62 63 166.98 145.30 -40.90
6 3817 8A 9L C N 65 67 -75.97 -70.70 21.47 1.44 -63.50 156.89 22.52
6 9L 9L N CA 67 68 162.41 141.60 -41.20
7 3820 11V 12L C N 87 89 -75.30 -70.70 4.73 0.46 -63.50 178.69 25.50
7 12L 12L N CA 89 90 140.50 141.60 -41.20
8 3823 14V 15G C N 108 110 -144.97 -167.20 22.64 0.54 82.20 -143.98 16.09
8 15G 15G N CA 110 111 178.86 174.60 8.50
9 3824 15G 16S C N 112 114 -74.71 -72.40 17.61 1.12 -64.10 170.28 11.75
9 16S 16S N CA 114 115 134.95 152.40 -35.00
10 3844 35F 36E C N 274 276 51.38 54.60 4.35 0.56 -63.60 139.94 24.06
10 36E 36E N CA 276 277 39.48 42.40 -40.30
11 3859 50E 51S C N 405 407 -136.07 -64.10 80.97 8.34 -64.10 80.97 8.34
11 51S 51S N CA 407 408 2.10 -35.00 -35.00
12 3860 51S 52S C N 411 413 60.56 56.90 5.28 0.31 -64.10 141.80 18.76
12 52S 52S N CA 413 414 32.59 36.40 -35.00
13 3871 62R 63N C N 499 501 -64.60 -119.90 69.59 3.72 -63.20 139.65 17.54
13 63N 63N N CA 501 502 179.26 137.00 -41.10
14 3872 63N 64G C N 507 509 -67.90 -62.40 20.43 2.83 82.20 153.08 11.21
14 64G 64G N CA 509 510 -21.52 -41.20 8.50
15 3893 84S 85P C N 675 677 -45.19 -58.70 58.54 3.86 -64.50 126.82 10.51
15 85P 85P N CA 677 678 -87.46 -30.50 147.20
16 3894 85P 86G C N 682 684 -66.52 -62.40 15.89 2.59 82.20 162.33 12.53
16 86G 86G N CA 684 685 -56.54 -41.20 8.50
17 3895 86G 87K C N 686 688 70.16 -70.20 140.39 10.32 -70.20 140.39 10.32
17 87K 87K N CA 688 689 143.65 140.40 140.40
18 3896 87K 88D C N 695 697 -157.35 -63.30 103.23 17.60 -63.30 103.23 17.60
18 88D 88D N CA 697 698 -82.55 -40.00 -40.00
19 3898 89C 90N C N 709 711 -175.99 -63.20 115.36 18.40 55.90 165.51 11.02
19 90N 90N N CA 711 712 -65.30 -41.10 39.50
20 3922 113K 114R C N 893 895 -64.95 -125.20 79.01 2.35 -63.00 130.60 17.51
20 114R 114R N CA 895 896 89.49 140.60 -41.10
21 3923 114R 115H C N 904 906 -175.17 -63.20 113.03 17.10 -63.20 113.03 17.10
21 115H 115H N CA 906 907 -26.88 -42.30 -42.30
22 3935 126H 127C C N 1020 1022 -127.74 -63.00 75.23 9.83 -63.00 75.23 9.83
22 127C 127C N CA 1022 1023 -2.77 -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 14 13 64 90 106 122 135 166 170 183
<< 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 : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12134 12134
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2340
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 : 1071.8582
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 : 1119 0 3 0.010 0.010 30.739 1.000
2 Bond angle potential : 1504 1 10 2.354 2.354 170.44 1.000
3 Stereochemical cosine torsion poten: 713 0 29 47.855 47.855 261.29 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.415 1.415 19.677 1.000
5 Soft-sphere overlap restraints : 2340 1 2 0.008 0.008 15.826 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) : 2215 0 6 0.290 0.290 98.479 1.000
10 Distance restraints 2 (N-O) : 2371 1 15 0.361 0.361 173.67 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: 136 0 4 4.440 4.440 31.614 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 74.818 74.818 38.166 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 71.771 71.771 29.504 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 77.879 77.879 26.552 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 82.187 82.187 15.312 1.000
18 Disulfide distance restraints : 3 0 0 0.030 0.030 0.47380 1.000
19 Disulfide angle restraints : 6 0 0 4.194 4.194 2.3308 1.000
20 Disulfide dihedral angle restraints: 3 0 0 17.815 17.815 1.0122 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) : 1316 0 0 0.315 0.315 20.548 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: 135 19 16 29.684 64.677 85.756 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.549 0.549 26.145 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 24.326 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: QUERY.V99990010
# 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: 15691.4600
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 2080 88D 88D N CA 697 698 130.52 107.00 23.52 6.76 107.00 23.52 6.76
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7531 65S 85P N O 513 683 8.90 6.49 2.41 4.58 6.49 2.41 4.58
-------------------------------------------------------------------------------------------------
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 3810 1M 2Q C N 7 9 -84.37 -73.00 15.73 0.91 -63.80 169.37 26.00
1 2Q 2Q N CA 9 10 151.58 140.70 -40.30
2 3811 2Q 3K C N 16 18 -82.32 -70.20 12.35 0.84 -62.90 177.50 24.16
2 3K 3K N CA 18 19 142.77 140.40 -40.80
3 3812 3K 4L C N 25 27 -104.06 -108.50 6.83 0.39 -63.50 -176.57 23.47
3 4L 4L N CA 27 28 137.69 132.50 -41.20
4 3815 6I 7F C N 49 51 -95.29 -71.40 31.63 2.75 -63.20 167.37 21.18
4 7F 7F N CA 51 52 119.97 140.70 -44.30
5 3816 7F 8A C N 60 62 -160.82 -134.00 37.25 1.10 -62.50 176.23 34.09
5 8A 8A N CA 62 63 172.84 147.00 -40.90
6 3817 8A 9L C N 65 67 -103.00 -70.70 77.96 4.92 -63.50 113.34 18.18
6 9L 9L N CA 67 68 -147.44 141.60 -41.20
7 3820 11V 12L C N 87 89 -131.94 -108.50 23.65 1.09 -63.50 -170.33 23.46
7 12L 12L N CA 89 90 135.70 132.50 -41.20
8 3821 12L 13C C N 95 97 -61.42 -63.00 3.70 0.38 -117.90 -176.64 7.91
8 13C 13C N CA 97 98 -44.45 -41.10 141.10
9 3823 14V 15G C N 108 110 -87.55 -80.20 20.76 0.51 82.20 -116.20 18.64
9 15G 15G N CA 110 111 -166.49 174.10 8.50
10 3824 15G 16S C N 112 114 -60.95 -72.40 30.72 1.47 -64.10 158.93 11.70
10 16S 16S N CA 114 115 123.90 152.40 -35.00
11 3844 35F 36E C N 274 276 56.35 54.60 9.80 0.62 -63.60 140.44 24.17
11 36E 36E N CA 276 277 32.76 42.40 -40.30
12 3859 50E 51S C N 405 407 -137.92 -64.10 85.13 8.50 -64.10 85.13 8.50
12 51S 51S N CA 407 408 7.41 -35.00 -35.00
13 3860 51S 52S C N 411 413 58.27 56.90 1.77 0.12 -64.10 141.13 18.60
13 52S 52S N CA 413 414 35.29 36.40 -35.00
14 3893 84S 85P C N 675 677 -46.58 -58.70 59.56 4.02 -64.50 125.28 10.32
14 85P 85P N CA 677 678 -88.81 -30.50 147.20
15 3894 85P 86G C N 682 684 -69.42 -62.40 13.10 2.33 82.20 163.35 12.55
15 86G 86G N CA 684 685 -52.26 -41.20 8.50
16 3895 86G 87K C N 686 688 43.53 -70.20 113.99 8.50 -70.20 113.99 8.50
16 87K 87K N CA 688 689 148.04 140.40 140.40
17 3896 87K 88D C N 695 697 -159.41 -63.30 97.07 14.69 -63.30 97.07 14.69
17 88D 88D N CA 697 698 -26.36 -40.00 -40.00
18 3920 111I 112Y C N 872 874 -35.42 -98.40 67.36 3.72 -63.50 150.56 25.33
18 112Y 112Y N CA 874 875 104.52 128.40 -43.40
19 3935 126H 127C C N 1020 1022 -116.91 -63.00 57.37 8.29 -63.00 57.37 8.29
19 127C 127C N CA 1022 1023 -21.47 -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 13 9 56 71 114 119 141 167 190 171
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
QUERY.B99990001.pdb 1038.51123
QUERY.B99990002.pdb 1175.59900
QUERY.B99990003.pdb 1160.81323
QUERY.B99990004.pdb 1106.07715
QUERY.B99990005.pdb 1049.37708
QUERY.B99990006.pdb 1017.08124
QUERY.B99990007.pdb 1054.98535
QUERY.B99990008.pdb 1229.94946
QUERY.B99990009.pdb 1205.64258
QUERY.B99990010.pdb 1071.85815
In [11]:
%ls
1lmp.pdb QUERY.B99990008.pdb QUERY.D00000008 QUERY.V99990008 Modeller.ipynb QUERY.B99990009.pdb QUERY.D00000009 QUERY.V99990009 P48816.fasta QUERY.B99990010.pdb QUERY.D00000010 QUERY.V99990010 QUERY.B99990001.pdb QUERY.D00000001 QUERY.V99990001 QUERY.ini QUERY.B99990002.pdb QUERY.D00000002 QUERY.V99990002 QUERY.rsr QUERY.B99990003.pdb QUERY.D00000003 QUERY.V99990003 QUERY.sch QUERY.B99990004.pdb QUERY.D00000004 QUERY.V99990004 bommo.ali QUERY.B99990005.pdb QUERY.D00000005 QUERY.V99990005 QUERY.B99990006.pdb QUERY.D00000006 QUERY.V99990006 QUERY.B99990007.pdb QUERY.D00000007 QUERY.V99990007
Совместим все структуры и посмотрим, что вышло. Слева исходная модель, справа сгенерированные структуры. Получилось неплохо, лиганд на месте.
In [12]:
display(Image('./modeller.png'))
