Гомологичное моделирование комплекса белка с лигандом¶
Используя известную структуру лизоцима форели в качестве образца, необходимо построить гомологичную модель комплекса белка с лигандом (LYS_BOMMO) в программном пакете "Modeller". Это программное обеспечение распространяется бесплатно для академических пользователей. Программе Modeller для построения структуры белков, в качестве входных файлов нужны: управляющий скрипт, файл pdb со структурой-образцом и файл выравнивания с дополнительной информацией.
LYS_BOMMO - лизоцим тутового шелкопряда:
In [1]:
from IPython.display import display,Image
In [2]:
# Загрузим модель
import sys
import modeller
import _modeller
import modeller.automodel
In [3]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.18, 2017/02/17, r11002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux srv 4.15.0-46-generic x86_64
Date and time of compilation : 2017/02/17 14:47:45
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2019/05/15 23:18:41
In [4]:
# Скачаем белок-заготовку: лизоцим форели
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2019-05-15 23:18:41-- http://www.pdb.org/pdb/files/1lmp.pdb Resolving www.pdb.org (www.pdb.org)... 128.6.244.52 Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following] --2019-05-15 23:18:41-- https://www.rcsb.org/pdb/files/1lmp.pdb Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65 Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: http://files.rcsb.org/view/1lmp.pdb [following] --2019-05-15 23:18:42-- http://files.rcsb.org/view/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 128.6.244.12 Connecting to files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb.11’ 1lmp.pdb.11 [ <=> ] 127.35K 349KB/s in 0.4s 2019-05-15 23:18:42 (349 KB/s) - ‘1lmp.pdb.11’ saved [130410]
In [5]:
# Скачаем последовательность лизоцима тутового шелкопряда (LYS_BOMMO) с сайта Uniprot
! wget http://www.uniprot.org/uniprot/P48816.fasta
--2019-05-15 23:18:42-- http://www.uniprot.org/uniprot/P48816.fasta Resolving www.uniprot.org (www.uniprot.org)... 193.62.193.81 Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/P48816.fasta [following] --2019-05-15 23:18:43-- https://www.uniprot.org/uniprot/P48816.fasta Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:443... connected. HTTP request sent, awaiting response... 200 Length: 203 [text/plain] Saving to: ‘P48816.fasta.10’ P48816.fasta.10 100%[===================>] 203 --.-KB/s in 0s 2019-05-15 23:18:43 (15.6 MB/s) - ‘P48816.fasta.10’ saved [203/203]
In [6]:
# Создадим объект-выравнивание
alignm=modeller.alignment(env)
In [7]:
# Добавим последовательность и структуру
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'))
# Добавим модель 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.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [8]:
alignm
Out[8]:
Alignment of Sequence 'sp|P48816|LYS_BOMMO', Structure '1lmp'
In [9]:
# Поправим идентификаторы
alignm[0].code = 'Sequence'
alignm[1].code = 'Structure'
In [10]:
# Сделаем выравнивание и сохраним в файл ("bommo.ali")
alignm.salign()
alignm.write(file='bommo.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [11]:
# Посмотрим содержимое "bommo.ali"
! cat bommo.ali
>P1;Sequence sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC-------* >P1;Structure structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Строчка, расположенная под именем моделируемого белка:
sequence:: : : : :::-1.00:-1.00
описывает входные параметры последовательности, требующиеся в Modeller.
Строчка:
structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16
описывает, какой файл содержит структуру белка с этой последовательностью, номера первой и последней аминокислот в структуре, идентификатор цепи и т.д. В конце каждой последовательности добавьте символы
Не хватает лиганда. Необходимо добавить "/..." в конец каждой последовательности: "/" означает конец цепи белка, "." указывает на то, что имеется один лиганд (две точки - два лиганда, три точки - три лиганда и т. д.).
In [12]:
with open("bommo.ali") as rf:
lines = rf.readlines()
with open("bommo.ali", "w+") as wf:
for line in lines:
if not line.find("*") == -1:
line = line[:-5] + "/...*"
wf.write(line)
In [13]:
# Посмотрим содержимое файла "bommo.ali"
! cat bommo.ali
>P1;Sequence sequence:: : : : :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC----/...* >P1;Structure structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINS RYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...*
In [14]:
# Построим модель
# Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
# Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='bommo.ali', knowns=pdb.code, sequence=s.code)
# Построим 5 моделей
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 5
a.make()
Sequence Structure
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13094 12134
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): 2423
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 : 1027.6055
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 0.010 0.010 30.737 1.000
2 Bond angle potential : 1504 1 10 2.284 2.284 158.37 1.000
3 Stereochemical cosine torsion poten: 713 0 28 47.588 47.588 252.47 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.335 1.335 17.981 1.000
5 Soft-sphere overlap restraints : 2423 1 2 0.008 0.008 17.773 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 0.296 0.296 99.363 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.345 0.345 140.66 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 5.007 5.007 40.209 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 75.855 75.855 30.657 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 75.252 75.252 38.129 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 58.370 58.370 19.384 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 97.960 97.960 14.234 1.000
18 Disulfide distance restraints : 3 0 0 0.031 0.031 0.50915 1.000
19 Disulfide angle restraints : 6 0 0 5.353 5.353 3.7960 1.000
20 Disulfide dihedral angle restraints: 3 0 0 34.285 34.285 2.7443 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 0.398 0.398 36.118 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 17 18 23.563 61.097 62.863 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.635 0.635 34.201 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.048 0.048 27.404 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: Sequence.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: 15754.6846
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 697 698 128.14 107.00 21.14 6.08 107.00 21.14 6.08
-------------------------------------------------------------------------------------------------
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 -88.22 -73.00 19.65 1.16 -63.80 168.35 26.06
1 2Q 2Q N CA 9 10 153.13 140.70 -40.30
2 3811 2Q 3K C N 16 18 -66.41 -70.20 9.46 0.60 -62.90 172.57 22.22
2 3K 3K N CA 18 19 131.73 140.40 -40.80
3 3812 3K 4L C N 25 27 -78.12 -70.70 7.58 0.63 -63.50 176.26 25.34
3 4L 4L N CA 27 28 143.14 141.60 -41.20
4 3815 6I 7F C N 49 51 -85.92 -71.40 28.33 2.52 -63.20 162.27 21.05
4 7F 7F N CA 51 52 116.37 140.70 -44.30
5 3816 7F 8A C N 60 62 -168.17 -134.00 36.32 0.84 -62.50 -168.42 37.00
5 8A 8A N CA 62 63 159.30 147.00 -40.90
6 3817 8A 9L C N 65 67 -75.17 -70.70 6.77 0.67 -63.50 178.10 24.08
6 9L 9L N CA 67 68 136.52 141.60 -41.20
7 3820 11V 12L C N 87 89 -81.43 -70.70 19.86 1.23 -63.50 161.49 23.49
7 12L 12L N CA 89 90 158.31 141.60 -41.20
8 3821 12L 13C C N 95 97 -61.01 -63.00 4.46 0.46 -117.90 -177.12 7.89
8 13C 13C N CA 97 98 -45.09 -41.10 141.10
9 3823 14V 15G C N 108 110 -68.08 -80.20 19.27 0.53 82.20 -147.24 6.65
9 15G 15G N CA 110 111 159.12 174.10 8.50
10 3824 15G 16S C N 112 114 -114.25 -136.60 26.74 0.82 -64.10 178.69 11.04
10 16S 16S N CA 114 115 136.51 151.20 -35.00
11 3844 35F 36E C N 274 276 61.71 54.60 16.51 0.84 -63.60 142.47 24.50
11 36E 36E N CA 276 277 27.50 42.40 -40.30
12 3859 50E 51S C N 405 407 -135.02 -64.10 79.17 8.23 -64.10 79.17 8.23
12 51S 51S N CA 407 408 0.20 -35.00 -35.00
13 3860 51S 52S C N 411 413 60.06 56.90 4.62 0.26 -64.10 141.57 18.72
13 52S 52S N CA 413 414 33.02 36.40 -35.00
14 3896 87K 88D C N 695 697 -143.77 -63.30 86.59 14.73 -63.30 86.59 14.73
14 88D 88D N CA 697 698 -71.97 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -42.39 -98.40 60.73 3.49 -63.50 149.82 24.86
15 112Y 112Y N CA 874 875 104.93 128.40 -43.40
16 3923 114R 115H C N 904 906 -91.54 -125.60 62.79 1.69 -63.20 131.44 14.88
16 115H 115H N CA 906 907 86.04 138.80 -42.30
17 3924 115H 116R C N 914 916 -56.31 -63.00 43.33 5.43 -125.20 152.01 8.36
17 116R 116R N CA 916 917 -83.90 -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 10 11 46 79 116 117 123 171 181 197
<< end of ENERGY.
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): 2515
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 : 1130.7329
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 30.075 1.000
2 Bond angle potential : 1504 1 10 2.355 2.355 165.80 1.000
3 Stereochemical cosine torsion poten: 713 0 32 48.808 48.808 266.16 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.373 1.373 18.778 1.000
5 Soft-sphere overlap restraints : 2515 2 2 0.008 0.008 19.256 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 0.332 0.332 123.64 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.363 0.363 161.81 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.714 4.714 35.647 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 75.938 75.938 43.240 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 69.665 69.665 37.138 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 88.625 88.625 27.276 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 99.122 99.122 16.146 1.000
18 Disulfide distance restraints : 3 0 0 0.026 0.026 0.35501 1.000
19 Disulfide angle restraints : 6 0 0 4.225 4.225 2.3650 1.000
20 Disulfide dihedral angle restraints: 3 0 0 10.820 10.820 0.40443 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 0.354 0.354 28.734 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 20 30.050 68.493 88.491 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 2 0.722 0.722 42.132 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.045 0.045 23.285 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: Sequence.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: 16558.5332
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 697 698 128.14 107.00 21.14 6.08 107.00 21.14 6.08
-------------------------------------------------------------------------------------------------
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 -71.00 -73.00 6.74 0.48 -63.80 172.71 25.77
1 2Q 2Q N CA 9 10 147.14 140.70 -40.30
2 3811 2Q 3K C N 16 18 -74.63 -70.20 28.26 1.94 -62.90 151.35 20.32
2 3K 3K N CA 18 19 168.31 140.40 -40.80
3 3812 3K 4L C N 25 27 -61.23 -70.70 18.36 1.14 -63.50 167.09 23.33
3 4L 4L N CA 27 28 125.88 141.60 -41.20
4 3815 6I 7F C N 49 51 178.15 -124.20 60.01 1.87 -63.20 -164.19 34.33
4 7F 7F N CA 51 52 159.93 143.30 -44.30
5 3816 7F 8A C N 60 62 177.85 -134.00 55.73 1.30 -62.50 -172.74 36.91
5 8A 8A N CA 62 63 175.05 147.00 -40.90
6 3817 8A 9L C N 65 67 -63.21 -70.70 13.34 0.83 -63.50 171.76 23.87
6 9L 9L N CA 67 68 130.56 141.60 -41.20
7 3819 10V 11V C N 80 82 -66.77 -62.40 6.03 1.01 -125.40 179.97 10.06
7 11V 11V N CA 82 83 -46.55 -42.40 143.30
8 3820 11V 12L C N 87 89 -155.05 -108.50 47.96 2.43 -63.50 -173.77 22.82
8 12L 12L N CA 89 90 120.97 132.50 -41.20
9 3823 14V 15G C N 108 110 -176.62 -167.20 14.03 0.33 82.20 -156.56 14.39
9 15G 15G N CA 110 111 -175.00 174.60 8.50
10 3824 15G 16S C N 112 114 -72.33 -72.40 33.17 1.95 -64.10 154.45 10.73
10 16S 16S N CA 114 115 119.23 152.40 -35.00
11 3844 35F 36E C N 274 276 49.04 54.60 5.74 0.73 -63.60 138.88 23.86
11 36E 36E N CA 276 277 40.93 42.40 -40.30
12 3859 50E 51S C N 405 407 -137.46 -64.10 84.50 8.45 -64.10 84.50 8.45
12 51S 51S N CA 407 408 6.94 -35.00 -35.00
13 3860 51S 52S C N 411 413 57.50 56.90 0.63 0.06 -64.10 140.91 18.55
13 52S 52S N CA 413 414 36.20 36.40 -35.00
14 3896 87K 88D C N 695 697 -144.37 -63.30 83.16 13.90 -63.30 83.16 13.90
14 88D 88D N CA 697 698 -58.55 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -45.12 -98.40 56.47 3.03 -63.50 154.22 25.42
15 112Y 112Y N CA 874 875 109.71 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -130.83 -63.20 89.50 10.36 -63.20 89.50 10.36
16 126H 126H N CA 1012 1013 16.33 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -133.54 -63.00 73.67 10.95 -63.00 73.67 10.95
17 127C 127C N CA 1022 1023 -19.85 -41.10 -41.10
18 3936 127C 128Q C N 1026 1028 -63.33 -63.80 7.04 1.06 -121.10 -177.63 7.55
18 128Q 128Q N CA 1028 1029 -33.28 -40.30 139.70
19 3937 128Q 129G C N 1035 1037 -60.97 -62.40 11.80 1.83 82.20 148.13 11.06
19 129G 129G N CA 1037 1038 -29.49 -41.20 8.50
20 3938 129G 130S C N 1039 1041 80.84 56.90 27.82 2.25 -72.40 -158.93 9.86
20 130S 130S N CA 1041 1042 22.23 36.40 152.40
21 3939 130S 131L C N 1045 1047 -66.34 -63.50 3.52 0.48 -108.50 176.73 9.05
21 131L 131L N CA 1047 1048 -39.13 -41.20 132.50
22 3940 131L 132P C N 1053 1055 -42.85 -64.50 77.79 4.82 -58.70 104.20 9.92
22 132P 132P N CA 1055 1056 72.49 147.20 -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 1 7 14 77 82 135 117 158 172 183 184
<< end of ENERGY.
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): 2403
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 : 1126.2100
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 0.010 0.010 29.427 1.000
2 Bond angle potential : 1504 1 13 2.321 2.321 162.91 1.000
3 Stereochemical cosine torsion poten: 713 0 28 47.548 47.548 253.37 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.331 1.331 18.373 1.000
5 Soft-sphere overlap restraints : 2403 2 2 0.008 0.008 18.502 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 0.301 0.301 111.13 1.000
10 Distance restraints 2 (N-O) : 2371 2 18 0.397 0.397 222.47 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 5.159 5.159 42.690 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 71.002 71.002 31.928 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 79.263 79.263 36.647 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 77.662 77.662 20.584 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 78.686 78.686 13.071 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.41128 1.000
19 Disulfide angle restraints : 6 0 0 3.026 3.026 1.2131 1.000
20 Disulfide dihedral angle restraints: 3 0 0 16.731 16.731 0.89599 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 0.283 0.283 17.449 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 18 24.875 62.965 99.397 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.505 0.505 21.545 1.000
27 Distance restraints 5 (X-Y) : 1389 0 0 0.045 0.045 24.195 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: Sequence.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: 15573.4941
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 697 698 126.93 107.00 19.93 5.73 107.00 19.93 5.73
-------------------------------------------------------------------------------------------------
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 10.68 7.27 3.41 4.81 7.27 3.41 4.81
2 8033 87K 63N N O 688 508 12.11 8.66 3.45 5.76 8.66 3.45 5.76
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -93.89 -73.00 22.45 1.72 -63.80 175.40 24.31
1 2Q 2Q N CA 9 10 132.49 140.70 -40.30
2 3811 2Q 3K C N 16 18 -94.69 -118.00 23.31 0.88 -62.90 -177.25 22.19
2 3K 3K N CA 18 19 139.16 139.10 -40.80
3 3812 3K 4L C N 25 27 -98.40 -108.50 17.27 0.98 -63.50 175.79 26.53
3 4L 4L N CA 27 28 146.51 132.50 -41.20
4 3815 6I 7F C N 49 51 -87.47 -71.40 16.29 1.19 -63.20 179.33 26.54
4 7F 7F N CA 51 52 138.02 140.70 -44.30
5 3816 7F 8A C N 60 62 -128.79 -134.00 10.48 0.64 -62.50 175.98 32.39
5 8A 8A N CA 62 63 156.09 147.00 -40.90
6 3820 11V 12L C N 87 89 -95.53 -108.50 37.76 1.88 -63.50 141.90 18.13
6 12L 12L N CA 89 90 97.04 132.50 -41.20
7 3823 14V 15G C N 108 110 -90.77 -80.20 19.68 0.48 82.20 -111.95 18.97
7 15G 15G N CA 110 111 -169.30 174.10 8.50
8 3824 15G 16S C N 112 114 -94.44 -72.40 31.75 2.52 -64.10 167.32 10.70
8 16S 16S N CA 114 115 129.55 152.40 -35.00
9 3841 32K 33H C N 249 251 -56.15 -63.20 7.99 1.03 -125.60 -171.59 8.23
9 33H 33H N CA 251 252 -46.06 -42.30 138.80
10 3842 33H 34G C N 259 261 -87.80 -62.40 30.76 4.58 82.20 173.06 12.63
10 34G 34G N CA 261 262 -23.86 -41.20 8.50
11 3844 35F 36E C N 274 276 50.78 54.60 5.27 0.67 -63.60 139.05 23.91
11 36E 36E N CA 276 277 38.77 42.40 -40.30
12 3859 50E 51S C N 405 407 -139.54 -64.10 88.83 8.65 -64.10 88.83 8.65
12 51S 51S N CA 407 408 11.90 -35.00 -35.00
13 3860 51S 52S C N 411 413 53.63 56.90 3.64 0.32 -64.10 138.53 18.16
13 52S 52S N CA 413 414 38.00 36.40 -35.00
14 3871 62R 63N C N 499 501 -73.07 -119.90 72.03 3.91 -63.20 127.56 16.50
14 63N 63N N CA 501 502 -168.27 137.00 -41.10
15 3872 63N 64G C N 507 509 -69.06 -62.40 23.16 3.20 82.20 153.74 11.19
15 64G 64G N CA 509 510 -19.02 -41.20 8.50
16 3896 87K 88D C N 695 697 -142.40 -63.30 84.21 14.29 -63.30 84.21 14.29
16 88D 88D N CA 697 698 -68.89 -40.00 -40.00
17 3923 114R 115H C N 904 906 -83.36 -125.60 59.72 1.48 -63.20 140.33 16.38
17 115H 115H N CA 906 907 96.58 138.80 -42.30
18 3924 115H 116R C N 914 916 -57.97 -63.00 64.18 8.34 -125.20 132.62 7.33
18 116R 116R N CA 916 917 -105.08 -41.10 140.60
19 3935 126H 127C C N 1020 1022 -115.10 -63.00 53.28 8.22 -63.00 53.28 8.22
19 127C 127C N CA 1022 1023 -29.96 -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 16 64 71 112 126 131 164 190 185
<< end of ENERGY.
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: -90.4098
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): 2432
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 : 1081.0306
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 31.799 1.000
2 Bond angle potential : 1504 1 14 2.413 2.413 175.05 1.000
3 Stereochemical cosine torsion poten: 713 0 23 47.560 47.560 254.06 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.344 1.344 18.101 1.000
5 Soft-sphere overlap restraints : 2432 1 2 0.008 0.008 18.654 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 0.303 103.79 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.335 0.335 135.27 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 4.456 4.456 31.840 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 85.907 85.907 47.804 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 75.698 75.698 39.574 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 72.832 72.832 21.100 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 83.134 83.134 14.840 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.38322 1.000
19 Disulfide angle restraints : 6 0 0 3.096 3.096 1.2703 1.000
20 Disulfide dihedral angle restraints: 3 0 0 18.929 18.929 1.1381 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 0.429 0.429 46.357 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 26.117 61.201 54.900 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.823 0.823 56.226 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.049 0.049 28.864 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: Sequence.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: 16566.9785
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 697 698 129.63 107.00 22.63 6.51 107.00 22.63 6.51
-------------------------------------------------------------------------------------------------
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 -72.72 -73.00 2.49 0.17 -63.80 176.75 26.46
1 2Q 2Q N CA 9 10 143.17 140.70 -40.30
2 3811 2Q 3K C N 16 18 -106.59 -118.00 40.46 2.08 -62.90 147.88 21.80
2 3K 3K N CA 18 19 177.92 139.10 -40.80
3 3812 3K 4L C N 25 27 -66.50 -70.70 13.58 1.19 -63.50 164.31 22.99
3 4L 4L N CA 27 28 154.52 141.60 -41.20
4 3815 6I 7F C N 49 51 -66.83 -71.40 14.26 1.01 -63.20 171.54 23.57
4 7F 7F N CA 51 52 127.20 140.70 -44.30
5 3816 7F 8A C N 60 62 -128.72 -134.00 5.76 0.13 -62.50 -173.44 34.12
5 8A 8A N CA 62 63 144.69 147.00 -40.90
6 3817 8A 9L C N 65 67 -73.85 -70.70 10.13 0.66 -63.50 167.89 23.92
6 9L 9L N CA 67 68 151.22 141.60 -41.20
7 3818 9L 10V C N 73 75 -58.64 -62.40 5.10 0.60 -125.40 -176.57 10.34
7 10V 10V N CA 75 76 -45.85 -42.40 143.30
8 3820 11V 12L C N 87 89 -71.99 -70.70 9.48 0.77 -63.50 173.62 23.63
8 12L 12L N CA 89 90 132.21 141.60 -41.20
9 3821 12L 13C C N 95 97 -68.25 -63.00 5.33 0.83 -117.90 -174.49 7.93
9 13C 13C N CA 97 98 -40.16 -41.10 141.10
10 3823 14V 15G C N 108 110 -162.39 -167.20 14.67 0.49 82.20 -168.96 14.17
10 15G 15G N CA 110 111 160.75 174.60 8.50
11 3824 15G 16S C N 112 114 -126.87 -136.60 16.24 0.57 -64.10 -175.78 11.36
11 16S 16S N CA 114 115 138.20 151.20 -35.00
12 3844 35F 36E C N 274 276 50.98 54.60 6.23 0.75 -63.60 138.40 23.80
12 36E 36E N CA 276 277 37.33 42.40 -40.30
13 3860 51S 52S C N 411 413 64.04 56.90 9.65 0.61 -64.10 143.64 19.07
13 52S 52S N CA 413 414 29.90 36.40 -35.00
14 3896 87K 88D C N 695 697 -141.47 -63.30 79.76 13.27 -63.30 79.76 13.27
14 88D 88D N CA 697 698 -55.83 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -28.46 -98.40 75.86 4.37 -63.50 146.66 25.06
15 112Y 112Y N CA 874 875 99.01 128.40 -43.40
16 3935 126H 127C C N 1020 1022 -121.33 -63.00 65.89 8.86 -63.00 65.89 8.86
16 127C 127C N CA 1022 1023 -10.45 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 12 14 54 92 137 125 147 165 163 184
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 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): 2463
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 : 1055.0023
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 0.010 0.010 29.772 1.000
2 Bond angle potential : 1504 1 11 2.258 2.258 156.75 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.336 47.336 251.98 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.188 1.188 15.203 1.000
5 Soft-sphere overlap restraints : 2463 1 2 0.008 0.008 18.001 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 0.313 0.313 107.96 1.000
10 Distance restraints 2 (N-O) : 2371 2 12 0.373 0.373 175.47 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 4.572 4.572 33.519 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 77.773 77.773 40.861 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 81.840 81.840 40.922 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 65.631 65.631 17.391 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 89.371 89.371 14.769 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.33519 1.000
19 Disulfide angle restraints : 6 0 0 4.895 4.895 3.1748 1.000
20 Disulfide dihedral angle restraints: 3 0 0 11.487 11.487 0.46254 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 0.299 0.299 21.801 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 17 15 27.476 63.960 67.281 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.629 0.629 33.543 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.047 0.047 25.816 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: Sequence.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: 15891.6094
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 697 698 127.60 107.00 20.60 5.92 107.00 20.60 5.92
-------------------------------------------------------------------------------------------------
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 10.83 7.27 3.56 5.02 7.27 3.56 5.02
2 8033 87K 63N N O 688 508 12.24 8.66 3.58 5.97 8.66 3.58 5.97
-------------------------------------------------------------------------------------------------
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 -66.51 -73.00 6.51 0.47 -63.80 178.49 26.39
1 2Q 2Q N CA 9 10 141.23 140.70 -40.30
2 3811 2Q 3K C N 16 18 -73.62 -70.20 14.25 0.95 -62.90 165.32 22.07
2 3K 3K N CA 18 19 154.23 140.40 -40.80
3 3812 3K 4L C N 25 27 -61.37 -70.70 9.33 0.85 -63.50 177.13 24.47
3 4L 4L N CA 27 28 141.68 141.60 -41.20
4 3815 6I 7F C N 49 51 -81.29 -71.40 24.11 2.13 -63.20 164.02 21.58
4 7F 7F N CA 51 52 118.72 140.70 -44.30
5 3816 7F 8A C N 60 62 -125.87 -134.00 9.83 0.24 -62.50 -171.41 34.29
5 8A 8A N CA 62 63 141.48 147.00 -40.90
6 3818 9L 10V C N 73 75 -64.12 -62.40 2.35 0.27 -125.40 -173.73 10.42
6 10V 10V N CA 75 76 -40.79 -42.40 143.30
7 3820 11V 12L C N 87 89 -99.29 -108.50 17.47 0.99 -63.50 175.15 26.50
7 12L 12L N CA 89 90 147.35 132.50 -41.20
8 3824 15G 16S C N 112 114 -108.50 -136.60 29.58 0.96 -64.10 -177.54 11.37
8 16S 16S N CA 114 115 141.97 151.20 -35.00
9 3844 35F 36E C N 274 276 56.53 54.60 8.75 0.53 -63.60 141.18 24.29
9 36E 36E N CA 276 277 33.86 42.40 -40.30
10 3859 50E 51S C N 405 407 -139.89 -64.10 87.25 8.73 -64.10 87.25 8.73
10 51S 51S N CA 407 408 8.23 -35.00 -35.00
11 3860 51S 52S C N 411 413 61.85 56.90 9.23 0.41 -64.10 141.11 18.73
11 52S 52S N CA 413 414 28.62 36.40 -35.00
12 3871 62R 63N C N 499 501 -71.56 -119.90 71.92 3.90 -63.20 128.92 16.58
12 63N 63N N CA 501 502 -169.74 137.00 -41.10
13 3872 63N 64G C N 507 509 -68.86 -62.40 21.66 2.99 82.20 153.83 11.24
13 64G 64G N CA 509 510 -20.53 -41.20 8.50
14 3896 87K 88D C N 695 697 -134.59 -63.30 73.88 12.42 -63.30 73.88 12.42
14 88D 88D N CA 697 698 -59.40 -40.00 -40.00
15 3920 111I 112Y C N 872 874 -48.04 -98.40 53.81 2.96 -63.50 153.64 25.17
15 112Y 112Y N CA 874 875 109.46 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -120.12 -63.20 79.63 8.99 -63.20 79.63 8.99
16 126H 126H N CA 1012 1013 13.37 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -126.79 -63.00 63.81 10.72 -63.00 63.81 10.72
17 127C 127C N CA 1022 1023 -42.84 -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 5 17 60 76 116 121 164 159 184 180
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
Sequence.B99990001.pdb 1027.60547
Sequence.B99990002.pdb 1130.73291
Sequence.B99990003.pdb 1126.20996
Sequence.B99990004.pdb 1081.03064
Sequence.B99990005.pdb 1055.00232
In [15]:
s.code
Out[15]:
'Sequence'
In [16]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('Sequence.B99990001.pdb')
w1
In [17]:
Image(filename='1lmp_hom_05_01.png')
Out[17]:
In [18]:
# Посмотрим названия атомов в остатках белка и лиганда
for x in pdb.residues[-6:]:
print (x)
print(" ")
for i in x.atoms:
print (i)
print(" ")
<Residue 127:A (type CYS)> <Atom N:127:A> <Atom CA:127:A> <Atom C:127:A> <Atom O:127:A> <Atom CB:127:A> <Atom SG:127:A> <Residue 128:A (type GLY)> <Atom N:128:A> <Atom CA:128:A> <Atom C:128:A> <Atom O:128:A> <Residue 129:A (type VAL)> <Atom N:129:A> <Atom CA:129:A> <Atom C:129:A> <Atom O:129:A> <Atom CB:129:A> <Atom CG1:129:A> <Atom CG2:129:A> <Residue 130:A (type NAG)> <Atom C1:130:A> <Atom C2:130:A> <Atom C3:130:A> <Atom C4:130:A> <Atom C5:130:A> <Atom C6:130:A> <Atom C7:130:A> <Atom C8:130:A> <Atom N2:130:A> <Atom O3:130:A> <Atom O4:130:A> <Atom O5:130:A> <Atom O6:130:A> <Atom O7:130:A> <Residue 131:A (type NAG)> <Atom C1:131:A> <Atom C2:131:A> <Atom C3:131:A> <Atom C4:131:A> <Atom C5:131:A> <Atom C6:131:A> <Atom C7:131:A> <Atom C8:131:A> <Atom N2:131:A> <Atom O3:131:A> <Atom O4:131:A> <Atom O5:131:A> <Atom O6:131:A> <Atom O7:131:A> <Residue 132:A (type NDG)> <Atom C1:132:A> <Atom C2:132:A> <Atom C3:132:A> <Atom C4:132:A> <Atom C5:132:A> <Atom C6:132:A> <Atom C7:132:A> <Atom C8:132:A> <Atom O:132:A> <Atom O3:132:A> <Atom O4:132:A> <Atom O6:132:A> <Atom O7:132:A> <Atom N2:132:A> <Atom O1L:132:A>
Поместим лиганд в другое место, переназначив объект automodel. В скрипте указано, что:
- нужно использовать стандартные валентные углы в полипептидной цепи (строчка 4)
- дополнительно нужно сохранять взаимное расположение определенных пар атомов (3.0 ангстрема); в данном случае трех атомов белка, образующих водородные связи с тремя атомами лиганда - строчки 5-7 с ID пар атомов (название атома:номер остатка:имя цепи); параметры взаимного расположения атомов пары описаны в строчке 9-10 (3 точки могут однозначно расположить сложную структуру в пространстве, поэтому мы выбираем водородные связи как источник данных точек)
- ковалентные связи в гетероатомах нужно вычислять по расстояниям между атомами, так же, как это делает Rasmol/PyMOL (строчка 12)
- имя файла с выравниванием и имена последовательностей образца и моделируемого белка; имя файла со структурой содержится в выравнивании (строчка 13)
- число и номера моделей, которые нужно построить; в данном случае - 5 моделей (строки 14-15)
- пора строить модель (строчка 16)
In [19]:
from modeller import *
from modeller.automodel import *
class mymodel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
for ids in (('O:101:A', 'N:130:A'),
('N:43:A', 'O:131:A'),
('N:60:A', 'O:132:A')):
atoms = [self.atoms[i] for i in ids]
rsr.add(forms.upper_bound(group=physical.upper_distance,
feature=features.distance(*atoms), mean=3.5, stdev=0.1))
env = environ()
env.io.hetatm = True
a = mymodel(env, alnfile='bommo.ali', knowns=pdb.code, sequence=s.code)
a.starting_model = 1
a.ending_model = 5
a.make()
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13097 12137
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2859
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 : 7227.1826
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 6 19 0.024 0.024 197.81 1.000
2 Bond angle potential : 1504 11 45 4.059 4.059 471.31 1.000
3 Stereochemical cosine torsion poten: 713 0 36 50.300 50.300 283.04 1.000
4 Stereochemical improper torsion pot: 461 1 4 2.230 2.230 53.955 1.000
5 Soft-sphere overlap restraints : 2859 7 9 0.018 0.018 104.00 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 81 193 1.154 1.154 2323.6 1.000
10 Distance restraints 2 (N-O) : 2371 71 159 0.985 0.985 1915.9 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 4 11 9.070 9.070 131.94 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 78.286 78.286 45.363 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 86.781 86.781 45.388 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 68.810 68.810 21.014 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 95.640 95.640 14.192 1.000
18 Disulfide distance restraints : 3 0 0 0.039 0.039 0.80268 1.000
19 Disulfide angle restraints : 6 0 1 6.098 6.098 4.9264 1.000
20 Disulfide dihedral angle restraints: 3 0 0 36.507 36.507 2.5557 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.444 3.444 1050.0 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.557 0.557 71.163 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 25 40.269 70.766 177.38 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 6 1.113 1.113 98.152 1.000
27 Distance restraints 5 (X-Y) : 1389 4 24 0.143 0.143 214.72 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: Sequence.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: 26642.1895
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.75 1.43 0.32 10.61 1.43 0.32 10.61
2 488 60T 60T C CA 480 476 1.73 1.49 0.24 6.96 1.49 0.24 6.96
3 489 60T 61N C N 480 482 1.48 1.35 0.14 4.93 1.35 0.14 4.93
4 717 88D 88D C CA 703 698 1.65 1.49 0.16 4.63 1.49 0.16 4.63
5 1078 132P 132P O C 1061 1060 1.40 1.23 0.17 7.62 1.23 0.17 7.62
6 1079 132P 132P C CA 1060 1056 1.74 1.49 0.25 7.37 1.49 0.25 7.37
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 130.54 107.00 23.54 6.77 107.00 23.54 6.77
2 1640 47V 48E C N 377 379 145.67 120.00 25.67 5.83 120.00 25.67 5.83
3 1773 60T 60T N CA 475 476 126.81 107.00 19.81 5.70 107.00 19.81 5.70
4 1783 61N 61N N CA 482 483 124.87 107.00 17.87 5.14 107.00 17.87 5.14
5 2080 88D 88D N CA 697 698 130.94 107.00 23.94 6.88 107.00 23.94 6.88
6 2214 101I 101I N CA 794 795 123.52 107.00 16.52 4.75 107.00 16.52 4.75
7 2222 101I 102T C N 800 802 144.60 120.00 24.60 5.59 120.00 24.60 5.59
8 2577 132P 132P N CA 1055 1056 148.59 108.20 40.39 9.18 108.20 40.39 9.18
9 2586 132P 133D C N 1060 1062 146.18 120.00 26.18 5.95 120.00 26.18 5.95
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.05 9.77 3.28 5.82 9.77 3.28 5.82
2 5022 41R 132P CA CA 319 1056 8.68 5.64 3.05 7.63 5.64 3.05 7.63
3 5023 41R 133D CA CA 319 1063 9.34 6.81 2.52 4.76 6.81 2.52 4.76
4 5571 60T 64G CA CA 476 510 10.31 6.93 3.38 6.33 6.93 3.38 6.33
5 5572 60T 65S CA CA 476 514 9.45 6.01 3.44 7.66 6.01 3.44 7.66
6 5573 60T 66K CA CA 476 520 6.89 4.22 2.67 6.65 4.22 2.67 6.65
7 5582 60T 81K CA CA 476 654 14.75 11.49 3.26 5.34 11.49 3.26 5.34
8 5583 60T 82G CA CA 476 663 17.31 13.44 3.88 4.92 13.44 3.88 4.92
9 5584 60T 83A CA CA 476 667 14.85 11.07 3.78 5.58 11.07 3.78 5.58
10 5585 60T 84S CA CA 476 672 14.05 10.32 3.73 6.61 10.32 3.73 6.61
11 5586 60T 85P CA CA 476 678 16.73 12.86 3.87 5.11 12.86 3.87 5.11
12 6505 124K 128Q CA CA 996 1029 7.21 5.18 2.02 5.03 5.18 2.02 5.03
13 6507 124K 130S CA CA 996 1042 13.23 10.06 3.17 4.89 10.06 3.17 4.89
14 6511 125N 128Q CA CA 1005 1029 9.01 6.66 2.35 4.74 6.66 2.35 4.74
15 6513 125N 130S CA CA 1005 1042 14.01 9.78 4.23 6.22 9.78 4.23 6.22
16 6518 126H 130S CA CA 1013 1042 12.18 7.42 4.76 9.09 7.42 4.76 9.09
17 6525 127C 130S CA CA 1023 1042 8.74 5.30 3.44 9.37 5.30 3.44 9.37
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 14.48 10.18 4.29 6.80 10.18 4.29 6.80
2 6967 40M 132P N O 310 1061 13.38 8.51 4.87 10.17 8.51 4.87 10.17
3 6991 41R 132P N O 318 1061 11.51 5.74 5.77 12.14 5.74 5.77 12.14
4 7019 42N 132P N O 329 1061 10.01 6.20 3.80 7.75 6.20 3.80 7.75
5 7179 48E 44V N O 379 357 5.28 3.06 2.22 5.01 3.06 2.22 5.01
6 7468 60T 64G N O 475 512 11.27 7.82 3.45 5.40 7.82 3.45 5.40
7 7469 60T 65S N O 475 518 8.11 4.76 3.35 6.88 4.76 3.35 6.88
8 7476 60T 83A N O 475 670 15.47 11.00 4.47 6.13 11.00 4.47 6.13
9 7482 61N 65S N O 482 518 4.77 2.59 2.17 5.49 2.59 2.17 5.49
10 8757 125N 128Q N O 1004 1036 10.23 6.57 3.66 6.17 6.57 3.66 6.17
11 8773 126H 128Q N O 1012 1036 8.90 6.16 2.73 5.21 6.16 2.73 5.21
12 8794 127C 130S N O 1022 1046 10.48 7.34 3.14 6.03 7.34 3.14 6.03
13 8808 128Q 123W N O 1028 994 4.50 2.79 1.71 4.64 2.79 1.71 4.64
14 8809 128Q 124K N O 1028 1003 7.18 4.29 2.89 6.07 4.29 2.89 6.07
15 8822 129G 124K N O 1037 1003 10.75 6.40 4.34 6.23 6.40 4.34 6.23
16 8831 130S 123W N O 1041 994 11.43 7.33 4.10 7.46 7.33 4.10 7.46
17 8832 130S 124K N O 1041 1003 14.17 7.82 6.35 9.96 7.82 6.35 9.96
18 8833 130S 125N N O 1041 1011 14.21 7.78 6.43 9.43 7.78 6.43 9.43
19 8834 130S 126H N O 1041 1021 11.03 5.94 5.09 9.24 5.94 5.09 9.24
20 8835 130S 127C N O 1041 1027 7.56 3.18 4.38 11.67 3.18 4.38 11.67
21 8843 131L 126H N O 1047 1021 10.08 6.80 3.28 4.74 6.80 3.28 4.74
22 8844 131L 127C N O 1047 1027 8.07 5.43 2.64 4.85 5.43 2.64 4.85
23 8857 132P 127C N O 1055 1027 8.79 6.04 2.76 7.66 6.04 2.76 7.66
24 8860 132P 130S N O 1055 1046 5.37 3.36 2.01 4.60 3.36 2.01 4.60
25 8884 134I 132P N O 1070 1061 6.06 3.18 2.88 5.16 3.18 2.88 5.16
26 8900 135S 132P N O 1078 1061 8.07 2.93 5.14 11.22 2.93 5.14 11.22
27 8917 136S 132P N O 1084 1061 10.59 4.11 6.48 11.96 4.11 6.48 11.96
28 8928 137C 132P N O 1090 1061 12.61 5.93 6.68 5.96 5.93 6.68 5.96
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4002 58T 58T CA C 461 465 -157.44 -180.00 22.56 4.51 -180.00 22.56 4.51
2 4003 59N 59N CA C 468 473 -112.43 -180.00 67.57 13.51 -180.00 67.57 13.51
3 4075 131L 131L CA C 1048 1053 -149.56 -180.00 30.44 6.08 -180.00 30.44 6.08
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.73 3.50 2.23 22.28 3.50 2.23 22.28
2 12136 43W 131L N O 337 1054 4.54 3.50 1.04 10.36 3.50 1.04 10.36
3 12137 60T 132P N O 475 1061 8.94 3.50 5.44 54.36 3.50 5.44 54.36
-------------------------------------------------------------------------------------------------
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 -74.02 -73.00 15.99 1.02 -63.80 163.36 24.56
1 2Q 2Q N CA 9 10 156.66 140.70 -40.30
2 3811 2Q 3K C N 16 18 -58.46 -70.20 14.96 0.90 -62.90 171.98 22.58
2 3K 3K N CA 18 19 131.12 140.40 -40.80
3 3812 3K 4L C N 25 27 -115.32 -108.50 26.86 1.37 -63.50 168.49 26.59
3 4L 4L N CA 27 28 158.48 132.50 -41.20
4 3815 6I 7F C N 49 51 -122.32 -124.20 3.19 0.09 -63.20 -175.31 29.57
4 7F 7F N CA 51 52 140.73 143.30 -44.30
5 3816 7F 8A C N 60 62 -155.68 -134.00 22.65 0.55 -62.50 -170.03 36.11
5 8A 8A N CA 62 63 153.55 147.00 -40.90
6 3817 8A 9L C N 65 67 -89.24 -108.50 41.89 2.02 -63.50 138.91 17.98
6 9L 9L N CA 67 68 95.30 132.50 -41.20
7 3820 11V 12L C N 87 89 -64.56 -70.70 6.14 0.56 -63.50 176.98 24.63
7 12L 12L N CA 89 90 141.82 141.60 -41.20
8 3821 12L 13C C N 95 97 -61.44 -63.00 2.90 0.30 -117.90 -175.78 7.94
8 13C 13C N CA 97 98 -43.54 -41.10 141.10
9 3823 14V 15G C N 108 110 177.43 -167.20 19.35 0.68 82.20 -178.65 13.00
9 15G 15G N CA 110 111 162.84 174.60 8.50
10 3824 15G 16S C N 112 114 -108.97 -136.60 35.78 1.11 -64.10 169.51 10.51
10 16S 16S N CA 114 115 128.46 151.20 -35.00
11 3844 35F 36E C N 274 276 47.23 54.60 7.62 0.77 -63.60 139.44 23.93
11 36E 36E N CA 276 277 44.32 42.40 -40.30
12 3859 50E 51S C N 405 407 -146.54 -64.10 92.86 9.54 -64.10 92.86 9.54
12 51S 51S N CA 407 408 7.74 -35.00 -35.00
13 3860 51S 52S C N 411 413 58.02 56.90 5.60 0.27 -64.10 138.77 18.36
13 52S 52S N CA 413 414 30.91 36.40 -35.00
14 3896 87K 88D C N 695 697 161.93 -96.50 102.88 4.19 -63.30 -167.23 21.68
14 88D 88D N CA 697 698 97.84 114.20 -40.00
15 3920 111I 112Y C N 872 874 -46.70 -98.40 57.52 3.53 -63.50 147.55 24.28
15 112Y 112Y N CA 874 875 103.19 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -147.34 -125.60 102.22 4.26 -63.20 116.95 13.24
16 126H 126H N CA 1012 1013 38.92 138.80 -42.30
17 3935 126H 127C C N 1020 1022 -159.54 -63.00 100.29 17.72 -63.00 100.29 17.72
17 127C 127C N CA 1022 1023 -68.28 -41.10 -41.10
18 3936 127C 128Q C N 1026 1028 63.75 55.10 84.37 6.77 -121.10 175.83 6.94
18 128Q 128Q N CA 1028 1029 124.23 40.30 139.70
19 3937 128Q 129G C N 1035 1037 91.52 82.20 178.37 8.19 82.20 178.37 8.19
19 129G 129G N CA 1037 1038 -169.63 8.50 8.50
20 3941 132P 133D C N 1060 1062 -153.18 -63.30 118.92 20.00 -63.30 118.92 20.00
20 133D 133D N CA 1062 1063 -117.87 -40.00 -40.00
21 3942 133D 134I C N 1068 1070 -98.40 -97.30 30.28 3.15 -63.40 144.84 22.65
21 134I 134I N CA 1070 1071 96.95 127.20 -43.60
22 3943 134I 135S C N 1076 1078 -151.16 -64.10 109.94 9.91 -64.10 109.94 9.91
22 135S 135S N CA 1078 1079 32.13 -35.00 -35.00
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 388 1061 2.281
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 1 2 2 18 33 104 97 151 151 173 174 195 211
<< end of ENERGY.
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3041
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 : 6941.1816
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 7 19 0.023 0.023 178.16 1.000
2 Bond angle potential : 1504 13 48 4.000 4.000 459.48 1.000
3 Stereochemical cosine torsion poten: 713 0 39 49.571 49.571 276.94 1.000
4 Stereochemical improper torsion pot: 461 1 5 2.649 2.649 67.194 1.000
5 Soft-sphere overlap restraints : 3041 3 9 0.014 0.014 68.950 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 91 191 1.166 1.166 2285.1 1.000
10 Distance restraints 2 (N-O) : 2371 71 164 1.019 1.019 1963.3 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 2 8 6.399 6.399 65.666 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 6 71.939 71.939 53.067 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 77.622 77.622 39.372 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 82.347 82.347 26.043 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 100.251 100.251 16.975 1.000
18 Disulfide distance restraints : 3 0 0 0.037 0.037 0.70426 1.000
19 Disulfide angle restraints : 6 0 0 4.881 4.881 3.1569 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.650 25.650 1.5930 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.243 3.243 930.77 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 1 0.505 0.505 60.097 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 24 26 40.138 70.209 160.78 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 2 10 1.264 1.264 131.16 1.000
27 Distance restraints 5 (X-Y) : 1389 5 9 0.120 0.120 152.73 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: Sequence.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: 26096.6719
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.74 1.43 0.31 10.08 1.43 0.31 10.08
2 488 60T 60T C CA 480 476 1.72 1.49 0.23 6.68 1.49 0.23 6.68
3 1078 132P 132P O C 1061 1060 1.37 1.23 0.14 6.50 1.23 0.14 6.50
4 1079 132P 132P C CA 1060 1056 1.65 1.49 0.16 4.60 1.49 0.16 4.60
5 1080 132P 133D C N 1060 1062 1.49 1.35 0.14 5.09 1.35 0.14 5.09
6 1090 133D 133D N CA 1062 1063 1.58 1.43 0.15 4.91 1.43 0.15 4.91
-------------------------------------------------------------------------------------------------
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 697 698 129.71 107.00 22.71 6.53 107.00 22.71 6.53
2 2214 101I 101I N CA 794 795 122.92 107.00 15.92 4.58 107.00 15.92 4.58
3 2222 101I 102T C N 800 802 144.98 120.00 24.98 5.68 120.00 24.98 5.68
4 2574 131L 132P C N 1053 1055 144.48 117.00 27.48 6.84 117.00 27.48 6.84
5 2576 132P 131L N C 1055 1053 139.70 122.50 17.20 4.95 122.50 17.20 4.95
6 2577 132P 132P N CA 1055 1056 146.91 108.20 38.72 8.80 108.20 38.72 8.80
7 2586 132P 133D C N 1060 1062 150.95 120.00 30.95 7.03 120.00 30.95 7.03
8 2589 133D 133D N CA 1062 1063 128.99 107.00 21.99 6.32 107.00 21.99 6.32
9 2611 135S 135S N CA 1078 1079 123.63 107.00 16.63 4.78 107.00 16.63 4.78
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4952 38N 132P CA CA 295 1056 14.72 11.84 2.87 5.53 11.84 2.87 5.53
2 4974 39L 132P CA CA 303 1056 14.23 9.77 4.46 7.93 9.77 4.46 7.93
3 4975 39L 133D CA CA 303 1063 15.29 10.76 4.53 6.04 10.76 4.53 6.04
4 4997 40M 132P CA CA 311 1056 11.80 9.28 2.53 5.68 9.28 2.53 5.68
5 4998 40M 133D CA CA 311 1063 12.74 9.89 2.85 4.63 9.89 2.85 4.63
6 5022 41R 132P CA CA 319 1056 10.94 5.64 5.30 13.27 5.64 5.30 13.27
7 5023 41R 133D CA CA 319 1063 10.78 6.81 3.96 7.47 6.81 3.96 7.47
8 5057 42N 132P CA CA 330 1056 10.17 7.04 3.13 7.08 7.04 3.13 7.08
9 6505 124K 128Q CA CA 996 1029 7.91 5.18 2.73 6.78 5.18 2.73 6.78
10 6507 124K 130S CA CA 996 1042 13.50 10.06 3.44 5.30 10.06 3.44 5.30
11 6511 125N 128Q CA CA 1005 1029 9.43 6.66 2.78 5.59 6.66 2.78 5.59
12 6512 125N 129G CA CA 1005 1038 12.89 9.45 3.44 4.51 9.45 3.44 4.51
13 6513 125N 130S CA CA 1005 1042 14.78 9.78 5.00 7.35 9.78 5.00 7.35
14 6518 126H 130S CA CA 1013 1042 13.12 7.42 5.70 10.89 7.42 5.70 10.89
15 6520 126H 132P CA CA 1013 1056 12.72 9.77 2.95 5.73 9.77 2.95 5.73
16 6525 127C 130S CA CA 1023 1042 9.66 5.30 4.36 11.89 5.30 4.36 11.89
17 6527 127C 132P CA CA 1023 1056 10.30 7.04 3.26 9.70 7.04 3.26 9.70
18 6552 132P 135S CA CA 1056 1079 8.76 5.61 3.15 6.32 5.61 3.15 6.32
19 6553 132P 136S CA CA 1056 1085 11.98 7.77 4.21 6.85 7.77 4.21 6.85
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 16.02 10.18 5.84 9.25 10.18 5.84 9.25
2 6967 40M 132P N O 310 1061 14.83 8.51 6.32 13.20 8.51 6.32 13.20
3 6991 41R 132P N O 318 1061 13.34 5.74 7.60 15.99 5.74 7.60 15.99
4 7019 42N 132P N O 329 1061 12.16 6.20 5.96 12.13 6.20 5.96 12.13
5 7535 66K 59N N O 519 474 7.28 4.44 2.84 5.66 4.44 2.84 5.66
6 7561 67D 59N N O 528 474 5.31 2.79 2.51 5.39 2.79 2.51 5.39
7 7801 75D 59N N O 596 474 10.27 7.52 2.74 4.94 7.52 2.74 4.94
8 8757 125N 128Q N O 1004 1036 10.51 6.57 3.95 6.66 6.57 3.95 6.66
9 8773 126H 128Q N O 1012 1036 9.08 6.16 2.92 5.56 6.16 2.92 5.56
10 8794 127C 130S N O 1022 1046 9.75 7.34 2.41 4.63 7.34 2.41 4.63
11 8808 128Q 123W N O 1028 994 4.85 2.79 2.06 5.59 2.79 2.06 5.59
12 8809 128Q 124K N O 1028 1003 7.37 4.29 3.08 6.48 4.29 3.08 6.48
13 8822 129G 124K N O 1037 1003 10.31 6.40 3.91 5.60 6.40 3.91 5.60
14 8831 130S 123W N O 1041 994 11.10 7.33 3.77 6.85 7.33 3.77 6.85
15 8832 130S 124K N O 1041 1003 13.76 7.82 5.94 9.32 7.82 5.94 9.32
16 8833 130S 125N N O 1041 1011 14.40 7.78 6.62 9.71 7.78 6.62 9.71
17 8834 130S 126H N O 1041 1021 11.43 5.94 5.50 9.98 5.94 5.50 9.98
18 8835 130S 127C N O 1041 1027 8.67 3.18 5.49 14.64 3.18 5.49 14.64
19 8842 131L 125N N O 1047 1011 14.37 9.93 4.44 4.86 9.93 4.44 4.86
20 8843 131L 126H N O 1047 1021 11.18 6.80 4.38 6.33 6.80 4.38 6.33
21 8844 131L 127C N O 1047 1027 9.42 5.43 3.99 7.34 5.43 3.99 7.34
22 8856 132P 126H N O 1055 1021 11.44 7.67 3.77 7.38 7.67 3.77 7.38
23 8857 132P 127C N O 1055 1027 10.61 6.04 4.57 12.71 6.04 4.57 12.71
24 8870 133D 127C N O 1062 1027 12.18 8.59 3.59 5.36 8.59 3.59 5.36
25 8884 134I 132P N O 1070 1061 6.41 3.18 3.23 5.79 3.18 3.23 5.79
26 8897 135S 127C N O 1078 1027 13.10 10.21 2.89 5.15 10.21 2.89 5.15
27 8900 135S 132P N O 1078 1061 9.34 2.93 6.41 14.00 2.93 6.41 14.00
28 8917 136S 132P N O 1084 1061 12.04 4.11 7.92 14.63 4.11 7.92 14.63
29 8928 137C 132P N O 1090 1061 14.09 5.93 8.16 7.28 5.93 8.16 7.28
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.63 3.50 2.13 21.27 3.50 2.13 21.27
2 12136 43W 131L N O 337 1054 4.92 3.50 1.42 14.16 3.50 1.42 14.16
3 12137 60T 132P N O 475 1061 8.50 3.50 5.00 50.01 3.50 5.00 50.01
-------------------------------------------------------------------------------------------------
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 -117.69 -121.10 51.50 2.51 -63.80 139.45 23.34
1 2Q 2Q N CA 9 10 -168.91 139.70 -40.30
2 3811 2Q 3K C N 16 18 -56.17 -70.20 15.79 1.29 -62.90 171.69 21.94
2 3K 3K N CA 18 19 147.65 140.40 -40.80
3 3812 3K 4L C N 25 27 -78.77 -108.50 54.41 2.56 -63.50 129.04 17.10
3 4L 4L N CA 27 28 86.93 132.50 -41.20
4 3815 6I 7F C N 49 51 -70.70 -71.40 3.92 0.30 -63.20 179.01 25.36
4 7F 7F N CA 51 52 136.84 140.70 -44.30
5 3816 7F 8A C N 60 62 -65.99 -68.20 22.58 1.74 -62.50 163.76 26.67
5 8A 8A N CA 62 63 122.83 145.30 -40.90
6 3817 8A 9L C N 65 67 -133.89 -108.50 25.72 1.28 -63.50 -176.34 22.64
6 9L 9L N CA 67 68 128.43 132.50 -41.20
7 3819 10V 11V C N 80 82 -61.77 -62.40 2.80 0.39 -125.40 -171.89 10.54
7 11V 11V N CA 82 83 -39.67 -42.40 143.30
8 3820 11V 12L C N 87 89 -75.64 -70.70 17.40 1.15 -63.50 160.97 23.07
8 12L 12L N CA 89 90 158.28 141.60 -41.20
9 3823 14V 15G C N 108 110 79.92 78.70 8.55 0.19 82.20 176.95 8.48
9 15G 15G N CA 110 111 -174.56 -166.10 8.50
10 3824 15G 16S C N 112 114 -108.76 -136.60 57.28 2.19 -64.10 143.28 8.83
10 16S 16S N CA 114 115 101.14 151.20 -35.00
11 3844 35F 36E C N 274 276 49.70 54.60 4.90 0.57 -63.60 140.29 24.10
11 36E 36E N CA 276 277 42.44 42.40 -40.30
12 3859 50E 51S C N 405 407 -159.81 -136.60 113.94 6.19 -64.10 121.38 10.89
12 51S 51S N CA 407 408 39.64 151.20 -35.00
13 3860 51S 52S C N 411 413 54.09 56.90 25.77 1.88 -64.10 126.75 16.95
13 52S 52S N CA 413 414 10.79 36.40 -35.00
14 3867 58T 59N C N 465 467 -70.58 -63.20 10.67 1.72 -119.90 -178.95 9.21
14 59N 59N N CA 467 468 -48.80 -41.10 137.00
15 3868 59N 60T C N 473 475 78.04 -78.10 156.97 9.85 -78.10 156.97 9.85
15 60T 60T N CA 475 476 165.89 149.80 149.80
16 3896 87K 88D C N 695 697 -149.70 -63.30 87.22 14.33 -63.30 87.22 14.33
16 88D 88D N CA 697 698 -51.92 -40.00 -40.00
17 3920 111I 112Y C N 872 874 -43.43 -98.40 61.07 3.74 -63.50 146.57 24.29
17 112Y 112Y N CA 874 875 101.79 128.40 -43.40
18 3934 125N 126H C N 1010 1012 -137.66 -63.20 90.46 11.02 -63.20 90.46 11.02
18 126H 126H N CA 1012 1013 9.05 -42.30 -42.30
19 3935 126H 127C C N 1020 1022 -140.67 -117.90 70.32 2.38 -63.00 135.69 22.29
19 127C 127C N CA 1022 1023 -152.37 141.10 -41.10
20 3937 128Q 129G C N 1035 1037 82.28 82.20 166.75 8.09 82.20 166.75 8.09
20 129G 129G N CA 1037 1038 -158.25 8.50 8.50
21 3938 129G 130S C N 1039 1041 -71.15 -64.10 27.24 2.46 -72.40 146.29 8.65
21 130S 130S N CA 1041 1042 -61.31 -35.00 152.40
22 3941 132P 133D C N 1060 1062 -156.25 -96.50 72.78 3.03 -63.30 -171.26 29.26
22 133D 133D N CA 1062 1063 155.74 114.20 -40.00
23 3942 133D 134I C N 1068 1070 25.18 -97.30 123.48 5.55 -63.40 178.65 32.48
23 134I 134I N CA 1070 1071 111.54 127.20 -43.60
24 3943 134I 135S C N 1076 1078 -158.35 -64.10 100.34 11.16 -64.10 100.34 11.16
24 135S 135S N CA 1078 1079 -0.57 -35.00 -35.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10349 41R 132P CB CB 320 1058 12.75 3.70 9.04 6.58 3.70 9.04 6.58
2 10419 47V 71F CB CE1 374 566 10.34 4.53 5.82 4.63 4.53 5.82 4.63
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 3 22 38 112 117 163 195 186 186 194 230
<< end of ENERGY.
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: -93.2466
>> 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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2877
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 : 7102.7695
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 8 27 0.024 0.024 191.84 1.000
2 Bond angle potential : 1504 14 56 4.018 4.018 466.76 1.000
3 Stereochemical cosine torsion poten: 713 0 36 49.746 49.746 275.37 1.000
4 Stereochemical improper torsion pot: 461 1 9 2.698 2.698 74.687 1.000
5 Soft-sphere overlap restraints : 2877 4 9 0.015 0.015 78.822 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 96 185 1.182 1.182 2376.5 1.000
10 Distance restraints 2 (N-O) : 2371 80 192 1.032 1.032 2052.9 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 3 6 7.814 7.814 97.939 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 7 72.266 72.266 57.518 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 79.363 79.363 51.525 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.859 80.859 23.944 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 80.543 80.543 13.754 1.000
18 Disulfide distance restraints : 3 0 0 0.031 0.031 0.50350 1.000
19 Disulfide angle restraints : 6 0 0 4.007 4.007 2.1271 1.000
20 Disulfide dihedral angle restraints: 3 0 0 31.497 31.497 2.1137 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 2.970 2.970 780.62 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 1 0.492 0.492 56.241 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 24 32 36.687 76.160 202.72 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 1 9 1.197 1.197 121.98 1.000
27 Distance restraints 5 (X-Y) : 1389 5 15 0.129 0.129 174.84 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: Sequence.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: 26369.1328
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.72 1.43 0.29 9.43 1.43 0.29 9.43
2 488 60T 60T C CA 480 476 1.66 1.49 0.17 5.06 1.49 0.17 5.06
3 1078 132P 132P O C 1061 1060 1.33 1.23 0.10 4.77 1.23 0.10 4.77
4 1079 132P 132P C CA 1060 1056 1.66 1.49 0.17 4.94 1.49 0.17 4.94
5 1080 132P 133D C N 1060 1062 1.50 1.35 0.15 5.38 1.35 0.15 5.38
6 1090 133D 133D N CA 1062 1063 1.59 1.43 0.16 5.31 1.43 0.16 5.31
7 1092 133D 133D C CA 1068 1063 1.67 1.49 0.18 5.21 1.49 0.18 5.21
8 1098 134I 134I N CA 1070 1071 1.57 1.43 0.14 4.56 1.43 0.14 4.56
-------------------------------------------------------------------------------------------------
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 697 698 128.76 107.00 21.76 6.26 107.00 21.76 6.26
2 2211 100D 101I C N 792 794 140.48 120.00 20.48 4.65 120.00 20.48 4.65
3 2214 101I 101I N CA 794 795 123.53 107.00 16.53 4.75 107.00 16.53 4.75
4 2222 101I 102T C N 800 802 145.78 120.00 25.78 5.86 120.00 25.78 5.86
5 2574 131L 132P C N 1053 1055 145.96 117.00 28.96 7.21 117.00 28.96 7.21
6 2576 132P 131L N C 1055 1053 140.60 122.50 18.10 5.21 122.50 18.10 5.21
7 2577 132P 132P N CA 1055 1056 145.28 108.20 37.09 8.43 108.20 37.09 8.43
8 2586 132P 133D C N 1060 1062 141.88 120.00 21.88 4.97 120.00 21.88 4.97
9 2589 133D 133D N CA 1062 1063 134.58 107.00 27.58 7.93 107.00 27.58 7.93
10 2592 133D 133D CA C 1063 1068 134.06 116.50 17.56 5.05 116.50 17.56 5.05
11 2600 134I 134I N CA 1070 1071 124.70 107.00 17.70 5.09 107.00 17.70 5.09
12 2611 135S 135S N CA 1078 1079 123.53 107.00 16.53 4.75 107.00 16.53 4.75
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4952 38N 132P CA CA 295 1056 14.30 11.84 2.46 4.74 11.84 2.46 4.74
2 4974 39L 132P CA CA 303 1056 14.13 9.77 4.35 7.74 9.77 4.35 7.74
3 4997 40M 132P CA CA 311 1056 12.29 9.28 3.01 6.77 9.28 3.01 6.77
4 5022 41R 132P CA CA 319 1056 11.17 5.64 5.53 13.85 5.64 5.53 13.85
5 5023 41R 133D CA CA 319 1063 10.34 6.81 3.53 6.65 6.81 3.53 6.65
6 5057 42N 132P CA CA 330 1056 9.71 7.04 2.67 6.03 7.04 2.67 6.03
7 6505 124K 128Q CA CA 996 1029 7.77 5.18 2.59 6.42 5.18 2.59 6.42
8 6511 125N 128Q CA CA 1005 1029 9.48 6.66 2.82 5.68 6.66 2.82 5.68
9 6512 125N 129G CA CA 1005 1038 12.90 9.45 3.45 4.53 9.45 3.45 4.53
10 6513 125N 130S CA CA 1005 1042 14.56 9.78 4.78 7.02 9.78 4.78 7.02
11 6518 126H 130S CA CA 1013 1042 12.36 7.42 4.94 9.44 7.42 4.94 9.44
12 6525 127C 130S CA CA 1023 1042 9.53 5.30 4.23 11.54 5.30 4.23 11.54
13 6527 127C 132P CA CA 1023 1056 9.28 7.04 2.24 6.67 7.04 2.24 6.67
14 6552 132P 135S CA CA 1056 1079 9.80 5.61 4.19 8.41 5.61 4.19 8.41
15 6553 132P 136S CA CA 1056 1085 12.30 7.77 4.53 7.38 7.77 4.53 7.38
16 6556 133D 136S CA CA 1063 1085 11.15 6.03 5.12 4.67 6.03 5.12 4.67
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 15.77 10.18 5.59 8.85 10.18 5.59 8.85
2 6967 40M 132P N O 310 1061 15.13 8.51 6.62 13.83 8.51 6.62 13.83
3 6991 41R 132P N O 318 1061 13.75 5.74 8.01 16.84 5.74 8.01 16.84
4 6992 41R 133D N O 318 1069 10.85 7.72 3.13 4.73 7.72 3.13 4.73
5 7019 42N 132P N O 329 1061 12.24 6.20 6.04 12.31 6.20 6.04 12.31
6 7107 45C 132P N O 358 1061 9.00 6.76 2.24 4.94 6.76 2.24 4.94
7 7201 49H 46L N O 388 371 5.52 3.52 2.00 4.56 3.52 2.00 4.56
8 7223 50E 46L N O 398 371 4.83 2.85 1.98 5.19 2.85 1.98 5.19
9 7516 65S 59N N O 513 474 9.41 6.93 2.48 4.54 6.93 2.48 4.54
10 7535 66K 59N N O 519 474 7.26 4.44 2.82 5.63 4.44 2.82 5.63
11 7561 67D 59N N O 528 474 5.30 2.79 2.51 5.37 2.79 2.51 5.37
12 7801 75D 59N N O 596 474 10.20 7.52 2.68 4.81 7.52 2.68 4.81
13 8023 86G 63N N O 684 508 10.95 7.27 3.67 5.19 7.27 3.67 5.19
14 8033 87K 63N N O 688 508 12.41 8.66 3.75 6.26 8.66 3.75 6.26
15 8757 125N 128Q N O 1004 1036 10.23 6.57 3.67 6.18 6.57 3.67 6.18
16 8773 126H 128Q N O 1012 1036 8.96 6.16 2.80 5.33 6.16 2.80 5.33
17 8808 128Q 123W N O 1028 994 4.75 2.79 1.96 5.32 2.79 1.96 5.32
18 8809 128Q 124K N O 1028 1003 6.92 4.29 2.62 5.51 4.29 2.62 5.51
19 8822 129G 124K N O 1037 1003 10.29 6.40 3.89 5.57 6.40 3.89 5.57
20 8831 130S 123W N O 1041 994 11.13 7.33 3.80 6.91 7.33 3.80 6.91
21 8832 130S 124K N O 1041 1003 13.59 7.82 5.77 9.05 7.82 5.77 9.05
22 8833 130S 125N N O 1041 1011 13.58 7.78 5.80 8.51 7.78 5.80 8.51
23 8834 130S 126H N O 1041 1021 11.52 5.94 5.58 10.13 5.94 5.58 10.13
24 8835 130S 127C N O 1041 1027 6.91 3.18 3.72 9.93 3.18 3.72 9.93
25 8843 131L 126H N O 1047 1021 11.40 6.80 4.60 6.66 6.80 4.60 6.66
26 8856 132P 126H N O 1055 1021 10.74 7.67 3.07 6.01 7.67 3.07 6.01
27 8884 134I 132P N O 1070 1061 6.33 3.18 3.15 5.65 3.18 3.15 5.65
28 8900 135S 132P N O 1078 1061 9.59 2.93 6.66 14.56 2.93 6.66 14.56
29 8917 136S 132P N O 1084 1061 12.83 4.11 8.72 16.09 4.11 8.72 16.09
30 8918 136S 133D N O 1084 1069 8.99 3.24 5.75 5.48 3.24 5.75 5.48
31 8928 137C 132P N O 1090 1061 14.57 5.93 8.64 7.71 5.93 8.64 7.71
32 8929 137C 133D N O 1090 1069 10.60 3.22 7.39 4.78 3.22 7.39 4.78
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4075 131L 131L CA C 1048 1053 -152.88 -180.00 27.12 5.42 -180.00 27.12 5.42
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.85 3.50 2.35 23.49 3.50 2.35 23.49
2 12136 43W 131L N O 337 1054 4.60 3.50 1.10 11.04 3.50 1.10 11.04
3 12137 60T 132P N O 475 1061 7.94 3.50 4.44 44.41 3.50 4.44 44.41
-------------------------------------------------------------------------------------------------
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 -110.15 -121.10 12.71 0.61 -63.80 179.62 28.89
1 2Q 2Q N CA 9 10 146.16 139.70 -40.30
2 3811 2Q 3K C N 16 18 -78.37 -70.20 14.12 0.85 -62.90 168.00 22.69
2 3K 3K N CA 18 19 151.91 140.40 -40.80
3 3812 3K 4L C N 25 27 -71.21 -70.70 2.39 0.20 -63.50 179.70 25.40
3 4L 4L N CA 27 28 139.27 141.60 -41.20
4 3815 6I 7F C N 49 51 -110.08 -124.20 19.65 0.52 -63.20 -179.85 22.10
4 7F 7F N CA 51 52 129.64 143.30 -44.30
5 3816 7F 8A C N 60 62 -139.44 -134.00 6.13 0.14 -62.50 -174.04 34.60
5 8A 8A N CA 62 63 149.81 147.00 -40.90
6 3817 8A 9L C N 65 67 -76.68 -70.70 7.26 0.50 -63.50 173.58 24.88
6 9L 9L N CA 67 68 145.72 141.60 -41.20
7 3820 11V 12L C N 87 89 -111.48 -108.50 6.00 0.29 -63.50 -174.77 23.44
7 12L 12L N CA 89 90 137.71 132.50 -41.20
8 3823 14V 15G C N 108 110 99.20 78.70 39.60 0.61 82.20 152.46 8.25
8 15G 15G N CA 110 111 160.01 -166.10 8.50
9 3824 15G 16S C N 112 114 -140.91 -136.60 9.38 0.53 -64.10 -166.26 12.08
9 16S 16S N CA 114 115 142.87 151.20 -35.00
10 3842 33H 34G C N 259 261 -90.45 -62.40 31.98 4.91 82.20 176.04 12.89
10 34G 34G N CA 261 262 -25.84 -41.20 8.50
11 3844 35F 36E C N 274 276 51.99 54.60 2.64 0.33 -63.60 141.89 24.38
11 36E 36E N CA 276 277 41.99 42.40 -40.30
12 3860 51S 52S C N 411 413 62.88 56.90 7.48 0.54 -64.10 143.53 19.02
12 52S 52S N CA 413 414 31.90 36.40 -35.00
13 3867 58T 59N C N 465 467 -77.69 -63.20 20.60 3.33 -119.90 172.50 8.69
13 59N 59N N CA 467 468 -55.74 -41.10 137.00
14 3868 59N 60T C N 473 475 91.36 -124.80 144.70 7.25 -78.10 169.73 10.50
14 60T 60T N CA 475 476 159.33 143.50 149.80
15 3871 62R 63N C N 499 501 -72.71 -119.90 65.46 3.54 -63.20 136.87 17.64
15 63N 63N N CA 501 502 -177.63 137.00 -41.10
16 3872 63N 64G C N 507 509 -63.24 -62.40 20.04 2.95 82.20 148.44 10.89
16 64G 64G N CA 509 510 -21.18 -41.20 8.50
17 3896 87K 88D C N 695 697 169.99 -96.50 96.60 3.93 -63.30 -178.47 20.41
17 88D 88D N CA 697 698 90.00 114.20 -40.00
18 3919 110K 111I C N 864 866 -58.38 -63.40 39.30 6.62 -63.40 39.30 6.62
18 111I 111I N CA 866 867 -4.62 -43.60 -43.60
19 3935 126H 127C C N 1020 1022 -166.55 -117.90 53.60 1.50 -63.00 -173.35 30.44
19 127C 127C N CA 1022 1023 163.61 141.10 -41.10
20 3937 128Q 129G C N 1035 1037 99.43 82.20 173.90 7.57 82.20 173.90 7.57
20 129G 129G N CA 1037 1038 -164.54 8.50 8.50
21 3938 129G 130S C N 1039 1041 -73.09 -64.10 34.29 3.10 -72.40 139.50 8.18
21 130S 130S N CA 1041 1042 -68.10 -35.00 152.40
22 3941 132P 133D C N 1060 1062 -178.39 -63.30 122.72 16.97 -63.30 122.72 16.97
22 133D 133D N CA 1062 1063 2.60 -40.00 -40.00
23 3942 133D 134I C N 1068 1070 -125.58 -63.40 68.69 12.93 -63.40 68.69 12.93
23 134I 134I N CA 1070 1071 -72.78 -43.60 -43.60
24 3943 134I 135S C N 1076 1078 -166.68 -136.60 33.14 1.03 -64.10 -170.03 21.17
24 135S 135S N CA 1078 1079 165.11 151.20 -35.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10349 41R 132P CB CB 320 1058 12.74 3.70 9.03 6.58 3.70 9.03 6.58
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 1 3 21 43 102 109 152 145 150 194 194 256
<< end of ENERGY.
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2929
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 : 7274.1895
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 6 17 0.024 0.024 192.89 1.000
2 Bond angle potential : 1504 13 46 4.116 4.116 478.56 1.000
3 Stereochemical cosine torsion poten: 713 0 38 49.739 49.739 274.45 1.000
4 Stereochemical improper torsion pot: 461 0 5 2.263 2.263 56.543 1.000
5 Soft-sphere overlap restraints : 2929 5 9 0.017 0.017 102.65 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 86 186 1.150 1.150 2304.5 1.000
10 Distance restraints 2 (N-O) : 2371 73 165 0.998 0.998 1976.7 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 4 8 9.627 9.627 148.64 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 81.019 81.019 49.456 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 78.119 78.119 42.972 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 81.060 81.060 27.044 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 80.280 80.280 13.844 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.44033 1.000
19 Disulfide angle restraints : 6 0 1 5.735 5.735 4.3572 1.000
20 Disulfide dihedral angle restraints: 3 0 0 43.432 43.432 4.0599 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.363 3.363 1001.3 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.572 0.572 78.329 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 25 38.732 70.049 160.80 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 7 1.245 1.245 124.50 1.000
27 Distance restraints 5 (X-Y) : 1389 6 25 0.149 0.149 232.14 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: Sequence.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: 26579.0684
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 384 47V 47V C CA 377 373 1.65 1.49 0.16 4.71 1.49 0.16 4.71
2 486 60T 60T N CA 475 476 1.75 1.43 0.32 10.66 1.43 0.32 10.66
3 488 60T 60T C CA 480 476 1.74 1.49 0.25 7.16 1.49 0.25 7.16
4 489 60T 61N C N 480 482 1.49 1.35 0.15 5.16 1.35 0.15 5.16
5 1078 132P 132P O C 1061 1060 1.39 1.23 0.16 7.52 1.23 0.16 7.52
6 1079 132P 132P C CA 1060 1056 1.73 1.49 0.24 7.07 1.49 0.24 7.07
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 129.10 107.00 22.10 6.35 107.00 22.10 6.35
2 1640 47V 48E C N 377 379 142.90 120.00 22.90 5.20 120.00 22.90 5.20
3 1773 60T 60T N CA 475 476 127.75 107.00 20.75 5.97 107.00 20.75 5.97
4 1783 61N 61N N CA 482 483 125.79 107.00 18.79 5.40 107.00 18.79 5.40
5 2080 88D 88D N CA 697 698 130.58 107.00 23.58 6.78 107.00 23.58 6.78
6 2214 101I 101I N CA 794 795 123.99 107.00 16.99 4.89 107.00 16.99 4.89
7 2222 101I 102T C N 800 802 143.43 120.00 23.43 5.32 120.00 23.43 5.32
8 2532 127C 127C N CA 1022 1023 122.83 107.00 15.83 4.55 107.00 15.83 4.55
9 2577 132P 132P N CA 1055 1056 148.52 108.20 40.32 9.16 108.20 40.32 9.16
10 2586 132P 133D C N 1060 1062 147.49 120.00 27.49 6.25 120.00 27.49 6.25
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.03 9.77 3.26 5.79 9.77 3.26 5.79
2 4975 39L 133D CA CA 303 1063 14.27 10.76 3.51 4.68 10.76 3.51 4.68
3 5022 41R 132P CA CA 319 1056 8.69 5.64 3.05 7.64 5.64 3.05 7.64
4 5023 41R 133D CA CA 319 1063 9.45 6.81 2.64 4.97 6.81 2.64 4.97
5 5571 60T 64G CA CA 476 510 10.34 6.93 3.41 6.40 6.93 3.41 6.40
6 5572 60T 65S CA CA 476 514 9.48 6.01 3.47 7.72 6.01 3.47 7.72
7 5573 60T 66K CA CA 476 520 6.88 4.22 2.66 6.62 4.22 2.66 6.62
8 5582 60T 81K CA CA 476 654 14.77 11.49 3.28 5.37 11.49 3.28 5.37
9 5583 60T 82G CA CA 476 663 17.43 13.44 3.99 5.06 13.44 3.99 5.06
10 5584 60T 83A CA CA 476 667 14.83 11.07 3.76 5.55 11.07 3.76 5.55
11 5585 60T 84S CA CA 476 672 14.14 10.32 3.82 6.76 10.32 3.82 6.76
12 5586 60T 85P CA CA 476 678 16.93 12.86 4.07 5.38 12.86 4.07 5.38
13 6505 124K 128Q CA CA 996 1029 7.92 5.18 2.73 6.79 5.18 2.73 6.79
14 6507 124K 130S CA CA 996 1042 13.24 10.06 3.18 4.90 10.06 3.18 4.90
15 6511 125N 128Q CA CA 1005 1029 9.60 6.66 2.95 5.93 6.66 2.95 5.93
16 6512 125N 129G CA CA 1005 1038 12.89 9.45 3.44 4.50 9.45 3.44 4.50
17 6513 125N 130S CA CA 1005 1042 14.09 9.78 4.31 6.33 9.78 4.31 6.33
18 6518 126H 130S CA CA 1013 1042 12.09 7.42 4.67 8.92 7.42 4.67 8.92
19 6525 127C 130S CA CA 1023 1042 8.80 5.30 3.51 9.56 5.30 3.51 9.56
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 14.52 10.18 4.33 6.87 10.18 4.33 6.87
2 6967 40M 132P N O 310 1061 13.38 8.51 4.87 10.17 8.51 4.87 10.17
3 6991 41R 132P N O 318 1061 11.51 5.74 5.77 12.14 5.74 5.77 12.14
4 7019 42N 132P N O 329 1061 10.00 6.20 3.79 7.73 6.20 3.79 7.73
5 7179 48E 44V N O 379 357 5.25 3.06 2.19 4.94 3.06 2.19 4.94
6 7468 60T 64G N O 475 512 11.22 7.82 3.40 5.31 7.82 3.40 5.31
7 7469 60T 65S N O 475 518 8.13 4.76 3.36 6.91 4.76 3.36 6.91
8 7476 60T 83A N O 475 670 15.42 11.00 4.43 6.06 11.00 4.43 6.06
9 7482 61N 65S N O 482 518 4.80 2.59 2.20 5.56 2.59 2.20 5.56
10 8757 125N 128Q N O 1004 1036 10.74 6.57 4.18 7.04 6.57 4.18 7.04
11 8773 126H 128Q N O 1012 1036 9.21 6.16 3.05 5.81 6.16 3.05 5.81
12 8794 127C 130S N O 1022 1046 10.22 7.34 2.88 5.54 7.34 2.88 5.54
13 8808 128Q 123W N O 1028 994 4.84 2.79 2.06 5.59 2.79 2.06 5.59
14 8809 128Q 124K N O 1028 1003 7.45 4.29 3.16 6.65 4.29 3.16 6.65
15 8810 128Q 125N N O 1028 1011 8.11 5.41 2.71 4.93 5.41 2.71 4.93
16 8822 129G 124K N O 1037 1003 10.59 6.40 4.19 6.00 6.40 4.19 6.00
17 8823 129G 125N N O 1037 1011 11.56 7.69 3.87 4.73 7.69 3.87 4.73
18 8831 130S 123W N O 1041 994 11.21 7.33 3.88 7.05 7.33 3.88 7.05
19 8832 130S 124K N O 1041 1003 13.91 7.82 6.09 9.56 7.82 6.09 9.56
20 8833 130S 125N N O 1041 1011 14.39 7.78 6.61 9.69 7.78 6.61 9.69
21 8834 130S 126H N O 1041 1021 11.48 5.94 5.54 10.06 5.94 5.54 10.06
22 8835 130S 127C N O 1041 1027 8.90 3.18 5.72 15.25 3.18 5.72 15.25
23 8843 131L 126H N O 1047 1021 10.68 6.80 3.88 5.61 6.80 3.88 5.61
24 8844 131L 127C N O 1047 1027 9.42 5.43 3.99 7.35 5.43 3.99 7.35
25 8857 132P 127C N O 1055 1027 9.95 6.04 3.91 10.86 6.04 3.91 10.86
26 8860 132P 130S N O 1055 1046 5.43 3.36 2.07 4.73 3.36 2.07 4.73
27 8884 134I 132P N O 1070 1061 5.95 3.18 2.77 4.97 3.18 2.77 4.97
28 8900 135S 132P N O 1078 1061 8.30 2.93 5.37 11.73 2.93 5.37 11.73
29 8917 136S 132P N O 1084 1061 10.83 4.11 6.71 12.39 4.11 6.71 12.39
30 8928 137C 132P N O 1090 1061 12.64 5.93 6.71 5.99 5.93 6.71 5.99
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 59N 59N CA C 468 473 -100.32 -180.00 79.68 15.93 -180.00 79.68 15.93
2 4070 126H 126H CA C 1013 1020 -152.98 -180.00 27.02 5.40 -180.00 27.02 5.40
3 4075 131L 131L CA C 1048 1053 -145.53 -180.00 34.47 6.89 -180.00 34.47 6.89
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.70 3.50 2.20 21.97 3.50 2.20 21.97
2 12136 43W 131L N O 337 1054 4.49 3.50 0.99 9.90 3.50 0.99 9.90
3 12137 60T 132P N O 475 1061 8.80 3.50 5.30 53.03 3.50 5.30 53.03
-------------------------------------------------------------------------------------------------
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 -73.87 -73.00 1.83 0.14 -63.80 179.68 25.90
1 2Q 2Q N CA 9 10 139.09 140.70 -40.30
2 3811 2Q 3K C N 16 18 -86.36 -70.20 16.17 1.19 -62.90 -179.18 24.83
2 3K 3K N CA 18 19 139.91 140.40 -40.80
3 3812 3K 4L C N 25 27 -84.67 -70.70 15.61 1.15 -63.50 171.56 25.09
3 4L 4L N CA 27 28 148.55 141.60 -41.20
4 3815 6I 7F C N 49 51 -96.53 -71.40 33.55 2.92 -63.20 166.15 20.94
4 7F 7F N CA 51 52 118.47 140.70 -44.30
5 3816 7F 8A C N 60 62 -145.54 -134.00 13.62 0.32 -62.50 -175.40 34.70
5 8A 8A N CA 62 63 154.23 147.00 -40.90
6 3817 8A 9L C N 65 67 -105.14 -108.50 20.56 1.14 -63.50 171.15 26.32
6 9L 9L N CA 67 68 152.79 132.50 -41.20
7 3818 9L 10V C N 73 75 -60.79 -62.40 1.65 0.24 -125.40 -174.47 10.42
7 10V 10V N CA 75 76 -42.78 -42.40 143.30
8 3820 11V 12L C N 87 89 -67.14 -70.70 3.56 0.32 -63.50 177.21 24.82
8 12L 12L N CA 89 90 141.62 141.60 -41.20
9 3823 14V 15G C N 108 110 -147.50 -167.20 43.13 1.31 82.20 -177.54 14.02
9 15G 15G N CA 110 111 136.23 174.60 8.50
10 3824 15G 16S C N 112 114 -125.04 -136.60 22.39 0.84 -64.10 177.80 10.96
10 16S 16S N CA 114 115 132.02 151.20 -35.00
11 3844 35F 36E C N 274 276 42.30 54.60 15.54 1.09 -63.60 140.41 23.98
11 36E 36E N CA 276 277 51.90 42.40 -40.30
12 3859 50E 51S C N 405 407 -148.55 -64.10 98.69 9.69 -64.10 98.69 9.69
12 51S 51S N CA 407 408 16.06 -35.00 -35.00
13 3860 51S 52S C N 411 413 56.21 56.90 2.20 0.20 -64.10 138.85 18.30
13 52S 52S N CA 413 414 34.31 36.40 -35.00
14 3896 87K 88D C N 695 697 165.21 -96.50 99.38 4.05 -63.30 -168.29 21.41
14 88D 88D N CA 697 698 99.51 114.20 -40.00
15 3920 111I 112Y C N 872 874 -33.86 -98.40 70.44 4.13 -63.50 146.60 24.78
15 112Y 112Y N CA 874 875 100.17 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -136.37 -63.20 76.07 10.86 -63.20 76.07 10.86
16 126H 126H N CA 1012 1013 -21.53 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -127.86 -117.90 71.78 2.67 -63.00 124.88 20.06
17 127C 127C N CA 1022 1023 -147.81 141.10 -41.10
18 3937 128Q 129G C N 1035 1037 73.23 82.20 178.82 8.23 82.20 178.82 8.23
18 129G 129G N CA 1037 1038 -172.90 8.50 8.50
19 3941 132P 133D C N 1060 1062 -158.30 -63.30 113.12 19.27 -63.30 113.12 19.27
19 133D 133D N CA 1062 1063 -101.40 -40.00 -40.00
20 3942 133D 134I C N 1068 1070 -79.32 -97.30 21.29 1.48 -63.40 160.19 25.72
20 134I 134I N CA 1070 1071 115.80 127.20 -43.60
21 3943 134I 135S C N 1076 1078 -51.59 -72.40 64.94 4.53 -64.10 111.78 7.44
21 135S 135S N CA 1078 1079 -146.08 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10801 63N 139. CA O6 502 1123 10.15 9.24 0.91 4.55 9.24 0.91 4.55
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 388 1061 2.284
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 1 1 7 13 42 99 109 181 139 174 199 171 227
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2765
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 : 7266.0586
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 8 20 0.025 0.025 207.06 1.000
2 Bond angle potential : 1504 12 49 4.107 4.107 482.06 1.000
3 Stereochemical cosine torsion poten: 713 0 35 49.553 49.553 277.33 1.000
4 Stereochemical improper torsion pot: 461 0 4 2.133 2.133 50.930 1.000
5 Soft-sphere overlap restraints : 2765 7 8 0.018 0.018 100.17 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 81 187 1.148 1.148 2304.3 1.000
10 Distance restraints 2 (N-O) : 2371 77 168 1.005 1.005 1981.9 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 3 11 9.821 9.821 154.70 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 77.026 77.026 42.651 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 77.393 77.393 43.204 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 1 90.904 90.904 26.926 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 1 75.147 75.147 13.600 1.000
18 Disulfide distance restraints : 3 0 0 0.041 0.041 0.88048 1.000
19 Disulfide angle restraints : 6 0 1 6.301 6.301 5.2605 1.000
20 Disulfide dihedral angle restraints: 3 0 0 16.733 16.733 0.85538 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.396 3.396 1020.5 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.500 0.500 57.501 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 24 26 39.595 73.025 160.42 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 7 1.148 1.148 104.42 1.000
27 Distance restraints 5 (X-Y) : 1389 7 23 0.149 0.149 231.30 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: Sequence.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: 26720.3770
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 384 47V 47V C CA 377 373 1.66 1.49 0.17 4.82 1.49 0.17 4.82
2 486 60T 60T N CA 475 476 1.76 1.43 0.33 10.71 1.43 0.33 10.71
3 488 60T 60T C CA 480 476 1.75 1.49 0.26 7.45 1.49 0.26 7.45
4 489 60T 61N C N 480 482 1.49 1.35 0.14 5.09 1.35 0.14 5.09
5 494 61N 61N N CA 482 483 1.57 1.43 0.14 4.63 1.43 0.14 4.63
6 717 88D 88D C CA 703 698 1.67 1.49 0.18 5.12 1.49 0.18 5.12
7 1078 132P 132P O C 1061 1060 1.39 1.23 0.16 7.55 1.23 0.16 7.55
8 1079 132P 132P C CA 1060 1056 1.73 1.49 0.24 7.03 1.49 0.24 7.03
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 128.98 107.00 21.98 6.32 107.00 21.98 6.32
2 1640 47V 48E C N 377 379 145.86 120.00 25.86 5.88 120.00 25.86 5.88
3 1773 60T 60T N CA 475 476 128.35 107.00 21.35 6.14 107.00 21.35 6.14
4 1783 61N 61N N CA 482 483 126.60 107.00 19.60 5.64 107.00 19.60 5.64
5 2080 88D 88D N CA 697 698 132.24 107.00 25.24 7.26 107.00 25.24 7.26
6 2214 101I 101I N CA 794 795 123.75 107.00 16.75 4.82 107.00 16.75 4.82
7 2222 101I 102T C N 800 802 145.94 120.00 25.94 5.89 120.00 25.94 5.89
8 2563 130S 131L C N 1045 1047 139.87 120.00 19.87 4.52 120.00 19.87 4.52
9 2577 132P 132P N CA 1055 1056 147.82 108.20 39.62 9.00 108.20 39.62 9.00
10 2586 132P 133D C N 1060 1062 147.41 120.00 27.41 6.23 120.00 27.41 6.23
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.04 9.77 3.26 5.80 9.77 3.26 5.80
2 4975 39L 133D CA CA 303 1063 14.16 10.76 3.40 4.53 10.76 3.40 4.53
3 5022 41R 132P CA CA 319 1056 8.68 5.64 3.04 7.61 5.64 3.04 7.61
4 5023 41R 133D CA CA 319 1063 9.28 6.81 2.47 4.66 6.81 2.47 4.66
5 5571 60T 64G CA CA 476 510 11.28 6.93 4.35 8.16 6.93 4.35 8.16
6 5572 60T 65S CA CA 476 514 9.63 6.01 3.62 8.06 6.01 3.62 8.06
7 5573 60T 66K CA CA 476 520 7.03 4.22 2.81 6.99 4.22 2.81 6.99
8 5582 60T 81K CA CA 476 654 14.89 11.49 3.39 5.56 11.49 3.39 5.56
9 5583 60T 82G CA CA 476 663 17.50 13.44 4.06 5.15 13.44 4.06 5.15
10 5584 60T 83A CA CA 476 667 14.99 11.07 3.92 5.78 11.07 3.92 5.78
11 5585 60T 84S CA CA 476 672 14.30 10.32 3.98 7.05 10.32 3.98 7.05
12 5586 60T 85P CA CA 476 678 16.98 12.86 4.12 5.45 12.86 4.12 5.45
13 6505 124K 128Q CA CA 996 1029 7.23 5.18 2.05 5.09 5.18 2.05 5.09
14 6507 124K 130S CA CA 996 1042 13.36 10.06 3.30 5.09 10.06 3.30 5.09
15 6511 125N 128Q CA CA 1005 1029 8.97 6.66 2.31 4.66 6.66 2.31 4.66
16 6513 125N 130S CA CA 1005 1042 14.08 9.78 4.30 6.32 9.78 4.30 6.32
17 6518 126H 130S CA CA 1013 1042 12.29 7.42 4.87 9.31 7.42 4.87 9.31
18 6525 127C 130S CA CA 1023 1042 8.85 5.30 3.55 9.68 5.30 3.55 9.68
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6949 39L 132P N O 302 1061 14.41 10.18 4.23 6.70 10.18 4.23 6.70
2 6967 40M 132P N O 310 1061 13.29 8.51 4.78 9.99 8.51 4.78 9.99
3 6991 41R 132P N O 318 1061 11.41 5.74 5.68 11.93 5.74 5.68 11.93
4 7019 42N 132P N O 329 1061 9.92 6.20 3.72 7.58 6.20 3.72 7.58
5 7179 48E 44V N O 379 357 5.23 3.06 2.18 4.91 3.06 2.18 4.91
6 7468 60T 64G N O 475 512 11.30 7.82 3.49 5.45 7.82 3.49 5.45
7 7469 60T 65S N O 475 518 8.33 4.76 3.57 7.33 4.76 3.57 7.33
8 7476 60T 83A N O 475 670 15.64 11.00 4.64 6.35 11.00 4.64 6.35
9 7482 61N 65S N O 482 518 4.93 2.59 2.33 5.89 2.59 2.33 5.89
10 7507 64G 61N N O 509 489 5.45 3.18 2.27 4.67 3.18 2.27 4.67
11 8023 86G 63N N O 684 508 11.16 7.27 3.88 5.49 7.27 3.88 5.49
12 8033 87K 63N N O 688 508 12.76 8.66 4.10 6.85 8.66 4.10 6.85
13 8757 125N 128Q N O 1004 1036 10.20 6.57 3.64 6.13 6.57 3.64 6.13
14 8773 126H 128Q N O 1012 1036 8.84 6.16 2.67 5.09 6.16 2.67 5.09
15 8794 127C 130S N O 1022 1046 10.14 7.34 2.80 5.38 7.34 2.80 5.38
16 8808 128Q 123W N O 1028 994 4.45 2.79 1.67 4.53 2.79 1.67 4.53
17 8809 128Q 124K N O 1028 1003 7.13 4.29 2.84 5.97 4.29 2.84 5.97
18 8822 129G 124K N O 1037 1003 10.67 6.40 4.27 6.12 6.40 4.27 6.12
19 8823 129G 125N N O 1037 1011 11.40 7.69 3.71 4.54 7.69 3.71 4.54
20 8831 130S 123W N O 1041 994 11.44 7.33 4.11 7.48 7.33 4.11 7.48
21 8832 130S 124K N O 1041 1003 14.13 7.82 6.31 9.89 7.82 6.31 9.89
22 8833 130S 125N N O 1041 1011 14.40 7.78 6.62 9.72 7.78 6.62 9.72
23 8834 130S 126H N O 1041 1021 11.12 5.94 5.18 9.41 5.94 5.18 9.41
24 8835 130S 127C N O 1041 1027 7.81 3.18 4.63 12.35 3.18 4.63 12.35
25 8843 131L 126H N O 1047 1021 10.16 6.80 3.36 4.87 6.80 3.36 4.87
26 8844 131L 127C N O 1047 1027 8.25 5.43 2.82 5.19 5.43 2.82 5.19
27 8857 132P 127C N O 1055 1027 8.87 6.04 2.83 7.88 6.04 2.83 7.88
28 8860 132P 130S N O 1055 1046 5.41 3.36 2.05 4.69 3.36 2.05 4.69
29 8884 134I 132P N O 1070 1061 6.03 3.18 2.85 5.11 3.18 2.85 5.11
30 8900 135S 132P N O 1078 1061 8.26 2.93 5.33 11.64 2.93 5.33 11.64
31 8917 136S 132P N O 1084 1061 10.70 4.11 6.59 12.16 4.11 6.59 12.16
32 8928 137C 132P N O 1090 1061 12.73 5.93 6.81 6.07 5.93 6.81 6.07
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 59N 59N CA C 468 473 -100.81 -180.00 79.19 15.83 -180.00 79.19 15.83
2 4075 131L 131L CA C 1048 1053 -146.73 -180.00 33.27 6.65 -180.00 33.27 6.65
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.81 3.50 2.31 23.13 3.50 2.31 23.13
2 12136 43W 131L N O 337 1054 4.54 3.50 1.04 10.41 3.50 1.04 10.41
3 12137 60T 132P N O 475 1061 8.81 3.50 5.31 53.06 3.50 5.31 53.06
-------------------------------------------------------------------------------------------------
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 -73.58 -73.00 3.74 0.23 -63.80 175.57 26.33
1 2Q 2Q N CA 9 10 144.40 140.70 -40.30
2 3811 2Q 3K C N 16 18 -109.93 -118.00 17.08 0.88 -62.90 171.62 25.07
2 3K 3K N CA 18 19 154.15 139.10 -40.80
3 3812 3K 4L C N 25 27 -95.81 -108.50 12.77 0.63 -63.50 178.06 23.07
3 4L 4L N CA 27 28 133.90 132.50 -41.20
4 3815 6I 7F C N 49 51 -103.29 -124.20 30.35 0.83 -63.20 170.39 21.14
4 7F 7F N CA 51 52 121.31 143.30 -44.30
5 3816 7F 8A C N 60 62 -131.61 -134.00 4.86 0.20 -62.50 -170.60 34.74
5 8A 8A N CA 62 63 142.76 147.00 -40.90
6 3817 8A 9L C N 65 67 -78.95 -70.70 10.63 0.71 -63.50 171.19 24.68
6 9L 9L N CA 67 68 148.31 141.60 -41.20
7 3818 9L 10V C N 73 75 -61.44 -62.40 2.71 0.30 -125.40 -176.71 10.30
7 10V 10V N CA 75 76 -44.93 -42.40 143.30
8 3820 11V 12L C N 87 89 -68.64 -70.70 2.06 0.18 -63.50 177.34 24.92
8 12L 12L N CA 89 90 141.54 141.60 -41.20
9 3823 14V 15G C N 108 110 -170.29 -167.20 32.07 1.29 82.20 171.93 12.85
9 15G 15G N CA 110 111 142.67 174.60 8.50
10 3824 15G 16S C N 112 114 -135.49 -136.60 14.19 0.70 -64.10 -173.73 11.57
10 16S 16S N CA 114 115 137.05 151.20 -35.00
11 3844 35F 36E C N 274 276 51.45 54.60 4.24 0.54 -63.60 140.05 24.08
11 36E 36E N CA 276 277 39.55 42.40 -40.30
12 3859 50E 51S C N 405 407 -150.63 -64.10 95.79 10.07 -64.10 95.79 10.07
12 51S 51S N CA 407 408 6.09 -35.00 -35.00
13 3860 51S 52S C N 411 413 55.52 56.90 1.56 0.20 -64.10 138.94 18.28
13 52S 52S N CA 413 414 35.67 36.40 -35.00
14 3871 62R 63N C N 499 501 -67.26 -119.90 62.91 3.32 -63.20 147.51 18.67
14 63N 63N N CA 501 502 171.45 137.00 -41.10
15 3872 63N 64G C N 507 509 -59.82 -62.40 16.68 2.62 82.20 145.85 10.80
15 64G 64G N CA 509 510 -24.73 -41.20 8.50
16 3896 87K 88D C N 695 697 177.50 -96.50 88.71 3.61 -63.30 178.19 19.74
16 88D 88D N CA 697 698 92.45 114.20 -40.00
17 3920 111I 112Y C N 872 874 -51.24 -98.40 52.10 3.14 -63.50 150.16 24.46
17 112Y 112Y N CA 874 875 106.26 128.40 -43.40
18 3934 125N 126H C N 1010 1012 -156.06 -125.60 110.97 4.72 -63.20 118.98 14.02
18 126H 126H N CA 1012 1013 32.09 138.80 -42.30
19 3935 126H 127C C N 1020 1022 -157.01 -63.00 101.24 18.05 -63.00 101.24 18.05
19 127C 127C N CA 1022 1023 -78.67 -41.10 -41.10
20 3936 127C 128Q C N 1026 1028 72.06 55.10 86.74 7.66 -121.10 167.45 6.60
20 128Q 128Q N CA 1028 1029 125.37 40.30 139.70
21 3937 128Q 129G C N 1035 1037 87.98 82.20 175.24 8.80 82.20 175.24 8.80
21 129G 129G N CA 1037 1038 -176.35 8.50 8.50
22 3941 132P 133D C N 1060 1062 -163.52 -63.30 123.22 20.93 -63.30 123.22 20.93
22 133D 133D N CA 1062 1063 -111.68 -40.00 -40.00
23 3942 133D 134I C N 1068 1070 -70.55 -97.30 31.26 2.13 -63.40 154.79 25.12
23 134I 134I N CA 1070 1071 111.03 127.20 -43.60
24 3943 134I 135S C N 1076 1078 -52.88 -72.40 67.76 4.66 -64.10 108.29 7.25
24 135S 135S N CA 1078 1079 -142.71 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10800 63N 139. CA C6 502 1116 10.87 9.85 1.02 5.08 9.85 1.02 5.08
2 10801 63N 139. CA O6 502 1123 10.42 9.24 1.18 5.91 9.24 1.18 5.91
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 350 1054 2.299
serious non-bonded atom clash: 388 1061 2.299
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 2 1 2 18 26 83 104 129 145 189 185 181 208
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
Sequence.B99990001.pdb 7227.18262
Sequence.B99990002.pdb 6941.18164
Sequence.B99990003.pdb 7102.76953
Sequence.B99990004.pdb 7274.18945
Sequence.B99990005.pdb 7266.05859
In [46]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('Sequence.B99990001.pdb')
w1
In [21]:
class mymodel(automodel):
def special_restraints(self, aln):
rsr = self.restraints
for ids in (('O:101:A', 'N:130:A'),
('N:43:A', 'O:131:A'),
('N:60:A', 'O:132:A')):
atoms = [self.atoms[i] for i in ids]
rsr.add(forms.upper_bound(group=physical.upper_distance,
feature=features.distance(*atoms), mean=3.5, stdev=0.1))
env = environ()
env.io.hetatm = True
a = mymodel(env, alnfile='bommo.ali', knowns=pdb.code, sequence=s.code)
a.starting_model = 1
a.ending_model = 5
a.make()
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
88 1 73 76 D C 8.895
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 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/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13097 12137
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2859
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 : 7227.1826
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 6 19 0.024 0.024 197.81 1.000
2 Bond angle potential : 1504 11 45 4.059 4.059 471.31 1.000
3 Stereochemical cosine torsion poten: 713 0 36 50.300 50.300 283.04 1.000
4 Stereochemical improper torsion pot: 461 1 4 2.230 2.230 53.955 1.000
5 Soft-sphere overlap restraints : 2859 7 9 0.018 0.018 104.00 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 81 193 1.154 1.154 2323.6 1.000
10 Distance restraints 2 (N-O) : 2371 71 159 0.985 0.985 1915.9 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 4 11 9.070 9.070 131.94 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 78.286 78.286 45.363 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 86.781 86.781 45.388 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 68.810 68.810 21.014 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 95.640 95.640 14.192 1.000
18 Disulfide distance restraints : 3 0 0 0.039 0.039 0.80268 1.000
19 Disulfide angle restraints : 6 0 1 6.098 6.098 4.9264 1.000
20 Disulfide dihedral angle restraints: 3 0 0 36.507 36.507 2.5557 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.444 3.444 1050.0 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.557 0.557 71.163 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 25 40.269 70.766 177.38 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 6 1.113 1.113 98.152 1.000
27 Distance restraints 5 (X-Y) : 1389 4 24 0.143 0.143 214.72 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: Sequence.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: 26642.1895
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.75 1.43 0.32 10.61 1.43 0.32 10.61
2 488 60T 60T C CA 480 476 1.73 1.49 0.24 6.96 1.49 0.24 6.96
3 489 60T 61N C N 480 482 1.48 1.35 0.14 4.93 1.35 0.14 4.93
4 717 88D 88D C CA 703 698 1.65 1.49 0.16 4.63 1.49 0.16 4.63
5 1078 132P 132P O C 1061 1060 1.40 1.23 0.17 7.62 1.23 0.17 7.62
6 1079 132P 132P C CA 1060 1056 1.74 1.49 0.25 7.37 1.49 0.25 7.37
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 130.54 107.00 23.54 6.77 107.00 23.54 6.77
2 1640 47V 48E C N 377 379 145.67 120.00 25.67 5.83 120.00 25.67 5.83
3 1773 60T 60T N CA 475 476 126.81 107.00 19.81 5.70 107.00 19.81 5.70
4 1783 61N 61N N CA 482 483 124.87 107.00 17.87 5.14 107.00 17.87 5.14
5 2080 88D 88D N CA 697 698 130.94 107.00 23.94 6.88 107.00 23.94 6.88
6 2214 101I 101I N CA 794 795 123.52 107.00 16.52 4.75 107.00 16.52 4.75
7 2222 101I 102T C N 800 802 144.60 120.00 24.60 5.59 120.00 24.60 5.59
8 2577 132P 132P N CA 1055 1056 148.59 108.20 40.39 9.18 108.20 40.39 9.18
9 2586 132P 133D C N 1060 1062 146.18 120.00 26.18 5.95 120.00 26.18 5.95
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.05 9.77 3.28 5.82 9.77 3.28 5.82
2 5022 41R 132P CA CA 319 1056 8.68 5.64 3.05 7.63 5.64 3.05 7.63
3 5023 41R 133D CA CA 319 1063 9.34 6.81 2.52 4.76 6.81 2.52 4.76
4 5571 60T 64G CA CA 476 510 10.31 6.93 3.38 6.33 6.93 3.38 6.33
5 5572 60T 65S CA CA 476 514 9.45 6.01 3.44 7.66 6.01 3.44 7.66
6 5573 60T 66K CA CA 476 520 6.89 4.22 2.67 6.65 4.22 2.67 6.65
7 5582 60T 81K CA CA 476 654 14.75 11.49 3.26 5.34 11.49 3.26 5.34
8 5583 60T 82G CA CA 476 663 17.31 13.44 3.88 4.92 13.44 3.88 4.92
9 5584 60T 83A CA CA 476 667 14.85 11.07 3.78 5.58 11.07 3.78 5.58
10 5585 60T 84S CA CA 476 672 14.05 10.32 3.73 6.61 10.32 3.73 6.61
11 5586 60T 85P CA CA 476 678 16.73 12.86 3.87 5.11 12.86 3.87 5.11
12 6505 124K 128Q CA CA 996 1029 7.21 5.18 2.02 5.03 5.18 2.02 5.03
13 6507 124K 130S CA CA 996 1042 13.23 10.06 3.17 4.89 10.06 3.17 4.89
14 6511 125N 128Q CA CA 1005 1029 9.01 6.66 2.35 4.74 6.66 2.35 4.74
15 6513 125N 130S CA CA 1005 1042 14.01 9.78 4.23 6.22 9.78 4.23 6.22
16 6518 126H 130S CA CA 1013 1042 12.18 7.42 4.76 9.09 7.42 4.76 9.09
17 6525 127C 130S CA CA 1023 1042 8.74 5.30 3.44 9.37 5.30 3.44 9.37
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 14.48 10.18 4.29 6.80 10.18 4.29 6.80
2 6967 40M 132P N O 310 1061 13.38 8.51 4.87 10.17 8.51 4.87 10.17
3 6991 41R 132P N O 318 1061 11.51 5.74 5.77 12.14 5.74 5.77 12.14
4 7019 42N 132P N O 329 1061 10.01 6.20 3.80 7.75 6.20 3.80 7.75
5 7179 48E 44V N O 379 357 5.28 3.06 2.22 5.01 3.06 2.22 5.01
6 7468 60T 64G N O 475 512 11.27 7.82 3.45 5.40 7.82 3.45 5.40
7 7469 60T 65S N O 475 518 8.11 4.76 3.35 6.88 4.76 3.35 6.88
8 7476 60T 83A N O 475 670 15.47 11.00 4.47 6.13 11.00 4.47 6.13
9 7482 61N 65S N O 482 518 4.77 2.59 2.17 5.49 2.59 2.17 5.49
10 8757 125N 128Q N O 1004 1036 10.23 6.57 3.66 6.17 6.57 3.66 6.17
11 8773 126H 128Q N O 1012 1036 8.90 6.16 2.73 5.21 6.16 2.73 5.21
12 8794 127C 130S N O 1022 1046 10.48 7.34 3.14 6.03 7.34 3.14 6.03
13 8808 128Q 123W N O 1028 994 4.50 2.79 1.71 4.64 2.79 1.71 4.64
14 8809 128Q 124K N O 1028 1003 7.18 4.29 2.89 6.07 4.29 2.89 6.07
15 8822 129G 124K N O 1037 1003 10.75 6.40 4.34 6.23 6.40 4.34 6.23
16 8831 130S 123W N O 1041 994 11.43 7.33 4.10 7.46 7.33 4.10 7.46
17 8832 130S 124K N O 1041 1003 14.17 7.82 6.35 9.96 7.82 6.35 9.96
18 8833 130S 125N N O 1041 1011 14.21 7.78 6.43 9.43 7.78 6.43 9.43
19 8834 130S 126H N O 1041 1021 11.03 5.94 5.09 9.24 5.94 5.09 9.24
20 8835 130S 127C N O 1041 1027 7.56 3.18 4.38 11.67 3.18 4.38 11.67
21 8843 131L 126H N O 1047 1021 10.08 6.80 3.28 4.74 6.80 3.28 4.74
22 8844 131L 127C N O 1047 1027 8.07 5.43 2.64 4.85 5.43 2.64 4.85
23 8857 132P 127C N O 1055 1027 8.79 6.04 2.76 7.66 6.04 2.76 7.66
24 8860 132P 130S N O 1055 1046 5.37 3.36 2.01 4.60 3.36 2.01 4.60
25 8884 134I 132P N O 1070 1061 6.06 3.18 2.88 5.16 3.18 2.88 5.16
26 8900 135S 132P N O 1078 1061 8.07 2.93 5.14 11.22 2.93 5.14 11.22
27 8917 136S 132P N O 1084 1061 10.59 4.11 6.48 11.96 4.11 6.48 11.96
28 8928 137C 132P N O 1090 1061 12.61 5.93 6.68 5.96 5.93 6.68 5.96
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4002 58T 58T CA C 461 465 -157.44 -180.00 22.56 4.51 -180.00 22.56 4.51
2 4003 59N 59N CA C 468 473 -112.43 -180.00 67.57 13.51 -180.00 67.57 13.51
3 4075 131L 131L CA C 1048 1053 -149.56 -180.00 30.44 6.08 -180.00 30.44 6.08
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.73 3.50 2.23 22.28 3.50 2.23 22.28
2 12136 43W 131L N O 337 1054 4.54 3.50 1.04 10.36 3.50 1.04 10.36
3 12137 60T 132P N O 475 1061 8.94 3.50 5.44 54.36 3.50 5.44 54.36
-------------------------------------------------------------------------------------------------
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 -74.02 -73.00 15.99 1.02 -63.80 163.36 24.56
1 2Q 2Q N CA 9 10 156.66 140.70 -40.30
2 3811 2Q 3K C N 16 18 -58.46 -70.20 14.96 0.90 -62.90 171.98 22.58
2 3K 3K N CA 18 19 131.12 140.40 -40.80
3 3812 3K 4L C N 25 27 -115.32 -108.50 26.86 1.37 -63.50 168.49 26.59
3 4L 4L N CA 27 28 158.48 132.50 -41.20
4 3815 6I 7F C N 49 51 -122.32 -124.20 3.19 0.09 -63.20 -175.31 29.57
4 7F 7F N CA 51 52 140.73 143.30 -44.30
5 3816 7F 8A C N 60 62 -155.68 -134.00 22.65 0.55 -62.50 -170.03 36.11
5 8A 8A N CA 62 63 153.55 147.00 -40.90
6 3817 8A 9L C N 65 67 -89.24 -108.50 41.89 2.02 -63.50 138.91 17.98
6 9L 9L N CA 67 68 95.30 132.50 -41.20
7 3820 11V 12L C N 87 89 -64.56 -70.70 6.14 0.56 -63.50 176.98 24.63
7 12L 12L N CA 89 90 141.82 141.60 -41.20
8 3821 12L 13C C N 95 97 -61.44 -63.00 2.90 0.30 -117.90 -175.78 7.94
8 13C 13C N CA 97 98 -43.54 -41.10 141.10
9 3823 14V 15G C N 108 110 177.43 -167.20 19.35 0.68 82.20 -178.65 13.00
9 15G 15G N CA 110 111 162.84 174.60 8.50
10 3824 15G 16S C N 112 114 -108.97 -136.60 35.78 1.11 -64.10 169.51 10.51
10 16S 16S N CA 114 115 128.46 151.20 -35.00
11 3844 35F 36E C N 274 276 47.23 54.60 7.62 0.77 -63.60 139.44 23.93
11 36E 36E N CA 276 277 44.32 42.40 -40.30
12 3859 50E 51S C N 405 407 -146.54 -64.10 92.86 9.54 -64.10 92.86 9.54
12 51S 51S N CA 407 408 7.74 -35.00 -35.00
13 3860 51S 52S C N 411 413 58.02 56.90 5.60 0.27 -64.10 138.77 18.36
13 52S 52S N CA 413 414 30.91 36.40 -35.00
14 3896 87K 88D C N 695 697 161.93 -96.50 102.88 4.19 -63.30 -167.23 21.68
14 88D 88D N CA 697 698 97.84 114.20 -40.00
15 3920 111I 112Y C N 872 874 -46.70 -98.40 57.52 3.53 -63.50 147.55 24.28
15 112Y 112Y N CA 874 875 103.19 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -147.34 -125.60 102.22 4.26 -63.20 116.95 13.24
16 126H 126H N CA 1012 1013 38.92 138.80 -42.30
17 3935 126H 127C C N 1020 1022 -159.54 -63.00 100.29 17.72 -63.00 100.29 17.72
17 127C 127C N CA 1022 1023 -68.28 -41.10 -41.10
18 3936 127C 128Q C N 1026 1028 63.75 55.10 84.37 6.77 -121.10 175.83 6.94
18 128Q 128Q N CA 1028 1029 124.23 40.30 139.70
19 3937 128Q 129G C N 1035 1037 91.52 82.20 178.37 8.19 82.20 178.37 8.19
19 129G 129G N CA 1037 1038 -169.63 8.50 8.50
20 3941 132P 133D C N 1060 1062 -153.18 -63.30 118.92 20.00 -63.30 118.92 20.00
20 133D 133D N CA 1062 1063 -117.87 -40.00 -40.00
21 3942 133D 134I C N 1068 1070 -98.40 -97.30 30.28 3.15 -63.40 144.84 22.65
21 134I 134I N CA 1070 1071 96.95 127.20 -43.60
22 3943 134I 135S C N 1076 1078 -151.16 -64.10 109.94 9.91 -64.10 109.94 9.91
22 135S 135S N CA 1078 1079 32.13 -35.00 -35.00
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 388 1061 2.281
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 1 2 2 18 33 104 97 151 151 173 174 195 211
<< end of ENERGY.
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3041
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 : 6941.1816
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 7 19 0.023 0.023 178.16 1.000
2 Bond angle potential : 1504 13 48 4.000 4.000 459.48 1.000
3 Stereochemical cosine torsion poten: 713 0 39 49.571 49.571 276.94 1.000
4 Stereochemical improper torsion pot: 461 1 5 2.649 2.649 67.194 1.000
5 Soft-sphere overlap restraints : 3041 3 9 0.014 0.014 68.950 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 91 191 1.166 1.166 2285.1 1.000
10 Distance restraints 2 (N-O) : 2371 71 164 1.019 1.019 1963.3 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 2 8 6.399 6.399 65.666 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 6 71.939 71.939 53.067 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 77.622 77.622 39.372 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 82.347 82.347 26.043 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 100.251 100.251 16.975 1.000
18 Disulfide distance restraints : 3 0 0 0.037 0.037 0.70426 1.000
19 Disulfide angle restraints : 6 0 0 4.881 4.881 3.1569 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.650 25.650 1.5930 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.243 3.243 930.77 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 1 0.505 0.505 60.097 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 24 26 40.138 70.209 160.78 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 2 10 1.264 1.264 131.16 1.000
27 Distance restraints 5 (X-Y) : 1389 5 9 0.120 0.120 152.73 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: Sequence.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: 26096.6719
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.74 1.43 0.31 10.08 1.43 0.31 10.08
2 488 60T 60T C CA 480 476 1.72 1.49 0.23 6.68 1.49 0.23 6.68
3 1078 132P 132P O C 1061 1060 1.37 1.23 0.14 6.50 1.23 0.14 6.50
4 1079 132P 132P C CA 1060 1056 1.65 1.49 0.16 4.60 1.49 0.16 4.60
5 1080 132P 133D C N 1060 1062 1.49 1.35 0.14 5.09 1.35 0.14 5.09
6 1090 133D 133D N CA 1062 1063 1.58 1.43 0.15 4.91 1.43 0.15 4.91
-------------------------------------------------------------------------------------------------
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 697 698 129.71 107.00 22.71 6.53 107.00 22.71 6.53
2 2214 101I 101I N CA 794 795 122.92 107.00 15.92 4.58 107.00 15.92 4.58
3 2222 101I 102T C N 800 802 144.98 120.00 24.98 5.68 120.00 24.98 5.68
4 2574 131L 132P C N 1053 1055 144.48 117.00 27.48 6.84 117.00 27.48 6.84
5 2576 132P 131L N C 1055 1053 139.70 122.50 17.20 4.95 122.50 17.20 4.95
6 2577 132P 132P N CA 1055 1056 146.91 108.20 38.72 8.80 108.20 38.72 8.80
7 2586 132P 133D C N 1060 1062 150.95 120.00 30.95 7.03 120.00 30.95 7.03
8 2589 133D 133D N CA 1062 1063 128.99 107.00 21.99 6.32 107.00 21.99 6.32
9 2611 135S 135S N CA 1078 1079 123.63 107.00 16.63 4.78 107.00 16.63 4.78
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4952 38N 132P CA CA 295 1056 14.72 11.84 2.87 5.53 11.84 2.87 5.53
2 4974 39L 132P CA CA 303 1056 14.23 9.77 4.46 7.93 9.77 4.46 7.93
3 4975 39L 133D CA CA 303 1063 15.29 10.76 4.53 6.04 10.76 4.53 6.04
4 4997 40M 132P CA CA 311 1056 11.80 9.28 2.53 5.68 9.28 2.53 5.68
5 4998 40M 133D CA CA 311 1063 12.74 9.89 2.85 4.63 9.89 2.85 4.63
6 5022 41R 132P CA CA 319 1056 10.94 5.64 5.30 13.27 5.64 5.30 13.27
7 5023 41R 133D CA CA 319 1063 10.78 6.81 3.96 7.47 6.81 3.96 7.47
8 5057 42N 132P CA CA 330 1056 10.17 7.04 3.13 7.08 7.04 3.13 7.08
9 6505 124K 128Q CA CA 996 1029 7.91 5.18 2.73 6.78 5.18 2.73 6.78
10 6507 124K 130S CA CA 996 1042 13.50 10.06 3.44 5.30 10.06 3.44 5.30
11 6511 125N 128Q CA CA 1005 1029 9.43 6.66 2.78 5.59 6.66 2.78 5.59
12 6512 125N 129G CA CA 1005 1038 12.89 9.45 3.44 4.51 9.45 3.44 4.51
13 6513 125N 130S CA CA 1005 1042 14.78 9.78 5.00 7.35 9.78 5.00 7.35
14 6518 126H 130S CA CA 1013 1042 13.12 7.42 5.70 10.89 7.42 5.70 10.89
15 6520 126H 132P CA CA 1013 1056 12.72 9.77 2.95 5.73 9.77 2.95 5.73
16 6525 127C 130S CA CA 1023 1042 9.66 5.30 4.36 11.89 5.30 4.36 11.89
17 6527 127C 132P CA CA 1023 1056 10.30 7.04 3.26 9.70 7.04 3.26 9.70
18 6552 132P 135S CA CA 1056 1079 8.76 5.61 3.15 6.32 5.61 3.15 6.32
19 6553 132P 136S CA CA 1056 1085 11.98 7.77 4.21 6.85 7.77 4.21 6.85
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 16.02 10.18 5.84 9.25 10.18 5.84 9.25
2 6967 40M 132P N O 310 1061 14.83 8.51 6.32 13.20 8.51 6.32 13.20
3 6991 41R 132P N O 318 1061 13.34 5.74 7.60 15.99 5.74 7.60 15.99
4 7019 42N 132P N O 329 1061 12.16 6.20 5.96 12.13 6.20 5.96 12.13
5 7535 66K 59N N O 519 474 7.28 4.44 2.84 5.66 4.44 2.84 5.66
6 7561 67D 59N N O 528 474 5.31 2.79 2.51 5.39 2.79 2.51 5.39
7 7801 75D 59N N O 596 474 10.27 7.52 2.74 4.94 7.52 2.74 4.94
8 8757 125N 128Q N O 1004 1036 10.51 6.57 3.95 6.66 6.57 3.95 6.66
9 8773 126H 128Q N O 1012 1036 9.08 6.16 2.92 5.56 6.16 2.92 5.56
10 8794 127C 130S N O 1022 1046 9.75 7.34 2.41 4.63 7.34 2.41 4.63
11 8808 128Q 123W N O 1028 994 4.85 2.79 2.06 5.59 2.79 2.06 5.59
12 8809 128Q 124K N O 1028 1003 7.37 4.29 3.08 6.48 4.29 3.08 6.48
13 8822 129G 124K N O 1037 1003 10.31 6.40 3.91 5.60 6.40 3.91 5.60
14 8831 130S 123W N O 1041 994 11.10 7.33 3.77 6.85 7.33 3.77 6.85
15 8832 130S 124K N O 1041 1003 13.76 7.82 5.94 9.32 7.82 5.94 9.32
16 8833 130S 125N N O 1041 1011 14.40 7.78 6.62 9.71 7.78 6.62 9.71
17 8834 130S 126H N O 1041 1021 11.43 5.94 5.50 9.98 5.94 5.50 9.98
18 8835 130S 127C N O 1041 1027 8.67 3.18 5.49 14.64 3.18 5.49 14.64
19 8842 131L 125N N O 1047 1011 14.37 9.93 4.44 4.86 9.93 4.44 4.86
20 8843 131L 126H N O 1047 1021 11.18 6.80 4.38 6.33 6.80 4.38 6.33
21 8844 131L 127C N O 1047 1027 9.42 5.43 3.99 7.34 5.43 3.99 7.34
22 8856 132P 126H N O 1055 1021 11.44 7.67 3.77 7.38 7.67 3.77 7.38
23 8857 132P 127C N O 1055 1027 10.61 6.04 4.57 12.71 6.04 4.57 12.71
24 8870 133D 127C N O 1062 1027 12.18 8.59 3.59 5.36 8.59 3.59 5.36
25 8884 134I 132P N O 1070 1061 6.41 3.18 3.23 5.79 3.18 3.23 5.79
26 8897 135S 127C N O 1078 1027 13.10 10.21 2.89 5.15 10.21 2.89 5.15
27 8900 135S 132P N O 1078 1061 9.34 2.93 6.41 14.00 2.93 6.41 14.00
28 8917 136S 132P N O 1084 1061 12.04 4.11 7.92 14.63 4.11 7.92 14.63
29 8928 137C 132P N O 1090 1061 14.09 5.93 8.16 7.28 5.93 8.16 7.28
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.63 3.50 2.13 21.27 3.50 2.13 21.27
2 12136 43W 131L N O 337 1054 4.92 3.50 1.42 14.16 3.50 1.42 14.16
3 12137 60T 132P N O 475 1061 8.50 3.50 5.00 50.01 3.50 5.00 50.01
-------------------------------------------------------------------------------------------------
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 -117.69 -121.10 51.50 2.51 -63.80 139.45 23.34
1 2Q 2Q N CA 9 10 -168.91 139.70 -40.30
2 3811 2Q 3K C N 16 18 -56.17 -70.20 15.79 1.29 -62.90 171.69 21.94
2 3K 3K N CA 18 19 147.65 140.40 -40.80
3 3812 3K 4L C N 25 27 -78.77 -108.50 54.41 2.56 -63.50 129.04 17.10
3 4L 4L N CA 27 28 86.93 132.50 -41.20
4 3815 6I 7F C N 49 51 -70.70 -71.40 3.92 0.30 -63.20 179.01 25.36
4 7F 7F N CA 51 52 136.84 140.70 -44.30
5 3816 7F 8A C N 60 62 -65.99 -68.20 22.58 1.74 -62.50 163.76 26.67
5 8A 8A N CA 62 63 122.83 145.30 -40.90
6 3817 8A 9L C N 65 67 -133.89 -108.50 25.72 1.28 -63.50 -176.34 22.64
6 9L 9L N CA 67 68 128.43 132.50 -41.20
7 3819 10V 11V C N 80 82 -61.77 -62.40 2.80 0.39 -125.40 -171.89 10.54
7 11V 11V N CA 82 83 -39.67 -42.40 143.30
8 3820 11V 12L C N 87 89 -75.64 -70.70 17.40 1.15 -63.50 160.97 23.07
8 12L 12L N CA 89 90 158.28 141.60 -41.20
9 3823 14V 15G C N 108 110 79.92 78.70 8.55 0.19 82.20 176.95 8.48
9 15G 15G N CA 110 111 -174.56 -166.10 8.50
10 3824 15G 16S C N 112 114 -108.76 -136.60 57.28 2.19 -64.10 143.28 8.83
10 16S 16S N CA 114 115 101.14 151.20 -35.00
11 3844 35F 36E C N 274 276 49.70 54.60 4.90 0.57 -63.60 140.29 24.10
11 36E 36E N CA 276 277 42.44 42.40 -40.30
12 3859 50E 51S C N 405 407 -159.81 -136.60 113.94 6.19 -64.10 121.38 10.89
12 51S 51S N CA 407 408 39.64 151.20 -35.00
13 3860 51S 52S C N 411 413 54.09 56.90 25.77 1.88 -64.10 126.75 16.95
13 52S 52S N CA 413 414 10.79 36.40 -35.00
14 3867 58T 59N C N 465 467 -70.58 -63.20 10.67 1.72 -119.90 -178.95 9.21
14 59N 59N N CA 467 468 -48.80 -41.10 137.00
15 3868 59N 60T C N 473 475 78.04 -78.10 156.97 9.85 -78.10 156.97 9.85
15 60T 60T N CA 475 476 165.89 149.80 149.80
16 3896 87K 88D C N 695 697 -149.70 -63.30 87.22 14.33 -63.30 87.22 14.33
16 88D 88D N CA 697 698 -51.92 -40.00 -40.00
17 3920 111I 112Y C N 872 874 -43.43 -98.40 61.07 3.74 -63.50 146.57 24.29
17 112Y 112Y N CA 874 875 101.79 128.40 -43.40
18 3934 125N 126H C N 1010 1012 -137.66 -63.20 90.46 11.02 -63.20 90.46 11.02
18 126H 126H N CA 1012 1013 9.05 -42.30 -42.30
19 3935 126H 127C C N 1020 1022 -140.67 -117.90 70.32 2.38 -63.00 135.69 22.29
19 127C 127C N CA 1022 1023 -152.37 141.10 -41.10
20 3937 128Q 129G C N 1035 1037 82.28 82.20 166.75 8.09 82.20 166.75 8.09
20 129G 129G N CA 1037 1038 -158.25 8.50 8.50
21 3938 129G 130S C N 1039 1041 -71.15 -64.10 27.24 2.46 -72.40 146.29 8.65
21 130S 130S N CA 1041 1042 -61.31 -35.00 152.40
22 3941 132P 133D C N 1060 1062 -156.25 -96.50 72.78 3.03 -63.30 -171.26 29.26
22 133D 133D N CA 1062 1063 155.74 114.20 -40.00
23 3942 133D 134I C N 1068 1070 25.18 -97.30 123.48 5.55 -63.40 178.65 32.48
23 134I 134I N CA 1070 1071 111.54 127.20 -43.60
24 3943 134I 135S C N 1076 1078 -158.35 -64.10 100.34 11.16 -64.10 100.34 11.16
24 135S 135S N CA 1078 1079 -0.57 -35.00 -35.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10349 41R 132P CB CB 320 1058 12.75 3.70 9.04 6.58 3.70 9.04 6.58
2 10419 47V 71F CB CE1 374 566 10.34 4.53 5.82 4.63 4.53 5.82 4.63
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 3 22 38 112 117 163 195 186 186 194 230
<< end of ENERGY.
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: -93.2466
>> 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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2877
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 : 7102.7695
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 8 27 0.024 0.024 191.84 1.000
2 Bond angle potential : 1504 14 56 4.018 4.018 466.76 1.000
3 Stereochemical cosine torsion poten: 713 0 36 49.746 49.746 275.37 1.000
4 Stereochemical improper torsion pot: 461 1 9 2.698 2.698 74.687 1.000
5 Soft-sphere overlap restraints : 2877 4 9 0.015 0.015 78.822 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 96 185 1.182 1.182 2376.5 1.000
10 Distance restraints 2 (N-O) : 2371 80 192 1.032 1.032 2052.9 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 3 6 7.814 7.814 97.939 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 7 72.266 72.266 57.518 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 79.363 79.363 51.525 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 80.859 80.859 23.944 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 80.543 80.543 13.754 1.000
18 Disulfide distance restraints : 3 0 0 0.031 0.031 0.50350 1.000
19 Disulfide angle restraints : 6 0 0 4.007 4.007 2.1271 1.000
20 Disulfide dihedral angle restraints: 3 0 0 31.497 31.497 2.1137 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 2.970 2.970 780.62 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 1 0.492 0.492 56.241 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 24 32 36.687 76.160 202.72 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 1 9 1.197 1.197 121.98 1.000
27 Distance restraints 5 (X-Y) : 1389 5 15 0.129 0.129 174.84 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: Sequence.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: 26369.1328
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 486 60T 60T N CA 475 476 1.72 1.43 0.29 9.43 1.43 0.29 9.43
2 488 60T 60T C CA 480 476 1.66 1.49 0.17 5.06 1.49 0.17 5.06
3 1078 132P 132P O C 1061 1060 1.33 1.23 0.10 4.77 1.23 0.10 4.77
4 1079 132P 132P C CA 1060 1056 1.66 1.49 0.17 4.94 1.49 0.17 4.94
5 1080 132P 133D C N 1060 1062 1.50 1.35 0.15 5.38 1.35 0.15 5.38
6 1090 133D 133D N CA 1062 1063 1.59 1.43 0.16 5.31 1.43 0.16 5.31
7 1092 133D 133D C CA 1068 1063 1.67 1.49 0.18 5.21 1.49 0.18 5.21
8 1098 134I 134I N CA 1070 1071 1.57 1.43 0.14 4.56 1.43 0.14 4.56
-------------------------------------------------------------------------------------------------
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 697 698 128.76 107.00 21.76 6.26 107.00 21.76 6.26
2 2211 100D 101I C N 792 794 140.48 120.00 20.48 4.65 120.00 20.48 4.65
3 2214 101I 101I N CA 794 795 123.53 107.00 16.53 4.75 107.00 16.53 4.75
4 2222 101I 102T C N 800 802 145.78 120.00 25.78 5.86 120.00 25.78 5.86
5 2574 131L 132P C N 1053 1055 145.96 117.00 28.96 7.21 117.00 28.96 7.21
6 2576 132P 131L N C 1055 1053 140.60 122.50 18.10 5.21 122.50 18.10 5.21
7 2577 132P 132P N CA 1055 1056 145.28 108.20 37.09 8.43 108.20 37.09 8.43
8 2586 132P 133D C N 1060 1062 141.88 120.00 21.88 4.97 120.00 21.88 4.97
9 2589 133D 133D N CA 1062 1063 134.58 107.00 27.58 7.93 107.00 27.58 7.93
10 2592 133D 133D CA C 1063 1068 134.06 116.50 17.56 5.05 116.50 17.56 5.05
11 2600 134I 134I N CA 1070 1071 124.70 107.00 17.70 5.09 107.00 17.70 5.09
12 2611 135S 135S N CA 1078 1079 123.53 107.00 16.53 4.75 107.00 16.53 4.75
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4952 38N 132P CA CA 295 1056 14.30 11.84 2.46 4.74 11.84 2.46 4.74
2 4974 39L 132P CA CA 303 1056 14.13 9.77 4.35 7.74 9.77 4.35 7.74
3 4997 40M 132P CA CA 311 1056 12.29 9.28 3.01 6.77 9.28 3.01 6.77
4 5022 41R 132P CA CA 319 1056 11.17 5.64 5.53 13.85 5.64 5.53 13.85
5 5023 41R 133D CA CA 319 1063 10.34 6.81 3.53 6.65 6.81 3.53 6.65
6 5057 42N 132P CA CA 330 1056 9.71 7.04 2.67 6.03 7.04 2.67 6.03
7 6505 124K 128Q CA CA 996 1029 7.77 5.18 2.59 6.42 5.18 2.59 6.42
8 6511 125N 128Q CA CA 1005 1029 9.48 6.66 2.82 5.68 6.66 2.82 5.68
9 6512 125N 129G CA CA 1005 1038 12.90 9.45 3.45 4.53 9.45 3.45 4.53
10 6513 125N 130S CA CA 1005 1042 14.56 9.78 4.78 7.02 9.78 4.78 7.02
11 6518 126H 130S CA CA 1013 1042 12.36 7.42 4.94 9.44 7.42 4.94 9.44
12 6525 127C 130S CA CA 1023 1042 9.53 5.30 4.23 11.54 5.30 4.23 11.54
13 6527 127C 132P CA CA 1023 1056 9.28 7.04 2.24 6.67 7.04 2.24 6.67
14 6552 132P 135S CA CA 1056 1079 9.80 5.61 4.19 8.41 5.61 4.19 8.41
15 6553 132P 136S CA CA 1056 1085 12.30 7.77 4.53 7.38 7.77 4.53 7.38
16 6556 133D 136S CA CA 1063 1085 11.15 6.03 5.12 4.67 6.03 5.12 4.67
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 15.77 10.18 5.59 8.85 10.18 5.59 8.85
2 6967 40M 132P N O 310 1061 15.13 8.51 6.62 13.83 8.51 6.62 13.83
3 6991 41R 132P N O 318 1061 13.75 5.74 8.01 16.84 5.74 8.01 16.84
4 6992 41R 133D N O 318 1069 10.85 7.72 3.13 4.73 7.72 3.13 4.73
5 7019 42N 132P N O 329 1061 12.24 6.20 6.04 12.31 6.20 6.04 12.31
6 7107 45C 132P N O 358 1061 9.00 6.76 2.24 4.94 6.76 2.24 4.94
7 7201 49H 46L N O 388 371 5.52 3.52 2.00 4.56 3.52 2.00 4.56
8 7223 50E 46L N O 398 371 4.83 2.85 1.98 5.19 2.85 1.98 5.19
9 7516 65S 59N N O 513 474 9.41 6.93 2.48 4.54 6.93 2.48 4.54
10 7535 66K 59N N O 519 474 7.26 4.44 2.82 5.63 4.44 2.82 5.63
11 7561 67D 59N N O 528 474 5.30 2.79 2.51 5.37 2.79 2.51 5.37
12 7801 75D 59N N O 596 474 10.20 7.52 2.68 4.81 7.52 2.68 4.81
13 8023 86G 63N N O 684 508 10.95 7.27 3.67 5.19 7.27 3.67 5.19
14 8033 87K 63N N O 688 508 12.41 8.66 3.75 6.26 8.66 3.75 6.26
15 8757 125N 128Q N O 1004 1036 10.23 6.57 3.67 6.18 6.57 3.67 6.18
16 8773 126H 128Q N O 1012 1036 8.96 6.16 2.80 5.33 6.16 2.80 5.33
17 8808 128Q 123W N O 1028 994 4.75 2.79 1.96 5.32 2.79 1.96 5.32
18 8809 128Q 124K N O 1028 1003 6.92 4.29 2.62 5.51 4.29 2.62 5.51
19 8822 129G 124K N O 1037 1003 10.29 6.40 3.89 5.57 6.40 3.89 5.57
20 8831 130S 123W N O 1041 994 11.13 7.33 3.80 6.91 7.33 3.80 6.91
21 8832 130S 124K N O 1041 1003 13.59 7.82 5.77 9.05 7.82 5.77 9.05
22 8833 130S 125N N O 1041 1011 13.58 7.78 5.80 8.51 7.78 5.80 8.51
23 8834 130S 126H N O 1041 1021 11.52 5.94 5.58 10.13 5.94 5.58 10.13
24 8835 130S 127C N O 1041 1027 6.91 3.18 3.72 9.93 3.18 3.72 9.93
25 8843 131L 126H N O 1047 1021 11.40 6.80 4.60 6.66 6.80 4.60 6.66
26 8856 132P 126H N O 1055 1021 10.74 7.67 3.07 6.01 7.67 3.07 6.01
27 8884 134I 132P N O 1070 1061 6.33 3.18 3.15 5.65 3.18 3.15 5.65
28 8900 135S 132P N O 1078 1061 9.59 2.93 6.66 14.56 2.93 6.66 14.56
29 8917 136S 132P N O 1084 1061 12.83 4.11 8.72 16.09 4.11 8.72 16.09
30 8918 136S 133D N O 1084 1069 8.99 3.24 5.75 5.48 3.24 5.75 5.48
31 8928 137C 132P N O 1090 1061 14.57 5.93 8.64 7.71 5.93 8.64 7.71
32 8929 137C 133D N O 1090 1069 10.60 3.22 7.39 4.78 3.22 7.39 4.78
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4075 131L 131L CA C 1048 1053 -152.88 -180.00 27.12 5.42 -180.00 27.12 5.42
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.85 3.50 2.35 23.49 3.50 2.35 23.49
2 12136 43W 131L N O 337 1054 4.60 3.50 1.10 11.04 3.50 1.10 11.04
3 12137 60T 132P N O 475 1061 7.94 3.50 4.44 44.41 3.50 4.44 44.41
-------------------------------------------------------------------------------------------------
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 -110.15 -121.10 12.71 0.61 -63.80 179.62 28.89
1 2Q 2Q N CA 9 10 146.16 139.70 -40.30
2 3811 2Q 3K C N 16 18 -78.37 -70.20 14.12 0.85 -62.90 168.00 22.69
2 3K 3K N CA 18 19 151.91 140.40 -40.80
3 3812 3K 4L C N 25 27 -71.21 -70.70 2.39 0.20 -63.50 179.70 25.40
3 4L 4L N CA 27 28 139.27 141.60 -41.20
4 3815 6I 7F C N 49 51 -110.08 -124.20 19.65 0.52 -63.20 -179.85 22.10
4 7F 7F N CA 51 52 129.64 143.30 -44.30
5 3816 7F 8A C N 60 62 -139.44 -134.00 6.13 0.14 -62.50 -174.04 34.60
5 8A 8A N CA 62 63 149.81 147.00 -40.90
6 3817 8A 9L C N 65 67 -76.68 -70.70 7.26 0.50 -63.50 173.58 24.88
6 9L 9L N CA 67 68 145.72 141.60 -41.20
7 3820 11V 12L C N 87 89 -111.48 -108.50 6.00 0.29 -63.50 -174.77 23.44
7 12L 12L N CA 89 90 137.71 132.50 -41.20
8 3823 14V 15G C N 108 110 99.20 78.70 39.60 0.61 82.20 152.46 8.25
8 15G 15G N CA 110 111 160.01 -166.10 8.50
9 3824 15G 16S C N 112 114 -140.91 -136.60 9.38 0.53 -64.10 -166.26 12.08
9 16S 16S N CA 114 115 142.87 151.20 -35.00
10 3842 33H 34G C N 259 261 -90.45 -62.40 31.98 4.91 82.20 176.04 12.89
10 34G 34G N CA 261 262 -25.84 -41.20 8.50
11 3844 35F 36E C N 274 276 51.99 54.60 2.64 0.33 -63.60 141.89 24.38
11 36E 36E N CA 276 277 41.99 42.40 -40.30
12 3860 51S 52S C N 411 413 62.88 56.90 7.48 0.54 -64.10 143.53 19.02
12 52S 52S N CA 413 414 31.90 36.40 -35.00
13 3867 58T 59N C N 465 467 -77.69 -63.20 20.60 3.33 -119.90 172.50 8.69
13 59N 59N N CA 467 468 -55.74 -41.10 137.00
14 3868 59N 60T C N 473 475 91.36 -124.80 144.70 7.25 -78.10 169.73 10.50
14 60T 60T N CA 475 476 159.33 143.50 149.80
15 3871 62R 63N C N 499 501 -72.71 -119.90 65.46 3.54 -63.20 136.87 17.64
15 63N 63N N CA 501 502 -177.63 137.00 -41.10
16 3872 63N 64G C N 507 509 -63.24 -62.40 20.04 2.95 82.20 148.44 10.89
16 64G 64G N CA 509 510 -21.18 -41.20 8.50
17 3896 87K 88D C N 695 697 169.99 -96.50 96.60 3.93 -63.30 -178.47 20.41
17 88D 88D N CA 697 698 90.00 114.20 -40.00
18 3919 110K 111I C N 864 866 -58.38 -63.40 39.30 6.62 -63.40 39.30 6.62
18 111I 111I N CA 866 867 -4.62 -43.60 -43.60
19 3935 126H 127C C N 1020 1022 -166.55 -117.90 53.60 1.50 -63.00 -173.35 30.44
19 127C 127C N CA 1022 1023 163.61 141.10 -41.10
20 3937 128Q 129G C N 1035 1037 99.43 82.20 173.90 7.57 82.20 173.90 7.57
20 129G 129G N CA 1037 1038 -164.54 8.50 8.50
21 3938 129G 130S C N 1039 1041 -73.09 -64.10 34.29 3.10 -72.40 139.50 8.18
21 130S 130S N CA 1041 1042 -68.10 -35.00 152.40
22 3941 132P 133D C N 1060 1062 -178.39 -63.30 122.72 16.97 -63.30 122.72 16.97
22 133D 133D N CA 1062 1063 2.60 -40.00 -40.00
23 3942 133D 134I C N 1068 1070 -125.58 -63.40 68.69 12.93 -63.40 68.69 12.93
23 134I 134I N CA 1070 1071 -72.78 -43.60 -43.60
24 3943 134I 135S C N 1076 1078 -166.68 -136.60 33.14 1.03 -64.10 -170.03 21.17
24 135S 135S N CA 1078 1079 165.11 151.20 -35.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10349 41R 132P CB CB 320 1058 12.74 3.70 9.03 6.58 3.70 9.03 6.58
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 1 3 21 43 102 109 152 145 150 194 194 256
<< end of ENERGY.
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 : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2929
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 : 7274.1895
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 6 17 0.024 0.024 192.89 1.000
2 Bond angle potential : 1504 13 46 4.116 4.116 478.56 1.000
3 Stereochemical cosine torsion poten: 713 0 38 49.739 49.739 274.45 1.000
4 Stereochemical improper torsion pot: 461 0 5 2.263 2.263 56.543 1.000
5 Soft-sphere overlap restraints : 2929 5 9 0.017 0.017 102.65 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 86 186 1.150 1.150 2304.5 1.000
10 Distance restraints 2 (N-O) : 2371 73 165 0.998 0.998 1976.7 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 4 8 9.627 9.627 148.64 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 81.019 81.019 49.456 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 78.119 78.119 42.972 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 81.060 81.060 27.044 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 80.280 80.280 13.844 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.44033 1.000
19 Disulfide angle restraints : 6 0 1 5.735 5.735 4.3572 1.000
20 Disulfide dihedral angle restraints: 3 0 0 43.432 43.432 4.0599 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.363 3.363 1001.3 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.572 0.572 78.329 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 25 38.732 70.049 160.80 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 7 1.245 1.245 124.50 1.000
27 Distance restraints 5 (X-Y) : 1389 6 25 0.149 0.149 232.14 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: Sequence.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: 26579.0684
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 384 47V 47V C CA 377 373 1.65 1.49 0.16 4.71 1.49 0.16 4.71
2 486 60T 60T N CA 475 476 1.75 1.43 0.32 10.66 1.43 0.32 10.66
3 488 60T 60T C CA 480 476 1.74 1.49 0.25 7.16 1.49 0.25 7.16
4 489 60T 61N C N 480 482 1.49 1.35 0.15 5.16 1.35 0.15 5.16
5 1078 132P 132P O C 1061 1060 1.39 1.23 0.16 7.52 1.23 0.16 7.52
6 1079 132P 132P C CA 1060 1056 1.73 1.49 0.24 7.07 1.49 0.24 7.07
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 129.10 107.00 22.10 6.35 107.00 22.10 6.35
2 1640 47V 48E C N 377 379 142.90 120.00 22.90 5.20 120.00 22.90 5.20
3 1773 60T 60T N CA 475 476 127.75 107.00 20.75 5.97 107.00 20.75 5.97
4 1783 61N 61N N CA 482 483 125.79 107.00 18.79 5.40 107.00 18.79 5.40
5 2080 88D 88D N CA 697 698 130.58 107.00 23.58 6.78 107.00 23.58 6.78
6 2214 101I 101I N CA 794 795 123.99 107.00 16.99 4.89 107.00 16.99 4.89
7 2222 101I 102T C N 800 802 143.43 120.00 23.43 5.32 120.00 23.43 5.32
8 2532 127C 127C N CA 1022 1023 122.83 107.00 15.83 4.55 107.00 15.83 4.55
9 2577 132P 132P N CA 1055 1056 148.52 108.20 40.32 9.16 108.20 40.32 9.16
10 2586 132P 133D C N 1060 1062 147.49 120.00 27.49 6.25 120.00 27.49 6.25
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.03 9.77 3.26 5.79 9.77 3.26 5.79
2 4975 39L 133D CA CA 303 1063 14.27 10.76 3.51 4.68 10.76 3.51 4.68
3 5022 41R 132P CA CA 319 1056 8.69 5.64 3.05 7.64 5.64 3.05 7.64
4 5023 41R 133D CA CA 319 1063 9.45 6.81 2.64 4.97 6.81 2.64 4.97
5 5571 60T 64G CA CA 476 510 10.34 6.93 3.41 6.40 6.93 3.41 6.40
6 5572 60T 65S CA CA 476 514 9.48 6.01 3.47 7.72 6.01 3.47 7.72
7 5573 60T 66K CA CA 476 520 6.88 4.22 2.66 6.62 4.22 2.66 6.62
8 5582 60T 81K CA CA 476 654 14.77 11.49 3.28 5.37 11.49 3.28 5.37
9 5583 60T 82G CA CA 476 663 17.43 13.44 3.99 5.06 13.44 3.99 5.06
10 5584 60T 83A CA CA 476 667 14.83 11.07 3.76 5.55 11.07 3.76 5.55
11 5585 60T 84S CA CA 476 672 14.14 10.32 3.82 6.76 10.32 3.82 6.76
12 5586 60T 85P CA CA 476 678 16.93 12.86 4.07 5.38 12.86 4.07 5.38
13 6505 124K 128Q CA CA 996 1029 7.92 5.18 2.73 6.79 5.18 2.73 6.79
14 6507 124K 130S CA CA 996 1042 13.24 10.06 3.18 4.90 10.06 3.18 4.90
15 6511 125N 128Q CA CA 1005 1029 9.60 6.66 2.95 5.93 6.66 2.95 5.93
16 6512 125N 129G CA CA 1005 1038 12.89 9.45 3.44 4.50 9.45 3.44 4.50
17 6513 125N 130S CA CA 1005 1042 14.09 9.78 4.31 6.33 9.78 4.31 6.33
18 6518 126H 130S CA CA 1013 1042 12.09 7.42 4.67 8.92 7.42 4.67 8.92
19 6525 127C 130S CA CA 1023 1042 8.80 5.30 3.51 9.56 5.30 3.51 9.56
-------------------------------------------------------------------------------------------------
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 6949 39L 132P N O 302 1061 14.52 10.18 4.33 6.87 10.18 4.33 6.87
2 6967 40M 132P N O 310 1061 13.38 8.51 4.87 10.17 8.51 4.87 10.17
3 6991 41R 132P N O 318 1061 11.51 5.74 5.77 12.14 5.74 5.77 12.14
4 7019 42N 132P N O 329 1061 10.00 6.20 3.79 7.73 6.20 3.79 7.73
5 7179 48E 44V N O 379 357 5.25 3.06 2.19 4.94 3.06 2.19 4.94
6 7468 60T 64G N O 475 512 11.22 7.82 3.40 5.31 7.82 3.40 5.31
7 7469 60T 65S N O 475 518 8.13 4.76 3.36 6.91 4.76 3.36 6.91
8 7476 60T 83A N O 475 670 15.42 11.00 4.43 6.06 11.00 4.43 6.06
9 7482 61N 65S N O 482 518 4.80 2.59 2.20 5.56 2.59 2.20 5.56
10 8757 125N 128Q N O 1004 1036 10.74 6.57 4.18 7.04 6.57 4.18 7.04
11 8773 126H 128Q N O 1012 1036 9.21 6.16 3.05 5.81 6.16 3.05 5.81
12 8794 127C 130S N O 1022 1046 10.22 7.34 2.88 5.54 7.34 2.88 5.54
13 8808 128Q 123W N O 1028 994 4.84 2.79 2.06 5.59 2.79 2.06 5.59
14 8809 128Q 124K N O 1028 1003 7.45 4.29 3.16 6.65 4.29 3.16 6.65
15 8810 128Q 125N N O 1028 1011 8.11 5.41 2.71 4.93 5.41 2.71 4.93
16 8822 129G 124K N O 1037 1003 10.59 6.40 4.19 6.00 6.40 4.19 6.00
17 8823 129G 125N N O 1037 1011 11.56 7.69 3.87 4.73 7.69 3.87 4.73
18 8831 130S 123W N O 1041 994 11.21 7.33 3.88 7.05 7.33 3.88 7.05
19 8832 130S 124K N O 1041 1003 13.91 7.82 6.09 9.56 7.82 6.09 9.56
20 8833 130S 125N N O 1041 1011 14.39 7.78 6.61 9.69 7.78 6.61 9.69
21 8834 130S 126H N O 1041 1021 11.48 5.94 5.54 10.06 5.94 5.54 10.06
22 8835 130S 127C N O 1041 1027 8.90 3.18 5.72 15.25 3.18 5.72 15.25
23 8843 131L 126H N O 1047 1021 10.68 6.80 3.88 5.61 6.80 3.88 5.61
24 8844 131L 127C N O 1047 1027 9.42 5.43 3.99 7.35 5.43 3.99 7.35
25 8857 132P 127C N O 1055 1027 9.95 6.04 3.91 10.86 6.04 3.91 10.86
26 8860 132P 130S N O 1055 1046 5.43 3.36 2.07 4.73 3.36 2.07 4.73
27 8884 134I 132P N O 1070 1061 5.95 3.18 2.77 4.97 3.18 2.77 4.97
28 8900 135S 132P N O 1078 1061 8.30 2.93 5.37 11.73 2.93 5.37 11.73
29 8917 136S 132P N O 1084 1061 10.83 4.11 6.71 12.39 4.11 6.71 12.39
30 8928 137C 132P N O 1090 1061 12.64 5.93 6.71 5.99 5.93 6.71 5.99
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 59N 59N CA C 468 473 -100.32 -180.00 79.68 15.93 -180.00 79.68 15.93
2 4070 126H 126H CA C 1013 1020 -152.98 -180.00 27.02 5.40 -180.00 27.02 5.40
3 4075 131L 131L CA C 1048 1053 -145.53 -180.00 34.47 6.89 -180.00 34.47 6.89
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.70 3.50 2.20 21.97 3.50 2.20 21.97
2 12136 43W 131L N O 337 1054 4.49 3.50 0.99 9.90 3.50 0.99 9.90
3 12137 60T 132P N O 475 1061 8.80 3.50 5.30 53.03 3.50 5.30 53.03
-------------------------------------------------------------------------------------------------
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 -73.87 -73.00 1.83 0.14 -63.80 179.68 25.90
1 2Q 2Q N CA 9 10 139.09 140.70 -40.30
2 3811 2Q 3K C N 16 18 -86.36 -70.20 16.17 1.19 -62.90 -179.18 24.83
2 3K 3K N CA 18 19 139.91 140.40 -40.80
3 3812 3K 4L C N 25 27 -84.67 -70.70 15.61 1.15 -63.50 171.56 25.09
3 4L 4L N CA 27 28 148.55 141.60 -41.20
4 3815 6I 7F C N 49 51 -96.53 -71.40 33.55 2.92 -63.20 166.15 20.94
4 7F 7F N CA 51 52 118.47 140.70 -44.30
5 3816 7F 8A C N 60 62 -145.54 -134.00 13.62 0.32 -62.50 -175.40 34.70
5 8A 8A N CA 62 63 154.23 147.00 -40.90
6 3817 8A 9L C N 65 67 -105.14 -108.50 20.56 1.14 -63.50 171.15 26.32
6 9L 9L N CA 67 68 152.79 132.50 -41.20
7 3818 9L 10V C N 73 75 -60.79 -62.40 1.65 0.24 -125.40 -174.47 10.42
7 10V 10V N CA 75 76 -42.78 -42.40 143.30
8 3820 11V 12L C N 87 89 -67.14 -70.70 3.56 0.32 -63.50 177.21 24.82
8 12L 12L N CA 89 90 141.62 141.60 -41.20
9 3823 14V 15G C N 108 110 -147.50 -167.20 43.13 1.31 82.20 -177.54 14.02
9 15G 15G N CA 110 111 136.23 174.60 8.50
10 3824 15G 16S C N 112 114 -125.04 -136.60 22.39 0.84 -64.10 177.80 10.96
10 16S 16S N CA 114 115 132.02 151.20 -35.00
11 3844 35F 36E C N 274 276 42.30 54.60 15.54 1.09 -63.60 140.41 23.98
11 36E 36E N CA 276 277 51.90 42.40 -40.30
12 3859 50E 51S C N 405 407 -148.55 -64.10 98.69 9.69 -64.10 98.69 9.69
12 51S 51S N CA 407 408 16.06 -35.00 -35.00
13 3860 51S 52S C N 411 413 56.21 56.90 2.20 0.20 -64.10 138.85 18.30
13 52S 52S N CA 413 414 34.31 36.40 -35.00
14 3896 87K 88D C N 695 697 165.21 -96.50 99.38 4.05 -63.30 -168.29 21.41
14 88D 88D N CA 697 698 99.51 114.20 -40.00
15 3920 111I 112Y C N 872 874 -33.86 -98.40 70.44 4.13 -63.50 146.60 24.78
15 112Y 112Y N CA 874 875 100.17 128.40 -43.40
16 3934 125N 126H C N 1010 1012 -136.37 -63.20 76.07 10.86 -63.20 76.07 10.86
16 126H 126H N CA 1012 1013 -21.53 -42.30 -42.30
17 3935 126H 127C C N 1020 1022 -127.86 -117.90 71.78 2.67 -63.00 124.88 20.06
17 127C 127C N CA 1022 1023 -147.81 141.10 -41.10
18 3937 128Q 129G C N 1035 1037 73.23 82.20 178.82 8.23 82.20 178.82 8.23
18 129G 129G N CA 1037 1038 -172.90 8.50 8.50
19 3941 132P 133D C N 1060 1062 -158.30 -63.30 113.12 19.27 -63.30 113.12 19.27
19 133D 133D N CA 1062 1063 -101.40 -40.00 -40.00
20 3942 133D 134I C N 1068 1070 -79.32 -97.30 21.29 1.48 -63.40 160.19 25.72
20 134I 134I N CA 1070 1071 115.80 127.20 -43.60
21 3943 134I 135S C N 1076 1078 -51.59 -72.40 64.94 4.53 -64.10 111.78 7.44
21 135S 135S N CA 1078 1079 -146.08 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10801 63N 139. CA O6 502 1123 10.15 9.24 0.91 4.55 9.24 0.91 4.55
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 388 1061 2.284
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 1 1 7 13 42 99 109 181 139 174 199 171 227
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1139 1139
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12137 12137
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2765
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 : 7266.0586
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 8 20 0.025 0.025 207.06 1.000
2 Bond angle potential : 1504 12 49 4.107 4.107 482.06 1.000
3 Stereochemical cosine torsion poten: 713 0 35 49.553 49.553 277.33 1.000
4 Stereochemical improper torsion pot: 461 0 4 2.133 2.133 50.930 1.000
5 Soft-sphere overlap restraints : 2765 7 8 0.018 0.018 100.17 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 81 187 1.148 1.148 2304.3 1.000
10 Distance restraints 2 (N-O) : 2371 77 168 1.005 1.005 1981.9 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 3 11 9.821 9.821 154.70 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 77.026 77.026 42.651 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 77.393 77.393 43.204 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 1 90.904 90.904 26.926 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 1 75.147 75.147 13.600 1.000
18 Disulfide distance restraints : 3 0 0 0.041 0.041 0.88048 1.000
19 Disulfide angle restraints : 6 0 1 6.301 6.301 5.2605 1.000
20 Disulfide dihedral angle restraints: 3 0 0 16.733 16.733 0.85538 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 3 3 3 3.396 3.396 1020.5 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 2 0.500 0.500 57.501 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 24 26 39.595 73.025 160.42 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 7 1.148 1.148 104.42 1.000
27 Distance restraints 5 (X-Y) : 1389 7 23 0.149 0.149 231.30 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: Sequence.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: 26720.3770
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 384 47V 47V C CA 377 373 1.66 1.49 0.17 4.82 1.49 0.17 4.82
2 486 60T 60T N CA 475 476 1.76 1.43 0.33 10.71 1.43 0.33 10.71
3 488 60T 60T C CA 480 476 1.75 1.49 0.26 7.45 1.49 0.26 7.45
4 489 60T 61N C N 480 482 1.49 1.35 0.14 5.09 1.35 0.14 5.09
5 494 61N 61N N CA 482 483 1.57 1.43 0.14 4.63 1.43 0.14 4.63
6 717 88D 88D C CA 703 698 1.67 1.49 0.18 5.12 1.49 0.18 5.12
7 1078 132P 132P O C 1061 1060 1.39 1.23 0.16 7.55 1.23 0.16 7.55
8 1079 132P 132P C CA 1060 1056 1.73 1.49 0.24 7.03 1.49 0.24 7.03
-------------------------------------------------------------------------------------------------
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 1633 47V 47V N CA 372 373 128.98 107.00 21.98 6.32 107.00 21.98 6.32
2 1640 47V 48E C N 377 379 145.86 120.00 25.86 5.88 120.00 25.86 5.88
3 1773 60T 60T N CA 475 476 128.35 107.00 21.35 6.14 107.00 21.35 6.14
4 1783 61N 61N N CA 482 483 126.60 107.00 19.60 5.64 107.00 19.60 5.64
5 2080 88D 88D N CA 697 698 132.24 107.00 25.24 7.26 107.00 25.24 7.26
6 2214 101I 101I N CA 794 795 123.75 107.00 16.75 4.82 107.00 16.75 4.82
7 2222 101I 102T C N 800 802 145.94 120.00 25.94 5.89 120.00 25.94 5.89
8 2563 130S 131L C N 1045 1047 139.87 120.00 19.87 4.52 120.00 19.87 4.52
9 2577 132P 132P N CA 1055 1056 147.82 108.20 39.62 9.00 108.20 39.62 9.00
10 2586 132P 133D C N 1060 1062 147.41 120.00 27.41 6.23 120.00 27.41 6.23
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4974 39L 132P CA CA 303 1056 13.04 9.77 3.26 5.80 9.77 3.26 5.80
2 4975 39L 133D CA CA 303 1063 14.16 10.76 3.40 4.53 10.76 3.40 4.53
3 5022 41R 132P CA CA 319 1056 8.68 5.64 3.04 7.61 5.64 3.04 7.61
4 5023 41R 133D CA CA 319 1063 9.28 6.81 2.47 4.66 6.81 2.47 4.66
5 5571 60T 64G CA CA 476 510 11.28 6.93 4.35 8.16 6.93 4.35 8.16
6 5572 60T 65S CA CA 476 514 9.63 6.01 3.62 8.06 6.01 3.62 8.06
7 5573 60T 66K CA CA 476 520 7.03 4.22 2.81 6.99 4.22 2.81 6.99
8 5582 60T 81K CA CA 476 654 14.89 11.49 3.39 5.56 11.49 3.39 5.56
9 5583 60T 82G CA CA 476 663 17.50 13.44 4.06 5.15 13.44 4.06 5.15
10 5584 60T 83A CA CA 476 667 14.99 11.07 3.92 5.78 11.07 3.92 5.78
11 5585 60T 84S CA CA 476 672 14.30 10.32 3.98 7.05 10.32 3.98 7.05
12 5586 60T 85P CA CA 476 678 16.98 12.86 4.12 5.45 12.86 4.12 5.45
13 6505 124K 128Q CA CA 996 1029 7.23 5.18 2.05 5.09 5.18 2.05 5.09
14 6507 124K 130S CA CA 996 1042 13.36 10.06 3.30 5.09 10.06 3.30 5.09
15 6511 125N 128Q CA CA 1005 1029 8.97 6.66 2.31 4.66 6.66 2.31 4.66
16 6513 125N 130S CA CA 1005 1042 14.08 9.78 4.30 6.32 9.78 4.30 6.32
17 6518 126H 130S CA CA 1013 1042 12.29 7.42 4.87 9.31 7.42 4.87 9.31
18 6525 127C 130S CA CA 1023 1042 8.85 5.30 3.55 9.68 5.30 3.55 9.68
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6949 39L 132P N O 302 1061 14.41 10.18 4.23 6.70 10.18 4.23 6.70
2 6967 40M 132P N O 310 1061 13.29 8.51 4.78 9.99 8.51 4.78 9.99
3 6991 41R 132P N O 318 1061 11.41 5.74 5.68 11.93 5.74 5.68 11.93
4 7019 42N 132P N O 329 1061 9.92 6.20 3.72 7.58 6.20 3.72 7.58
5 7179 48E 44V N O 379 357 5.23 3.06 2.18 4.91 3.06 2.18 4.91
6 7468 60T 64G N O 475 512 11.30 7.82 3.49 5.45 7.82 3.49 5.45
7 7469 60T 65S N O 475 518 8.33 4.76 3.57 7.33 4.76 3.57 7.33
8 7476 60T 83A N O 475 670 15.64 11.00 4.64 6.35 11.00 4.64 6.35
9 7482 61N 65S N O 482 518 4.93 2.59 2.33 5.89 2.59 2.33 5.89
10 7507 64G 61N N O 509 489 5.45 3.18 2.27 4.67 3.18 2.27 4.67
11 8023 86G 63N N O 684 508 11.16 7.27 3.88 5.49 7.27 3.88 5.49
12 8033 87K 63N N O 688 508 12.76 8.66 4.10 6.85 8.66 4.10 6.85
13 8757 125N 128Q N O 1004 1036 10.20 6.57 3.64 6.13 6.57 3.64 6.13
14 8773 126H 128Q N O 1012 1036 8.84 6.16 2.67 5.09 6.16 2.67 5.09
15 8794 127C 130S N O 1022 1046 10.14 7.34 2.80 5.38 7.34 2.80 5.38
16 8808 128Q 123W N O 1028 994 4.45 2.79 1.67 4.53 2.79 1.67 4.53
17 8809 128Q 124K N O 1028 1003 7.13 4.29 2.84 5.97 4.29 2.84 5.97
18 8822 129G 124K N O 1037 1003 10.67 6.40 4.27 6.12 6.40 4.27 6.12
19 8823 129G 125N N O 1037 1011 11.40 7.69 3.71 4.54 7.69 3.71 4.54
20 8831 130S 123W N O 1041 994 11.44 7.33 4.11 7.48 7.33 4.11 7.48
21 8832 130S 124K N O 1041 1003 14.13 7.82 6.31 9.89 7.82 6.31 9.89
22 8833 130S 125N N O 1041 1011 14.40 7.78 6.62 9.72 7.78 6.62 9.72
23 8834 130S 126H N O 1041 1021 11.12 5.94 5.18 9.41 5.94 5.18 9.41
24 8835 130S 127C N O 1041 1027 7.81 3.18 4.63 12.35 3.18 4.63 12.35
25 8843 131L 126H N O 1047 1021 10.16 6.80 3.36 4.87 6.80 3.36 4.87
26 8844 131L 127C N O 1047 1027 8.25 5.43 2.82 5.19 5.43 2.82 5.19
27 8857 132P 127C N O 1055 1027 8.87 6.04 2.83 7.88 6.04 2.83 7.88
28 8860 132P 130S N O 1055 1046 5.41 3.36 2.05 4.69 3.36 2.05 4.69
29 8884 134I 132P N O 1070 1061 6.03 3.18 2.85 5.11 3.18 2.85 5.11
30 8900 135S 132P N O 1078 1061 8.26 2.93 5.33 11.64 2.93 5.33 11.64
31 8917 136S 132P N O 1084 1061 10.70 4.11 6.59 12.16 4.11 6.59 12.16
32 8928 137C 132P N O 1090 1061 12.73 5.93 6.81 6.07 5.93 6.81 6.07
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 4003 59N 59N CA C 468 473 -100.81 -180.00 79.19 15.83 -180.00 79.19 15.83
2 4075 131L 131L CA C 1048 1053 -146.73 -180.00 33.27 6.65 -180.00 33.27 6.65
-------------------------------------------------------------------------------------------------
Feature 22 : Upper bound distance restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12135 101I 130S O N 801 1041 5.81 3.50 2.31 23.13 3.50 2.31 23.13
2 12136 43W 131L N O 337 1054 4.54 3.50 1.04 10.41 3.50 1.04 10.41
3 12137 60T 132P N O 475 1061 8.81 3.50 5.31 53.06 3.50 5.31 53.06
-------------------------------------------------------------------------------------------------
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 -73.58 -73.00 3.74 0.23 -63.80 175.57 26.33
1 2Q 2Q N CA 9 10 144.40 140.70 -40.30
2 3811 2Q 3K C N 16 18 -109.93 -118.00 17.08 0.88 -62.90 171.62 25.07
2 3K 3K N CA 18 19 154.15 139.10 -40.80
3 3812 3K 4L C N 25 27 -95.81 -108.50 12.77 0.63 -63.50 178.06 23.07
3 4L 4L N CA 27 28 133.90 132.50 -41.20
4 3815 6I 7F C N 49 51 -103.29 -124.20 30.35 0.83 -63.20 170.39 21.14
4 7F 7F N CA 51 52 121.31 143.30 -44.30
5 3816 7F 8A C N 60 62 -131.61 -134.00 4.86 0.20 -62.50 -170.60 34.74
5 8A 8A N CA 62 63 142.76 147.00 -40.90
6 3817 8A 9L C N 65 67 -78.95 -70.70 10.63 0.71 -63.50 171.19 24.68
6 9L 9L N CA 67 68 148.31 141.60 -41.20
7 3818 9L 10V C N 73 75 -61.44 -62.40 2.71 0.30 -125.40 -176.71 10.30
7 10V 10V N CA 75 76 -44.93 -42.40 143.30
8 3820 11V 12L C N 87 89 -68.64 -70.70 2.06 0.18 -63.50 177.34 24.92
8 12L 12L N CA 89 90 141.54 141.60 -41.20
9 3823 14V 15G C N 108 110 -170.29 -167.20 32.07 1.29 82.20 171.93 12.85
9 15G 15G N CA 110 111 142.67 174.60 8.50
10 3824 15G 16S C N 112 114 -135.49 -136.60 14.19 0.70 -64.10 -173.73 11.57
10 16S 16S N CA 114 115 137.05 151.20 -35.00
11 3844 35F 36E C N 274 276 51.45 54.60 4.24 0.54 -63.60 140.05 24.08
11 36E 36E N CA 276 277 39.55 42.40 -40.30
12 3859 50E 51S C N 405 407 -150.63 -64.10 95.79 10.07 -64.10 95.79 10.07
12 51S 51S N CA 407 408 6.09 -35.00 -35.00
13 3860 51S 52S C N 411 413 55.52 56.90 1.56 0.20 -64.10 138.94 18.28
13 52S 52S N CA 413 414 35.67 36.40 -35.00
14 3871 62R 63N C N 499 501 -67.26 -119.90 62.91 3.32 -63.20 147.51 18.67
14 63N 63N N CA 501 502 171.45 137.00 -41.10
15 3872 63N 64G C N 507 509 -59.82 -62.40 16.68 2.62 82.20 145.85 10.80
15 64G 64G N CA 509 510 -24.73 -41.20 8.50
16 3896 87K 88D C N 695 697 177.50 -96.50 88.71 3.61 -63.30 178.19 19.74
16 88D 88D N CA 697 698 92.45 114.20 -40.00
17 3920 111I 112Y C N 872 874 -51.24 -98.40 52.10 3.14 -63.50 150.16 24.46
17 112Y 112Y N CA 874 875 106.26 128.40 -43.40
18 3934 125N 126H C N 1010 1012 -156.06 -125.60 110.97 4.72 -63.20 118.98 14.02
18 126H 126H N CA 1012 1013 32.09 138.80 -42.30
19 3935 126H 127C C N 1020 1022 -157.01 -63.00 101.24 18.05 -63.00 101.24 18.05
19 127C 127C N CA 1022 1023 -78.67 -41.10 -41.10
20 3936 127C 128Q C N 1026 1028 72.06 55.10 86.74 7.66 -121.10 167.45 6.60
20 128Q 128Q N CA 1028 1029 125.37 40.30 139.70
21 3937 128Q 129G C N 1035 1037 87.98 82.20 175.24 8.80 82.20 175.24 8.80
21 129G 129G N CA 1037 1038 -176.35 8.50 8.50
22 3941 132P 133D C N 1060 1062 -163.52 -63.30 123.22 20.93 -63.30 123.22 20.93
22 133D 133D N CA 1062 1063 -111.68 -40.00 -40.00
23 3942 133D 134I C N 1068 1070 -70.55 -97.30 31.26 2.13 -63.40 154.79 25.12
23 134I 134I N CA 1070 1071 111.03 127.20 -43.60
24 3943 134I 135S C N 1076 1078 -52.88 -72.40 67.76 4.66 -64.10 108.29 7.25
24 135S 135S N CA 1078 1079 -142.71 152.40 -35.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10800 63N 139. CA C6 502 1116 10.87 9.85 1.02 5.08 9.85 1.02 5.08
2 10801 63N 139. CA O6 502 1123 10.42 9.24 1.18 5.91 9.24 1.18 5.91
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 350 1054 2.299
serious non-bonded atom clash: 388 1061 2.299
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 2 1 2 18 26 83 104 129 145 189 185 181 208
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
Sequence.B99990001.pdb 7227.18262
Sequence.B99990002.pdb 6941.18164
Sequence.B99990003.pdb 7102.76953
Sequence.B99990004.pdb 7274.18945
Sequence.B99990005.pdb 7266.05859
In [40]:
import nglview
import ipywidgets
w1 = nglview.show_structure_file('Sequence.B99990001.pdb')
w1
In [23]:
Image(filename='1hom_lmp_02.png')
IOErrorTraceback (most recent call last) <ipython-input-23-722c3712c2a1> in <module>() ----> 1 Image(filename='1hom_lmp_02.png') /usr/local/lib/python2.7/dist-packages/IPython/core/display.pyc in __init__(self, data, url, filename, format, embed, width, height, retina, unconfined, metadata) 749 self.unconfined = unconfined 750 self.metadata = metadata --> 751 super(Image, self).__init__(data=data, url=url, filename=filename) 752 753 if retina: /usr/local/lib/python2.7/dist-packages/IPython/core/display.pyc in __init__(self, data, url, filename) 386 self.filename = None if filename is None else unicode_type(filename) 387 --> 388 self.reload() 389 self._check_data() 390 /usr/local/lib/python2.7/dist-packages/IPython/core/display.pyc in reload(self) 771 """Reload the raw data from file or URL.""" 772 if self.embed: --> 773 super(Image,self).reload() 774 if self.retina: 775 self._retina_shape() /usr/local/lib/python2.7/dist-packages/IPython/core/display.pyc in reload(self) 404 """Reload the raw data from file or URL.""" 405 if self.filename is not None: --> 406 with open(self.filename, self._read_flags) as f: 407 self.data = f.read() 408 elif self.url is not None: IOError: [Errno 2] No such file or directory: u'1hom_lmp_02.png'
Построим структуру лизоцима с лигандом, в котором все аминокислоты - аланин
In [35]:
with open("P48816.fasta") as rf:
lines = rf.readlines()
with open("polyA.fasta", "w+") as wf:
strip_lines = [line.strip("\n") for line in lines[1:]]
wf.write(lines[0])
for l in strip_lines:
wf.write("A" * len(l) + "\n")
In [36]:
# Посмотрим содержимое "polyA.fasta"
! cat polyA.fasta
>sp|P48816|LYS_BOMMO Lysozyme OS=Bombyx mori OX=7091 PE=1 SV=1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA
In [26]:
# Создадим объект-выравнивание
alignma=modeller.alignment(env)
In [27]:
# Добавим последовательность и структуру
alignma.append(file='polyA.fasta', align_codes='all',alignment_format='FASTA')
# Создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
# Добавим модель в выравнивание
alignma.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
In [28]:
# Поправим идентификаторы
alignma[0].code = 'PolyA'
alignma[1].code = 'Structure'
In [29]:
# Сделаем выравнивание и сохраним в файл ("polyA.ali")
alignma.salign()
alignma.write(file='polyA.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [30]:
# Посмотрим содержимое "polyA.ali"
! cat polyA.ali
>P1;PolyA sequence:: : : : :::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA* >P1;Structure structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY-----WCDDGRTP GAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
In [37]:
# Добавим лиганд
with open("polyA.ali") as rf:
lines = rf.readlines()
with open("polyA.ali", "w+") as wf:
for line in lines:
if not line.find("*") == -1:
line = line[:-5] + "/...*"
wf.write(line)
In [38]:
! cat polyA.ali
>P1;PolyA sequence:: : : : :::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/...* >P1;Structure structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRY-----WCDDGRTP GAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV/...*
In [39]:
# Построим модель
# Выбираем объект для моделирования
s = alignma[0]
pdb = alignma[1]
print s.code, pdb.code
# Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='polyA.ali', knowns=pdb.code, sequence=s.code)
# Построим 5 моделей
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 5
a.make()
PolyA Structure
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10230 9567
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 714 714
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9567 9567
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1371
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 : 929.2953
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 : 670 0 0 0.008 0.008 14.688 1.000
2 Bond angle potential : 937 2 10 2.590 2.590 130.04 1.000
3 Stereochemical cosine torsion poten: 272 0 40 77.553 77.553 265.66 1.000
4 Stereochemical improper torsion pot: 268 0 0 1.223 1.223 11.225 1.000
5 Soft-sphere overlap restraints : 1371 2 2 0.013 0.013 26.456 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.257 0.257 61.433 1.000
10 Distance restraints 2 (N-O) : 2564 0 16 0.416 0.416 177.51 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 133 1 4 5.533 5.533 48.016 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.285 0.285 6.9736 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: 132 25 27 40.461 72.870 149.27 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.463 0.463 1.3613 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.057 0.057 36.654 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: PolyA.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: 12925.7266
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 1099 62A 62A N CA 306 307 127.24 107.00 20.24 5.82 107.00 20.24 5.82
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2341 62A 62A CA C 307 309 -157.02 -180.00 22.98 4.59 -180.00 22.98 4.59
-------------------------------------------------------------------------------------------------
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 2162 15A 16A C N 74 76 78.04 55.40 26.02 1.94 -62.50 155.39 31.57
1 16A 16A N CA 76 77 25.38 38.20 -40.90
2 2165 18A 19A C N 89 91 65.01 55.40 20.05 0.74 -62.50 141.57 28.77
2 19A 19A N CA 91 92 20.60 38.20 -40.90
3 2167 20A 21A C N 99 101 62.10 -68.20 145.80 14.10 -62.50 165.13 25.94
3 21A 21A N CA 101 102 -149.26 145.30 -40.90
4 2168 21A 22A C N 104 106 -105.67 -134.00 84.69 3.97 -62.50 116.38 17.55
4 22A 22A N CA 106 107 67.18 147.00 -40.90
5 2169 22A 23A C N 109 111 -70.97 -62.50 11.42 2.29 -134.00 176.11 10.85
5 23A 23A N CA 111 112 -48.56 -40.90 147.00
6 2183 36A 37A C N 179 181 66.60 55.40 13.27 0.94 -62.50 147.81 30.06
6 37A 37A N CA 181 182 31.08 38.20 -40.90
7 2184 37A 38A C N 184 186 62.09 55.40 9.93 0.49 -62.50 143.78 29.24
7 38A 38A N CA 186 187 30.86 38.20 -40.90
8 2195 48A 49A C N 239 241 85.67 55.40 40.56 2.32 -62.50 157.06 31.74
8 49A 49A N CA 241 242 11.20 38.20 -40.90
9 2200 53A 54A C N 264 266 91.32 -134.00 139.72 3.43 -62.50 -155.40 32.11
9 54A 54A N CA 266 267 -175.81 147.00 -40.90
10 2203 56A 57A C N 279 281 60.39 55.40 12.16 1.13 -62.50 152.43 30.88
10 57A 57A N CA 281 282 49.28 38.20 -40.90
11 2208 61A 62A C N 304 306 -105.26 -62.50 56.97 11.46 -62.50 56.97 11.46
11 62A 62A N CA 306 307 -78.54 -40.90 -40.90
12 2209 62A 63A C N 309 311 52.30 -68.20 133.37 12.85 -62.50 163.67 25.26
12 63A 63A N CA 311 312 -157.55 145.30 -40.90
13 2210 63A 64A C N 314 316 -153.22 -134.00 21.88 1.12 -62.50 -160.71 29.87
13 64A 64A N CA 316 317 136.54 147.00 -40.90
14 2211 64A 65A C N 319 321 44.19 -68.20 116.54 8.78 -62.50 -171.53 36.53
14 65A 65A N CA 321 322 114.47 145.30 -40.90
15 2212 65A 66A C N 324 326 110.78 -134.00 156.56 4.49 -62.50 -174.54 32.30
15 66A 66A N CA 326 327 -107.00 147.00 -40.90
16 2213 66A 67A C N 329 331 -157.68 -134.00 40.29 2.45 -62.50 -177.86 27.31
16 67A 67A N CA 331 332 114.40 147.00 -40.90
17 2218 71A 72A C N 354 356 79.01 55.40 61.13 2.23 -62.50 143.31 28.37
17 72A 72A N CA 356 357 -18.19 38.20 -40.90
18 2222 75A 76A C N 374 376 51.90 55.40 15.04 0.64 -62.50 147.89 29.85
18 76A 76A N CA 376 377 52.83 38.20 -40.90
19 2225 78A 79A C N 389 391 54.28 55.40 56.00 3.28 -62.50 178.56 35.30
19 79A 79A N CA 391 392 94.19 38.20 -40.90
20 2228 81A 82A C N 404 406 73.41 55.40 18.03 1.92 -62.50 156.82 31.89
20 82A 82A N CA 406 407 37.33 38.20 -40.90
21 2255 108A 109A C N 539 541 78.55 -134.00 161.83 3.68 -62.50 176.10 28.20
21 109A 109A N CA 541 542 -146.33 147.00 -40.90
22 2268 121A 122A C N 604 606 49.62 55.40 11.65 0.43 -62.50 143.28 28.95
22 122A 122A N CA 606 607 48.31 38.20 -40.90
23 2276 129A 130A C N 644 646 55.99 -68.20 130.37 12.22 -68.20 130.37 12.22
23 130A 130A N CA 646 647 -175.05 145.30 145.30
24 2277 130A 131A C N 649 651 -87.11 -68.20 81.98 7.25 -62.50 109.24 16.87
24 131A 131A N CA 651 652 65.53 145.30 -40.90
25 2279 132A 133A C N 659 661 149.97 -134.00 107.80 3.26 -62.50 175.85 35.72
25 133A 133A N CA 661 662 -136.59 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 11 11 49 52 77 62 90 116 110 89
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 714 714
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9567 9567
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1409
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 : 970.4614
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 : 670 0 1 0.010 0.010 19.399 1.000
2 Bond angle potential : 937 3 8 2.765 2.765 151.00 1.000
3 Stereochemical cosine torsion poten: 272 0 37 77.893 77.893 267.24 1.000
4 Stereochemical improper torsion pot: 268 0 0 1.352 1.352 11.696 1.000
5 Soft-sphere overlap restraints : 1409 2 3 0.013 0.013 26.206 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 1 0.319 0.319 93.093 1.000
10 Distance restraints 2 (N-O) : 2564 1 13 0.441 0.441 188.22 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 133 0 9 5.589 5.589 49.002 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.292 0.292 7.0043 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: 132 28 25 37.004 72.878 119.85 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.648 0.648 2.5682 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.055 0.055 35.189 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: PolyA.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: 13386.2275
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 1099 62A 62A N CA 306 307 133.56 107.00 26.56 7.64 107.00 26.56 7.64
2 1127 66A 66A N CA 326 327 123.99 107.00 16.99 4.88 107.00 16.99 4.88
-------------------------------------------------------------------------------------------------
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 5855 52A 44A N O 256 220 5.73 2.79 2.94 5.72 2.79 2.94 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 2149 2A 3A C N 9 11 -59.91 -62.50 14.24 2.22 -68.20 160.01 13.20
1 3A 3A N CA 11 12 -54.90 -40.90 145.30
2 2150 3A 4A C N 14 16 25.68 -68.20 103.98 7.23 -68.20 103.98 7.23
2 4A 4A N CA 16 17 100.58 145.30 145.30
3 2162 15A 16A C N 74 76 78.09 55.40 25.70 1.98 -62.50 155.75 31.65
3 16A 16A N CA 76 77 26.13 38.20 -40.90
4 2165 18A 19A C N 89 91 64.97 55.40 21.63 0.78 -62.50 140.76 28.60
4 19A 19A N CA 91 92 18.80 38.20 -40.90
5 2167 20A 21A C N 99 101 53.01 55.40 3.29 0.37 -62.50 138.73 28.17
5 21A 21A N CA 101 102 35.94 38.20 -40.90
6 2168 21A 22A C N 104 106 61.88 55.40 11.99 0.47 -62.50 142.24 28.93
6 22A 22A N CA 106 107 28.11 38.20 -40.90
7 2183 36A 37A C N 179 181 67.59 55.40 16.09 0.94 -62.50 147.07 29.91
7 37A 37A N CA 181 182 27.69 38.20 -40.90
8 2184 37A 38A C N 184 186 55.60 55.40 1.83 0.13 -62.50 143.16 29.05
8 38A 38A N CA 186 187 40.02 38.20 -40.90
9 2190 43A 44A C N 214 216 -77.79 -62.50 15.71 3.14 -134.00 177.62 10.90
9 44A 44A N CA 216 217 -44.51 -40.90 147.00
10 2191 44A 45A C N 219 221 72.18 -68.20 140.54 11.68 -68.20 140.54 11.68
10 45A 45A N CA 221 222 138.61 145.30 145.30
11 2195 48A 49A C N 239 241 84.35 55.40 38.79 2.22 -62.50 156.22 31.60
11 49A 49A N CA 241 242 12.38 38.20 -40.90
12 2200 53A 54A C N 264 266 93.61 -134.00 137.66 3.36 -62.50 -154.02 32.40
12 54A 54A N CA 266 267 -175.27 147.00 -40.90
13 2203 56A 57A C N 279 281 59.84 55.40 13.81 1.19 -62.50 153.17 31.01
13 57A 57A N CA 281 282 51.27 38.20 -40.90
14 2208 61A 62A C N 304 306 -99.09 -62.50 40.37 8.20 -62.50 40.37 8.20
14 62A 62A N CA 306 307 -57.97 -40.90 -40.90
15 2209 62A 63A C N 309 311 38.16 -68.20 116.13 11.13 -62.50 162.19 24.57
15 63A 63A N CA 311 312 -168.08 145.30 -40.90
16 2210 63A 64A C N 314 316 -128.40 -134.00 26.94 1.38 -62.50 174.47 26.29
16 64A 64A N CA 316 317 120.65 147.00 -40.90
17 2211 64A 65A C N 319 321 111.87 -134.00 139.78 3.49 -62.50 -163.13 33.05
17 65A 65A N CA 321 322 -132.30 147.00 -40.90
18 2213 66A 67A C N 329 331 -152.38 -134.00 39.51 2.44 -62.50 177.39 26.58
18 67A 67A N CA 331 332 112.03 147.00 -40.90
19 2218 71A 72A C N 354 356 77.91 55.40 56.97 2.07 -62.50 142.94 28.42
19 72A 72A N CA 356 357 -14.13 38.20 -40.90
20 2222 75A 76A C N 374 376 53.27 55.40 4.34 0.16 -62.50 142.38 28.87
20 76A 76A N CA 376 377 41.98 38.20 -40.90
21 2225 78A 79A C N 389 391 66.75 55.40 76.98 5.58 -62.50 -158.00 39.82
21 79A 79A N CA 391 392 114.34 38.20 -40.90
22 2226 79A 80A C N 394 396 -141.59 -62.50 85.18 14.76 -62.50 85.18 14.76
22 80A 80A N CA 396 397 -9.26 -40.90 -40.90
23 2228 81A 82A C N 404 406 74.91 55.40 19.68 2.24 -62.50 159.88 32.51
23 82A 82A N CA 406 407 40.84 38.20 -40.90
24 2255 108A 109A C N 539 541 79.73 -134.00 160.81 3.65 -62.50 176.96 28.38
24 109A 109A N CA 541 542 -146.18 147.00 -40.90
25 2267 120A 121A C N 599 601 -56.51 -62.50 15.68 2.36 -68.20 159.74 13.30
25 121A 121A N CA 601 602 -55.39 -40.90 145.30
26 2276 129A 130A C N 644 646 59.30 -68.20 135.53 12.81 -68.20 135.53 12.81
26 130A 130A N CA 646 647 -168.74 145.30 145.30
27 2277 130A 131A C N 649 651 -82.94 -68.20 72.10 6.32 -62.50 117.42 18.35
27 131A 131A N CA 651 652 74.73 145.30 -40.90
28 2279 132A 133A C N 659 661 60.12 55.40 4.74 0.49 -62.50 145.67 29.60
28 133A 133A N CA 661 662 37.75 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 12 43 65 84 70 82 104 116 96
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 714 714
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9567 9567
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1354
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 : 973.7703
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 : 670 0 0 0.008 0.008 12.069 1.000
2 Bond angle potential : 937 3 12 2.717 2.717 142.47 1.000
3 Stereochemical cosine torsion poten: 272 0 38 78.405 78.405 271.22 1.000
4 Stereochemical improper torsion pot: 268 0 2 1.622 1.622 15.783 1.000
5 Soft-sphere overlap restraints : 1354 2 3 0.012 0.012 24.696 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 4 0.305 0.305 85.810 1.000
10 Distance restraints 2 (N-O) : 2564 0 18 0.469 0.469 203.50 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: 133 2 6 6.332 6.332 62.890 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.277 0.277 6.7157 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: 132 27 26 38.644 74.530 121.49 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.493 0.493 1.2741 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.047 0.047 25.860 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: PolyA.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: 13266.4990
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 1099 62A 62A N CA 306 307 126.70 107.00 19.70 5.66 107.00 19.70 5.66
2 1218 79A 79A N CA 391 392 123.88 107.00 16.88 4.85 107.00 16.88 4.85
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2340 61A 61A CA C 302 304 -151.58 -180.00 28.42 5.68 -180.00 28.42 5.68
2 2357 78A 78A CA C 387 389 -144.40 -180.00 35.60 7.12 -180.00 35.60 7.12
-------------------------------------------------------------------------------------------------
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 2162 15A 16A C N 74 76 78.66 55.40 26.69 2.00 -62.50 155.83 31.66
1 16A 16A N CA 76 77 25.10 38.20 -40.90
2 2165 18A 19A C N 89 91 59.52 55.40 10.06 0.36 -62.50 140.64 28.60
2 19A 19A N CA 91 92 29.03 38.20 -40.90
3 2166 19A 20A C N 94 96 -63.26 -62.50 22.54 3.73 -68.20 151.36 12.38
3 20A 20A N CA 96 97 -63.42 -40.90 145.30
4 2168 21A 22A C N 104 106 156.74 55.40 102.38 10.37 -62.50 154.87 26.43
4 22A 22A N CA 106 107 23.67 38.20 -40.90
5 2183 36A 37A C N 179 181 66.40 55.40 13.44 0.90 -62.50 147.33 29.96
5 37A 37A N CA 181 182 30.47 38.20 -40.90
6 2184 37A 38A C N 184 186 62.02 55.40 10.33 0.48 -62.50 143.43 29.17
6 38A 38A N CA 186 187 30.28 38.20 -40.90
7 2195 48A 49A C N 239 241 83.70 55.40 37.79 2.17 -62.50 155.87 31.54
7 49A 49A N CA 241 242 13.15 38.20 -40.90
8 2200 53A 54A C N 264 266 91.21 -134.00 139.81 3.44 -62.50 -155.43 32.10
8 54A 54A N CA 266 267 -175.90 147.00 -40.90
9 2203 56A 57A C N 279 281 60.62 55.40 13.39 1.23 -62.50 153.36 31.06
9 57A 57A N CA 281 282 50.53 38.20 -40.90
10 2209 62A 63A C N 309 311 74.24 -68.20 142.56 12.28 -62.50 -143.45 32.87
10 63A 63A N CA 311 312 151.19 145.30 -40.90
11 2210 63A 64A C N 314 316 105.49 -134.00 132.34 3.01 -62.50 -155.04 33.12
11 64A 64A N CA 316 317 -158.32 147.00 -40.90
12 2211 64A 65A C N 319 321 -113.16 -134.00 44.09 1.82 -62.50 157.41 23.89
12 65A 65A N CA 321 322 108.14 147.00 -40.90
13 2212 65A 66A C N 324 326 139.04 -134.00 105.89 2.62 -62.50 -166.14 39.32
13 66A 66A N CA 326 327 -152.57 147.00 -40.90
14 2213 66A 67A C N 329 331 -146.56 -134.00 12.81 0.52 -62.50 -166.19 36.26
14 67A 67A N CA 331 332 144.48 147.00 -40.90
15 2218 71A 72A C N 354 356 79.49 55.40 54.93 1.99 -62.50 145.07 28.92
15 72A 72A N CA 356 357 -11.16 38.20 -40.90
16 2220 73A 74A C N 364 366 -63.05 -62.50 0.94 0.14 -134.00 -173.14 11.52
16 74A 74A N CA 366 367 -40.14 -40.90 147.00
17 2221 74A 75A C N 369 371 69.51 -68.20 137.76 11.55 -68.20 137.76 11.55
17 75A 75A N CA 371 372 141.50 145.30 145.30
18 2222 75A 76A C N 374 376 59.15 55.40 11.55 0.44 -62.50 139.45 28.36
18 76A 76A N CA 376 377 27.27 38.20 -40.90
19 2224 77A 78A C N 384 386 -84.63 -62.50 46.44 6.96 -62.50 46.44 6.96
19 78A 78A N CA 386 387 -0.08 -40.90 -40.90
20 2226 79A 80A C N 394 396 110.24 -62.50 173.10 32.78 -62.50 173.10 32.78
20 80A 80A N CA 396 397 -52.11 -40.90 -40.90
21 2228 81A 82A C N 404 406 63.38 55.40 9.67 1.14 -62.50 151.64 30.79
21 82A 82A N CA 406 407 43.65 38.20 -40.90
22 2255 108A 109A C N 539 541 80.21 -134.00 159.66 3.63 -62.50 178.38 28.56
22 109A 109A N CA 541 542 -147.91 147.00 -40.90
23 2267 120A 121A C N 599 601 -55.71 -62.50 14.04 2.10 -68.20 162.00 13.51
23 121A 121A N CA 601 602 -53.18 -40.90 145.30
24 2268 121A 122A C N 604 606 -113.65 -134.00 57.21 2.64 -62.50 143.83 21.72
24 122A 122A N CA 606 607 93.53 147.00 -40.90
25 2269 122A 123A C N 609 611 -167.07 -134.00 37.39 0.86 -68.20 100.71 7.86
25 123A 123A N CA 611 612 164.43 147.00 145.30
26 2277 130A 131A C N 649 651 70.17 55.40 37.35 1.36 -62.50 140.03 28.27
26 131A 131A N CA 651 652 3.90 38.20 -40.90
27 2279 132A 133A C N 659 661 70.33 55.40 22.11 1.09 -62.50 146.92 29.85
27 133A 133A N CA 661 662 21.89 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 7 8 52 55 88 57 85 113 106 97
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 714 714
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9567 9567
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1381
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 : 828.3361
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 : 670 0 0 0.009 0.009 14.837 1.000
2 Bond angle potential : 937 3 9 2.655 2.655 137.56 1.000
3 Stereochemical cosine torsion poten: 272 0 36 76.659 76.659 261.14 1.000
4 Stereochemical improper torsion pot: 268 0 1 1.204 1.204 10.454 1.000
5 Soft-sphere overlap restraints : 1381 2 3 0.013 0.013 28.958 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 1 0.242 0.242 57.767 1.000
10 Distance restraints 2 (N-O) : 2564 1 11 0.364 0.364 134.32 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: 133 1 4 5.330 5.330 44.553 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.238 0.238 4.8792 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: 132 21 21 33.211 63.554 99.526 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.487 0.487 1.5087 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.054 0.054 32.836 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: PolyA.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: 12032.8818
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 1099 62A 62A N CA 306 307 128.02 107.00 21.02 6.04 107.00 21.02 6.04
2 1225 80A 80A N CA 396 397 124.07 107.00 17.07 4.91 107.00 17.07 4.91
-------------------------------------------------------------------------------------------------
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 6410 81A 68A N O 401 340 4.80 2.92 1.88 4.70 2.92 1.88 4.70
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2341 62A 62A CA C 307 309 -156.91 -180.00 23.09 4.62 -180.00 23.09 4.62
-------------------------------------------------------------------------------------------------
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 2162 15A 16A C N 74 76 77.88 55.40 25.53 1.95 -62.50 155.54 31.61
1 16A 16A N CA 76 77 26.09 38.20 -40.90
2 2165 18A 19A C N 89 91 63.99 55.40 22.61 0.83 -62.50 139.22 28.28
2 19A 19A N CA 91 92 17.28 38.20 -40.90
3 2167 20A 21A C N 99 101 62.72 -68.20 144.31 13.88 -62.50 168.74 26.39
3 21A 21A N CA 101 102 -154.00 145.30 -40.90
4 2168 21A 22A C N 104 106 -108.36 -134.00 75.85 3.55 -62.50 125.21 18.89
4 22A 22A N CA 106 107 75.61 147.00 -40.90
5 2183 36A 37A C N 179 181 66.61 55.40 13.40 0.93 -62.50 147.70 30.04
5 37A 37A N CA 181 182 30.85 38.20 -40.90
6 2184 37A 38A C N 184 186 62.53 55.40 11.90 0.51 -62.50 143.08 29.10
6 38A 38A N CA 186 187 28.67 38.20 -40.90
7 2195 48A 49A C N 239 241 85.68 55.40 41.30 2.30 -62.50 156.71 31.66
7 49A 49A N CA 241 242 10.12 38.20 -40.90
8 2200 53A 54A C N 264 266 89.47 -134.00 142.23 3.45 -62.50 -158.55 31.64
8 54A 54A N CA 266 267 -173.14 147.00 -40.90
9 2203 56A 57A C N 279 281 60.42 55.40 11.37 1.09 -62.50 151.93 30.79
9 57A 57A N CA 281 282 48.41 38.20 -40.90
10 2208 61A 62A C N 304 306 -104.53 -62.50 46.48 9.44 -62.50 46.48 9.44
10 62A 62A N CA 306 307 -60.74 -40.90 -40.90
11 2209 62A 63A C N 309 311 53.33 -62.50 134.52 22.24 -62.50 134.52 22.24
11 63A 63A N CA 311 312 -109.32 -40.90 -40.90
12 2210 63A 64A C N 314 316 -161.35 -134.00 92.77 4.48 -62.50 129.37 26.08
12 64A 64A N CA 316 317 -124.36 147.00 -40.90
13 2213 66A 67A C N 329 331 -177.88 -134.00 55.88 3.13 -62.50 -168.12 28.98
13 67A 67A N CA 331 332 112.41 147.00 -40.90
14 2218 71A 72A C N 354 356 78.85 55.40 57.53 2.08 -62.50 143.82 28.59
14 72A 72A N CA 356 357 -14.34 38.20 -40.90
15 2222 75A 76A C N 374 376 49.66 55.40 16.56 0.62 -62.50 146.74 29.58
15 76A 76A N CA 376 377 53.73 38.20 -40.90
16 2225 78A 79A C N 389 391 50.62 55.40 58.55 3.14 -62.50 178.01 35.06
16 79A 79A N CA 391 392 96.55 38.20 -40.90
17 2228 81A 82A C N 404 406 79.30 55.40 25.35 2.24 -62.50 158.42 32.21
17 82A 82A N CA 406 407 29.76 38.20 -40.90
18 2255 108A 109A C N 539 541 80.39 -134.00 159.55 3.63 -62.50 178.44 28.58
18 109A 109A N CA 541 542 -147.77 147.00 -40.90
19 2268 121A 122A C N 604 606 51.49 55.40 6.32 0.28 -62.50 141.63 28.69
19 122A 122A N CA 606 607 43.17 38.20 -40.90
20 2277 130A 131A C N 649 651 72.77 55.40 42.53 1.54 -62.50 141.13 28.40
20 131A 131A N CA 651 652 -0.63 38.20 -40.90
21 2279 132A 133A C N 659 661 62.92 55.40 10.13 0.58 -62.50 144.77 29.44
21 133A 133A N CA 661 662 31.41 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 9 11 44 59 76 64 96 111 108 102
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 714 714
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 9567 9567
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1404
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 : 1052.4282
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 : 670 0 5 0.013 0.013 35.481 1.000
2 Bond angle potential : 937 5 15 3.240 3.240 195.91 1.000
3 Stereochemical cosine torsion poten: 272 0 35 77.233 77.233 263.06 1.000
4 Stereochemical improper torsion pot: 268 0 1 1.609 1.609 17.280 1.000
5 Soft-sphere overlap restraints : 1404 3 7 0.016 0.016 44.942 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 3 0.274 0.274 74.144 1.000
10 Distance restraints 2 (N-O) : 2564 2 17 0.428 0.428 182.68 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: 133 2 10 7.550 7.550 89.415 1.000
14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 722 0 0 0.244 0.244 5.2174 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: 132 21 23 34.902 67.047 87.119 1.000
26 Distance restraints 4 (SDCH-SDCH) : 63 0 0 0.487 0.487 1.4264 1.000
27 Distance restraints 5 (X-Y) : 1401 0 3 0.071 0.071 55.753 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: PolyA.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: 12863.8818
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 1109 63A 63A C CA 314 312 131.61 108.00 23.61 5.47 108.00 23.61 5.47
2 1110 63A 64A C N 314 316 142.94 120.00 22.94 5.21 120.00 22.94 5.21
3 1131 66A 67A C N 329 331 153.40 120.00 33.40 7.59 120.00 33.40 7.59
4 1134 67A 67A N CA 331 332 130.37 107.00 23.37 6.72 107.00 23.37 6.72
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6409 81A 62A N O 401 310 7.68 4.80 2.88 4.54 4.80 2.88 4.54
2 6410 81A 68A N O 401 340 4.74 2.92 1.81 4.55 2.92 1.81 4.55
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2341 62A 62A CA C 307 309 -127.87 -180.00 52.13 10.42 -180.00 52.13 10.42
-------------------------------------------------------------------------------------------------
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 2162 15A 16A C N 74 76 78.51 55.40 25.96 2.03 -62.50 156.24 31.75
1 16A 16A N CA 76 77 26.39 38.20 -40.90
2 2164 17A 18A C N 84 86 -57.03 -62.50 6.34 1.05 -134.00 -174.40 11.45
2 18A 18A N CA 86 87 -44.11 -40.90 147.00
3 2167 20A 21A C N 99 101 63.95 -68.20 148.30 14.35 -62.50 165.32 26.07
3 21A 21A N CA 101 102 -147.39 145.30 -40.90
4 2168 21A 22A C N 104 106 -117.51 -134.00 80.15 4.11 -62.50 122.51 18.36
4 22A 22A N CA 106 107 68.56 147.00 -40.90
5 2183 36A 37A C N 179 181 66.25 55.40 13.51 0.87 -62.50 147.05 29.91
5 37A 37A N CA 181 182 30.14 38.20 -40.90
6 2184 37A 38A C N 184 186 63.09 55.40 12.11 0.55 -62.50 143.66 29.22
6 38A 38A N CA 186 187 28.85 38.20 -40.90
7 2195 48A 49A C N 239 241 85.34 55.40 41.08 2.27 -62.50 156.38 31.59
7 49A 49A N CA 241 242 10.08 38.20 -40.90
8 2200 53A 54A C N 264 266 91.18 -134.00 140.15 3.42 -62.50 -156.21 32.01
8 54A 54A N CA 266 267 -174.73 147.00 -40.90
9 2203 56A 57A C N 279 281 60.19 55.40 14.86 1.29 -62.50 154.06 31.18
9 57A 57A N CA 281 282 52.27 38.20 -40.90
10 2210 63A 64A C N 314 316 38.25 -68.20 111.61 8.26 -62.50 -177.08 35.32
10 64A 64A N CA 316 317 111.77 145.30 -40.90
11 2211 64A 65A C N 319 321 133.61 -134.00 141.35 4.64 -62.50 176.36 35.74
11 65A 65A N CA 321 322 -106.04 147.00 -40.90
12 2212 65A 66A C N 324 326 -141.16 -134.00 31.80 1.93 -62.50 175.52 26.31
12 66A 66A N CA 326 327 116.01 147.00 -40.90
13 2213 66A 67A C N 329 331 31.41 -68.20 109.85 7.67 -62.50 168.49 32.58
13 67A 67A N CA 331 332 98.99 145.30 -40.90
14 2218 71A 72A C N 354 356 76.75 55.40 52.40 1.90 -62.50 142.71 28.50
14 72A 72A N CA 356 357 -9.65 38.20 -40.90
15 2222 75A 76A C N 374 376 55.25 55.40 3.04 0.17 -62.50 143.56 29.12
15 76A 76A N CA 376 377 41.24 38.20 -40.90
16 2225 78A 79A C N 389 391 48.78 55.40 63.77 3.31 -62.50 -179.18 35.45
16 79A 79A N CA 391 392 101.63 38.20 -40.90
17 2228 81A 82A C N 404 406 85.11 55.40 30.52 2.92 -62.50 164.28 33.39
17 82A 82A N CA 406 407 31.22 38.20 -40.90
18 2255 108A 109A C N 539 541 80.39 -134.00 159.75 3.63 -62.50 178.15 28.55
18 109A 109A N CA 541 542 -147.31 147.00 -40.90
19 2268 121A 122A C N 604 606 51.96 55.40 8.33 0.30 -62.50 143.58 29.06
19 122A 122A N CA 606 607 45.79 38.20 -40.90
20 2277 130A 131A C N 649 651 68.69 55.40 37.40 1.39 -62.50 138.42 27.94
20 131A 131A N CA 651 652 3.24 38.20 -40.90
21 2279 132A 133A C N 659 661 59.70 55.40 4.31 0.47 -62.50 145.57 29.57
21 133A 133A N CA 661 662 38.21 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 10 11 49 72 68 68 91 122 114 99
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
PolyA.B99990001.pdb 929.29529
PolyA.B99990002.pdb 970.46143
PolyA.B99990003.pdb 973.77032
PolyA.B99990004.pdb 828.33612
PolyA.B99990005.pdb 1052.42822
In [45]:
Image(filename='1lmp_hom_polya.png')
Out[45]:
По выдаче Modeller видно, что даже визульно незначительные изменения в конформации в структуре приводят к существенным различиям в score:
1027.60547 7227.18262
1130.73291 6941.18164
1126.20996 7102.76953
1081.03064 7274.18945
1055.00232 7266.05859Ссылки¶
Визуализация: PyMOLWiki, NGL Viewer
https://pymolwiki.org/index.php/Main_Page
https://github.com/arose/nglviewГомологичное моделирование: Modeller
Псевдокод
In [ ]: