Гомологичное моделирование комплекса белка с лигандом¶
Импортируем Modeller
In [4]:
import sys
import modeller
import _modeller
import modeller.automodel
env=modeller.Environ()
env.io.hetatm=True
MODELLER 10.1, 2021/03/12, r12156
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 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 tskir-jupyter 5.11.0-1020-gcp x86_64
Date and time of compilation : 2021/03/12 00:18:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/10/24 18:55:38
Скачиваем белок заготовку 1lmp и последовательность для моделирования LYS_BOMMO
In [5]:
! wget -q -O template.pdb http://www.pdb.org/pdb/files/1lmp.pdb
! wget -q -O sequence.fasta http://www.uniprot.org/uniprot/P48816.fasta
In [6]:
alignm = modeller.Alignment(env)
In [7]:
# Читаем последовательность для моделирования
alignm.append(file='sequence.fasta', alignment_format='FASTA')
# Создадим модель, читаем цепь А с белком и цепь B с лигандом
mdl = modeller.Model(env, file='template.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
# И добавим в выравнивание
alignm.append_model(mdl, atom_files='template.pdb', align_codes='1lmp')
read_pd_459W> Residue type NDG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NAG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [10]:
# Правим идентификаторы
alignm[0].code = 'sequence'
alignm[1].code = 'template'
Modeller может сохранить выравнивание в форматах PIR или PAP. Более удобен для визуального просмотра PAP, поэтому посмотрим на него.
In [11]:
# Делаем выравнивание и сохраняем:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
alignm.write(file='all_in_one.pap', alignment_format='PAP')
! cat all_in_one.pap
SALIGN_____> adding the next group to the alignment; iteration 1 _aln.pos 10 20 30 40 50 60 sequence MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDY template ---------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDY _consrvd * * ***** *** * ** * ** ** _aln.p 70 80 90 100 110 120 130 sequence GLFQINDRYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPD template GIFQINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLR _consrvd * **** **** * ** * ** ***** * * *** ** * *** _aln.pos 140 sequence ISSC-------- template SYVAGCGV/... _consrvd
Выравнивание выглядит неплохо: интересующая нас последовательность содержит всего одну большую вставку и одну небольшую делецию.
Но нет лиганда (его остатки обозначаются точками), поэтому добавим его в файл с выравниванием. Редактируем именно PIR, потому что он будет использоваться в расчётах.
In [12]:
with open('all_in_one.ali','r') as old:
lines = old.readlines()
with open('all_in_one_lig.ali','w') as new:
for c, line in enumerate(lines):
if c == 4:
line = line[:-6] + '/...*'
new.write(line)
%cat all_in_one_lig.ali
>P1;sequence sequence::: :: :::-1.00:-1.00 MQKLIIFALVVLCVGSEAKTFTRCGLVHELRKHGFEENLMRNWVCLVEHESSRDTSKTNTNRNGSKDYGLFQIND RYWCSKGASPGKD--CNVKCSDLLTDDITKAAKCAKKI-YKRHRFDAWYGWKNHCQGSLPDISSC----/...* >P1;template structureX:template.pdb:1:A:+132:B: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/...*
Лиганд появился. Теперь запустим 10 итераций моделирования, чтобы было из чего выбирать:
In [15]:
## Выбираем объект для моделирования
sequence = alignm[0]
template = alignm[1]
## Создаем объект automodel
a = modeller.automodel.AutoModel(env, alnfile='all_in_one_lig.ali',
knowns=template.code,
sequence=sequence.code,
assess_methods=(modeller.automodel.assess.DOPE, modeller.automodel.assess.GA341))
a.name='mod'+sequence.code
a.starting_model = 1
a.ending_model = 10
a.make()
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied 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
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.
iupac_m_484W> Dihedral still outside +-90: -92.4636
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 197444
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11354.3828
<< end of ENERGY.
DOPE score : -11354.382812
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.111861
Native energy (pair) : -16.072391
Native energy (surface) : -1.161401
Native energy (combined) : -0.993498
Z score (pair) : -3.640282
Z score (surface) : -3.404358
Z score (combined) : -4.445635
GA341 score : 0.967816
>> 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): 2575
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 : 1157.5469
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 29.543 1.000
2 Bond angle potential : 1504 1 9 2.350 2.350 168.02 1.000
3 Stereochemical cosine torsion poten: 713 0 29 48.737 48.737 265.14 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.413 1.413 20.061 1.000
5 Soft-sphere overlap restraints : 2575 1 2 0.008 0.008 19.377 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 5 0.292 0.292 97.768 1.000
10 Distance restraints 2 (N-O) : 2371 0 16 0.371 0.371 178.75 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 1 5 5.289 5.289 44.861 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 82.943 82.943 38.097 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 68.372 68.372 37.539 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 90.870 90.870 29.880 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 98.694 98.694 14.089 1.000
18 Disulfide distance restraints : 3 0 0 0.025 0.025 0.32991 1.000
19 Disulfide angle restraints : 6 0 0 2.592 2.592 0.89016 1.000
20 Disulfide dihedral angle restraints: 3 0 0 26.382 26.382 2.0928 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 0.366 0.366 29.295 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 20 22 32.771 67.954 117.00 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 1 0.692 0.692 39.770 1.000
27 Distance restraints 5 (X-Y) : 1389 0 1 0.046 0.046 25.048 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: 16842.8184
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 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 697 698 129.70 107.00 22.70 6.53 107.00 22.70 6.53
-------------------------------------------------------------------------------------------------
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 4029 85P 85P CA C 678 682 -156.22 -180.00 23.78 4.75 -180.00 23.78 4.75
-------------------------------------------------------------------------------------------------
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 -73.69 -73.00 4.59 0.29 -63.80 174.74 26.22
1 2Q 2Q N CA 9 10 145.24 140.70 -40.30
2 3811 2Q 3K C N 16 18 -76.94 -70.20 15.81 1.28 -62.90 167.49 21.02
2 3K 3K N CA 18 19 126.10 140.40 -40.80
3 3812 3K 4L C N 25 27 -130.98 -108.50 22.67 1.05 -63.50 -170.89 23.41
3 4L 4L N CA 27 28 135.46 132.50 -41.20
4 3815 6I 7F C N 49 51 -142.33 -124.20 20.48 1.05 -63.20 -165.12 22.62
4 7F 7F N CA 51 52 133.79 143.30 -44.30
5 3816 7F 8A C N 60 62 -76.32 -68.20 8.13 0.68 -62.50 174.11 29.23
5 8A 8A N CA 62 63 145.54 145.30 -40.90
6 3817 8A 9L C N 65 67 -72.08 -70.70 2.61 0.25 -63.50 179.61 25.44
6 9L 9L N CA 67 68 139.39 141.60 -41.20
7 3820 11V 12L C N 87 89 -66.69 -70.70 5.49 0.36 -63.50 179.08 24.68
7 12L 12L N CA 89 90 137.85 141.60 -41.20
8 3823 14V 15G C N 108 110 -147.95 -167.20 22.17 0.36 82.20 -157.72 15.21
8 15G 15G N CA 110 111 163.60 174.60 8.50
9 3824 15G 16S C N 112 114 -110.67 -136.60 30.88 0.94 -64.10 175.71 10.89
9 16S 16S N CA 114 115 134.42 151.20 -35.00
10 3844 35F 36E C N 274 276 49.09 54.60 5.51 0.66 -63.60 139.64 23.99
10 36E 36E N CA 276 277 42.16 42.40 -40.30
11 3859 50E 51S C N 405 407 -141.66 -64.10 90.10 8.91 -64.10 90.10 8.91
11 51S 51S N CA 407 408 10.85 -35.00 -35.00
12 3860 51S 52S C N 411 413 53.87 56.90 3.40 0.29 -64.10 138.70 18.18
12 52S 52S N CA 413 414 37.94 36.40 -35.00
13 3894 85P 86G C N 682 684 -41.23 -62.40 30.33 4.26 82.20 142.61 11.13
13 86G 86G N CA 684 685 -62.92 -41.20 8.50
14 3895 86G 87K C N 686 688 75.46 -70.20 145.84 10.81 -70.20 145.84 10.81
14 87K 87K N CA 688 689 147.67 140.40 140.40
15 3896 87K 88D C N 695 697 162.13 -96.50 105.49 4.29 -63.30 -176.32 21.06
15 88D 88D N CA 697 698 85.02 114.20 -40.00
16 3922 113K 114R C N 893 895 -62.96 -125.20 77.47 2.29 -63.00 135.57 18.32
16 114R 114R N CA 895 896 94.47 140.60 -41.10
17 3923 114R 115H C N 904 906 -179.44 -63.20 116.37 18.18 -63.20 116.37 18.18
17 115H 115H N CA 906 907 -36.72 -42.30 -42.30
18 3935 126H 127C C N 1020 1022 -122.59 -63.00 64.16 9.13 -63.00 64.16 9.13
18 127C 127C N CA 1022 1023 -17.33 -41.10 -41.10
19 3936 127C 128Q C N 1026 1028 -55.83 -63.80 20.75 2.71 -121.10 173.58 9.01
19 128Q 128Q N CA 1028 1029 -59.46 -40.30 139.70
20 3937 128Q 129G C N 1035 1037 -75.00 -62.40 13.56 2.17 82.20 163.42 12.26
20 129G 129G N CA 1037 1038 -36.17 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 9 13 81 85 135 129 146 192 200 182
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 200443
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11830.9600
<< end of ENERGY.
DOPE score : -11830.959961
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.287749
Native energy (pair) : 10.980228
Native energy (surface) : 0.787957
Native energy (combined) : 0.696589
Z score (pair) : -3.035395
Z score (surface) : -2.929085
Z score (combined) : -3.632633
GA341 score : 0.871788
>> 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): 2489
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 : 1024.4296
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1119 0 5 0.009 0.009 28.608 1.000
2 Bond angle potential : 1504 1 12 2.229 2.229 152.30 1.000
3 Stereochemical cosine torsion poten: 713 0 29 48.367 48.367 261.32 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.212 1.212 15.574 1.000
5 Soft-sphere overlap restraints : 2489 1 2 0.008 0.008 17.978 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 3 0.309 0.309 102.91 1.000
10 Distance restraints 2 (N-O) : 2371 0 7 0.344 0.344 137.14 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 4.450 4.450 31.761 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 0 75.973 75.973 33.405 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 80.791 80.791 42.781 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 76.709 76.709 20.822 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 96.352 96.352 16.250 1.000
18 Disulfide distance restraints : 3 0 0 0.026 0.026 0.35999 1.000
19 Disulfide angle restraints : 6 0 0 4.307 4.307 2.4576 1.000
20 Disulfide dihedral angle restraints: 3 0 0 16.211 16.211 0.82361 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 0.331 0.331 25.732 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 14 17 28.347 59.804 71.496 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 2 0.685 0.685 37.537 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.046 0.046 25.179 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: 15966.2256
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 697 698 127.59 107.00 20.59 5.92 107.00 20.59 5.92
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -64.14 -73.00 16.19 1.23 -63.80 165.45 24.34
1 2Q 2Q N CA 9 10 154.25 140.70 -40.30
2 3811 2Q 3K C N 16 18 -65.50 -70.20 13.52 0.87 -62.90 168.54 21.75
2 3K 3K N CA 18 19 127.72 140.40 -40.80
3 3812 3K 4L C N 25 27 -131.04 -108.50 27.61 1.22 -63.50 -176.75 29.63
3 4L 4L N CA 27 28 148.45 132.50 -41.20
4 3815 6I 7F C N 49 51 -143.34 -124.20 25.75 0.68 -63.20 174.64 29.38
4 7F 7F N CA 51 52 160.54 143.30 -44.30
5 3816 7F 8A C N 60 62 -62.87 -68.20 10.76 0.70 -62.50 176.85 28.96
5 8A 8A N CA 62 63 135.96 145.30 -40.90
6 3817 8A 9L C N 65 67 -92.59 -108.50 16.15 0.74 -63.50 173.40 22.57
6 9L 9L N CA 67 68 129.74 132.50 -41.20
7 3820 11V 12L C N 87 89 177.98 -108.50 76.09 3.43 -63.50 -155.47 35.60
7 12L 12L N CA 89 90 152.11 132.50 -41.20
8 3824 15G 16S C N 112 114 -65.72 -72.40 23.58 1.18 -64.10 164.79 11.84
8 16S 16S N CA 114 115 129.78 152.40 -35.00
9 3844 35F 36E C N 274 276 53.27 54.60 7.72 0.70 -63.60 138.91 23.90
9 36E 36E N CA 276 277 34.79 42.40 -40.30
10 3860 51S 52S C N 411 413 65.22 56.90 12.36 0.69 -64.10 143.53 19.09
10 52S 52S N CA 413 414 27.26 36.40 -35.00
11 3896 87K 88D C N 695 697 -143.03 -63.30 82.17 13.77 -63.30 82.17 13.77
11 88D 88D N CA 697 698 -59.87 -40.00 -40.00
12 3920 111I 112Y C N 872 874 -45.27 -98.40 55.47 2.81 -63.50 156.94 25.84
12 112Y 112Y N CA 874 875 112.47 128.40 -43.40
13 3934 125N 126H C N 1010 1012 -122.19 -63.20 75.97 8.92 -63.20 75.97 8.92
13 126H 126H N CA 1012 1013 5.56 -42.30 -42.30
14 3935 126H 127C C N 1020 1022 -121.30 -63.00 58.70 9.40 -63.00 58.70 9.40
14 127C 127C N CA 1022 1023 -34.21 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 16 62 87 115 119 130 169 186 190
<< end of ENERGY.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 198139
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11941.0049
<< end of ENERGY.
DOPE score : -11941.004883
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.142881
Native energy (pair) : -13.086745
Native energy (surface) : 2.228922
Native energy (combined) : 0.038085
Z score (pair) : -3.794193
Z score (surface) : -2.540723
Z score (combined) : -3.934947
GA341 score : 0.887918
>> 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): 2444
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 : 997.5089
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 28.772 1.000
2 Bond angle potential : 1504 1 8 2.197 2.197 146.43 1.000
3 Stereochemical cosine torsion poten: 713 0 29 47.687 47.687 253.84 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.335 1.335 17.372 1.000
5 Soft-sphere overlap restraints : 2444 1 2 0.008 0.008 18.506 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 4 0.291 0.291 98.499 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.320 0.320 126.46 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 4.472 4.472 32.069 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 85.277 85.277 37.432 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 64.727 64.727 31.579 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 63.339 63.339 21.395 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 93.893 93.893 15.453 1.000
18 Disulfide distance restraints : 3 0 0 0.030 0.030 0.46020 1.000
19 Disulfide angle restraints : 6 0 0 2.957 2.957 1.1581 1.000
20 Disulfide dihedral angle restraints: 3 0 0 25.927 25.927 2.0250 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 0.415 0.415 42.325 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 15 27.451 57.638 65.711 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.666 0.666 35.131 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.044 0.044 22.890 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: 15596.3828
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 697 698 127.65 107.00 20.65 5.94 107.00 20.65 5.94
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -78.30 -73.00 6.27 0.38 -63.80 176.25 26.68
1 2Q 2Q N CA 9 10 144.04 140.70 -40.30
2 3811 2Q 3K C N 16 18 -64.85 -70.20 7.96 0.67 -62.90 172.92 22.56
2 3K 3K N CA 18 19 146.29 140.40 -40.80
3 3812 3K 4L C N 25 27 -86.13 -70.70 21.05 2.10 -63.50 170.00 22.41
3 4L 4L N CA 27 28 127.28 141.60 -41.20
4 3815 6I 7F C N 49 51 -117.32 -124.20 11.09 0.32 -63.20 -173.09 22.64
4 7F 7F N CA 51 52 134.60 143.30 -44.30
5 3816 7F 8A C N 60 62 -66.62 -68.20 1.75 0.12 -62.50 174.60 28.82
5 8A 8A N CA 62 63 144.55 145.30 -40.90
6 3817 8A 9L C N 65 67 -77.99 -70.70 13.29 0.82 -63.50 166.71 24.00
6 9L 9L N CA 67 68 152.71 141.60 -41.20
7 3821 12L 13C C N 95 97 -64.46 -63.00 1.51 0.23 -117.90 -173.98 7.99
7 13C 13C N CA 97 98 -40.72 -41.10 141.10
8 3823 14V 15G C N 108 110 94.97 78.70 37.21 0.55 82.20 152.46 8.04
8 15G 15G N CA 110 111 160.43 -166.10 8.50
9 3824 15G 16S C N 112 114 -107.91 -136.60 33.30 1.02 -64.10 174.87 10.88
9 16S 16S N CA 114 115 134.29 151.20 -35.00
10 3844 35F 36E C N 274 276 57.72 54.60 9.50 0.52 -63.60 141.96 24.43
10 36E 36E N CA 276 277 33.42 42.40 -40.30
11 3859 50E 51S C N 405 407 -131.71 -64.10 75.96 7.83 -64.10 75.96 7.83
11 51S 51S N CA 407 408 -0.37 -35.00 -35.00
12 3860 51S 52S C N 411 413 61.31 56.90 6.46 0.37 -64.10 142.03 18.81
12 52S 52S N CA 413 414 31.67 36.40 -35.00
13 3896 87K 88D C N 695 697 -142.10 -63.30 84.39 14.34 -63.30 84.39 14.34
13 88D 88D N CA 697 698 -70.20 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -41.13 -98.40 63.44 3.85 -63.50 146.23 24.35
14 112Y 112Y N CA 874 875 101.11 128.40 -43.40
15 3934 125N 126H C N 1010 1012 -121.59 -63.20 73.85 8.77 -63.20 73.85 8.77
15 126H 126H N CA 1012 1013 2.92 -42.30 -42.30
16 3935 126H 127C C N 1020 1022 -121.82 -63.00 58.89 9.66 -63.00 58.89 9.66
16 127C 127C N CA 1022 1023 -38.10 -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 1 7 16 57 92 110 108 129 185 196 176
<< 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: -90.1074
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 193985
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11715.8184
<< end of ENERGY.
DOPE score : -11715.818359
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.163823
Native energy (pair) : -2.471409
Native energy (surface) : 0.956297
Native energy (combined) : 0.151168
Z score (pair) : -3.341868
Z score (surface) : -2.925178
Z score (combined) : -3.929518
GA341 score : 0.895815
>> 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): 2328
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 : 1057.1034
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 30.071 1.000
2 Bond angle potential : 1504 1 11 2.265 2.265 156.36 1.000
3 Stereochemical cosine torsion poten: 713 0 35 48.713 48.713 263.33 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.289 1.289 16.803 1.000
5 Soft-sphere overlap restraints : 2328 1 2 0.008 0.008 18.656 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 1 0.305 0.305 98.254 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.352 0.352 138.30 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 2 4.335 4.335 30.142 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 77.509 77.509 40.209 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 1 84.111 84.111 40.658 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 73.454 73.454 21.742 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 105.387 105.387 14.500 1.000
18 Disulfide distance restraints : 3 0 0 0.029 0.029 0.43348 1.000
19 Disulfide angle restraints : 6 0 0 4.309 4.309 2.4600 1.000
20 Disulfide dihedral angle restraints: 3 0 0 12.741 12.741 0.54439 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 0.407 0.407 41.205 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 18 17 25.178 58.655 75.050 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.737 0.737 45.450 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.044 0.044 22.934 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: 16032.9658
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 697 698 128.62 107.00 21.62 6.22 107.00 21.62 6.22
-------------------------------------------------------------------------------------------------
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 -72.59 -73.00 3.07 0.21 -63.80 176.18 26.37
1 2Q 2Q N CA 9 10 143.74 140.70 -40.30
2 3811 2Q 3K C N 16 18 -97.99 -118.00 50.18 2.09 -62.90 138.41 16.40
2 3K 3K N CA 18 19 93.08 139.10 -40.80
3 3812 3K 4L C N 25 27 -141.88 -108.50 36.54 1.93 -63.50 177.11 21.71
3 4L 4L N CA 27 28 117.62 132.50 -41.20
4 3815 6I 7F C N 49 51 -128.10 -124.20 10.32 0.56 -63.20 -170.48 22.48
4 7F 7F N CA 51 52 133.75 143.30 -44.30
5 3816 7F 8A C N 60 62 -80.40 -68.20 14.53 0.96 -62.50 166.88 28.26
5 8A 8A N CA 62 63 153.18 145.30 -40.90
6 3817 8A 9L C N 65 67 -73.79 -70.70 13.86 1.17 -63.50 169.60 22.98
6 9L 9L N CA 67 68 128.09 141.60 -41.20
7 3820 11V 12L C N 87 89 -62.52 -70.70 28.11 1.85 -63.50 155.91 21.70
7 12L 12L N CA 89 90 114.71 141.60 -41.20
8 3823 14V 15G C N 108 110 -85.90 -80.20 6.33 0.47 82.20 -125.97 7.45
8 15G 15G N CA 110 111 171.33 174.10 8.50
9 3824 15G 16S C N 112 114 -68.37 -72.40 17.73 0.91 -64.10 170.19 12.08
9 16S 16S N CA 114 115 135.13 152.40 -35.00
10 3844 35F 36E C N 274 276 59.63 54.60 13.99 0.74 -63.60 141.55 24.35
10 36E 36E N CA 276 277 29.35 42.40 -40.30
11 3859 50E 51S C N 405 407 -141.02 -64.10 88.79 8.85 -64.10 88.79 8.85
11 51S 51S N CA 407 408 9.35 -35.00 -35.00
12 3860 51S 52S C N 411 413 58.50 56.90 2.75 0.13 -64.10 140.77 18.58
12 52S 52S N CA 413 414 34.17 36.40 -35.00
13 3896 87K 88D C N 695 697 -147.21 -63.30 86.10 14.39 -63.30 86.10 14.39
13 88D 88D N CA 697 698 -59.30 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -41.56 -98.40 62.94 3.82 -63.50 146.43 24.36
14 112Y 112Y N CA 874 875 101.38 128.40 -43.40
15 3923 114R 115H C N 904 906 -90.02 -125.60 53.09 1.33 -63.20 144.21 16.52
15 115H 115H N CA 906 907 99.39 138.80 -42.30
16 3924 115H 116R C N 914 916 -56.40 -63.00 70.57 9.11 -125.20 128.09 7.10
16 116R 116R N CA 916 917 -111.35 -41.10 140.60
17 3934 125N 126H C N 1010 1012 -118.70 -63.20 70.81 8.36 -63.20 70.81 8.36
17 126H 126H N CA 1012 1013 1.67 -42.30 -42.30
18 3935 126H 127C C N 1020 1022 -125.19 -63.00 64.77 9.67 -63.00 64.77 9.67
18 127C 127C N CA 1022 1023 -22.99 -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 1 5 11 65 82 94 110 132 170 171 180
<< 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.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 197754
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11733.7490
<< end of ENERGY.
DOPE score : -11733.749023
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.256744
Native energy (pair) : -17.040306
Native energy (surface) : 1.192380
Native energy (combined) : -0.419560
Z score (pair) : -3.798421
Z score (surface) : -2.892603
Z score (combined) : -4.196624
GA341 score : 0.968132
>> 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): 2419
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 : 1016.0260
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 1 0.009 0.009 26.882 1.000
2 Bond angle potential : 1504 1 11 2.240 2.240 153.41 1.000
3 Stereochemical cosine torsion poten: 713 0 27 46.825 46.825 246.21 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.307 1.307 17.511 1.000
5 Soft-sphere overlap restraints : 2419 1 2 0.008 0.008 18.333 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 3 0.295 0.295 102.76 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.346 0.346 145.75 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 4.694 4.694 35.332 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 76.056 76.056 37.791 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 2 73.292 73.292 42.073 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 73.796 73.796 20.118 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 89.084 89.084 14.700 1.000
18 Disulfide distance restraints : 3 0 0 0.028 0.028 0.39581 1.000
19 Disulfide angle restraints : 6 0 0 2.834 2.834 1.0640 1.000
20 Disulfide dihedral angle restraints: 3 0 0 32.101 32.101 2.6917 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 0.373 0.373 30.262 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 17 25.740 59.899 70.206 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.575 0.575 26.146 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.046 0.046 24.380 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: 15636.1982
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 697 698 127.37 107.00 20.37 5.86 107.00 20.37 5.86
-------------------------------------------------------------------------------------------------
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 -73.13 -73.00 8.83 0.58 -63.80 172.43 24.87
1 2Q 2Q N CA 9 10 131.88 140.70 -40.30
2 3811 2Q 3K C N 16 18 -94.81 -118.00 29.97 1.48 -62.90 164.23 23.19
2 3K 3K N CA 18 19 158.10 139.10 -40.80
3 3812 3K 4L C N 25 27 -101.78 -108.50 6.73 0.32 -63.50 178.22 22.85
3 4L 4L N CA 27 28 132.86 132.50 -41.20
4 3815 6I 7F C N 49 51 -142.04 -124.20 18.68 0.57 -63.20 -175.46 30.72
4 7F 7F N CA 51 52 148.85 143.30 -44.30
5 3816 7F 8A C N 60 62 -133.90 -134.00 11.08 0.63 -62.50 176.14 32.69
5 8A 8A N CA 62 63 158.08 147.00 -40.90
6 3817 8A 9L C N 65 67 -75.72 -70.70 46.47 3.72 -63.50 137.15 18.38
6 9L 9L N CA 67 68 95.40 141.60 -41.20
7 3820 11V 12L C N 87 89 -57.45 -70.70 15.35 1.09 -63.50 175.16 24.67
7 12L 12L N CA 89 90 133.85 141.60 -41.20
8 3823 14V 15G C N 108 110 -88.90 -80.20 33.93 0.93 82.20 -124.64 18.14
8 15G 15G N CA 110 111 -153.10 174.10 8.50
9 3824 15G 16S C N 112 114 -62.31 -72.40 42.55 2.18 -64.10 146.08 10.69
9 16S 16S N CA 114 115 111.06 152.40 -35.00
10 3844 35F 36E C N 274 276 51.74 54.60 5.38 0.63 -63.60 139.31 23.96
10 36E 36E N CA 276 277 37.84 42.40 -40.30
11 3860 51S 52S C N 411 413 63.40 56.90 8.58 0.57 -64.10 143.49 19.03
11 52S 52S N CA 413 414 30.80 36.40 -35.00
12 3896 87K 88D C N 695 697 -145.98 -63.30 91.71 15.65 -63.30 91.71 15.65
12 88D 88D N CA 697 698 -79.69 -40.00 -40.00
13 3898 89C 90N C N 709 711 -176.60 -63.20 116.70 18.70 55.90 167.21 10.92
13 90N 90N N CA 711 712 -68.67 -41.10 39.50
14 3920 111I 112Y C N 872 874 -50.38 -98.40 53.30 3.25 -63.50 149.26 24.36
14 112Y 112Y N CA 874 875 105.28 128.40 -43.40
15 3923 114R 115H C N 904 906 -90.89 -125.60 54.03 1.37 -63.20 142.41 16.26
15 115H 115H N CA 906 907 97.39 138.80 -42.30
16 3924 115H 116R C N 914 916 -57.78 -63.00 71.12 9.27 -125.20 126.78 7.02
16 116R 116R N CA 916 917 -112.03 -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 1 13 8 62 78 112 124 127 180 176 187
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 200918
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11783.3291
<< end of ENERGY.
DOPE score : -11783.329102
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.154557
Native energy (pair) : -4.167381
Native energy (surface) : 1.806173
Native energy (combined) : 0.297246
Z score (pair) : -3.379564
Z score (surface) : -2.617596
Z score (combined) : -3.731996
GA341 score : 0.838845
>> 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): 2488
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 : 984.1353
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1119 0 2 0.009 0.009 25.559 1.000
2 Bond angle potential : 1504 1 9 2.178 2.178 144.75 1.000
3 Stereochemical cosine torsion poten: 713 0 26 47.748 47.748 254.81 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.339 1.339 17.874 1.000
5 Soft-sphere overlap restraints : 2488 2 2 0.008 0.008 18.035 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 0.308 0.308 98.276 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.345 0.345 134.68 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: 136 0 2 4.274 4.274 29.292 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 79.627 79.627 35.824 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 78.390 78.390 34.769 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 79.688 79.688 21.536 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 86.388 86.388 12.105 1.000
18 Disulfide distance restraints : 3 0 0 0.026 0.026 0.34371 1.000
19 Disulfide angle restraints : 6 0 0 3.810 3.810 1.9231 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.832 22.832 1.5234 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 0.346 0.346 28.367 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 16 16 27.705 57.711 63.944 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.674 0.674 36.680 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.045 0.045 23.844 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.V99990006
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15352.0312
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 697 698 127.58 107.00 20.58 5.92 107.00 20.58 5.92
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -77.61 -73.00 21.01 1.29 -63.80 159.10 24.13
1 2Q 2Q N CA 9 10 161.20 140.70 -40.30
2 3811 2Q 3K C N 16 18 -63.98 -70.20 6.38 0.50 -62.90 177.41 23.10
2 3K 3K N CA 18 19 141.80 140.40 -40.80
3 3812 3K 4L C N 25 27 -76.26 -70.70 6.06 0.46 -63.50 175.25 25.08
3 4L 4L N CA 27 28 144.01 141.60 -41.20
4 3815 6I 7F C N 49 51 -116.21 -124.20 8.29 0.39 -63.20 178.27 28.28
4 7F 7F N CA 51 52 145.50 143.30 -44.30
5 3816 7F 8A C N 60 62 -103.59 -134.00 36.08 0.87 -62.50 173.41 26.72
5 8A 8A N CA 62 63 127.57 147.00 -40.90
6 3817 8A 9L C N 65 67 -113.76 -108.50 5.61 0.25 -63.50 -177.29 23.02
6 9L 9L N CA 67 68 134.46 132.50 -41.20
7 3821 12L 13C C N 95 97 -59.33 -63.00 6.19 0.66 -117.90 -177.53 7.89
7 13C 13C N CA 97 98 -46.09 -41.10 141.10
8 3823 14V 15G C N 108 110 87.81 78.70 24.29 0.38 82.20 162.97 8.19
8 15G 15G N CA 110 111 171.38 -166.10 8.50
9 3824 15G 16S C N 112 114 -107.10 -136.60 36.27 1.11 -64.10 170.60 10.61
9 16S 16S N CA 114 115 130.09 151.20 -35.00
10 3844 35F 36E C N 274 276 49.68 54.60 5.75 0.75 -63.60 138.52 23.81
10 36E 36E N CA 276 277 39.42 42.40 -40.30
11 3859 50E 51S C N 405 407 -141.37 -64.10 89.94 8.88 -64.10 89.94 8.88
11 51S 51S N CA 407 408 11.02 -35.00 -35.00
12 3860 51S 52S C N 411 413 54.20 56.90 2.71 0.31 -64.10 138.23 18.15
12 52S 52S N CA 413 414 36.51 36.40 -35.00
13 3896 87K 88D C N 695 697 -140.11 -63.30 79.80 13.43 -63.30 79.80 13.43
13 88D 88D N CA 697 698 -61.64 -40.00 -40.00
14 3920 111I 112Y C N 872 874 -45.07 -98.40 59.02 3.58 -63.50 147.66 24.38
14 112Y 112Y N CA 874 875 103.11 128.40 -43.40
15 3934 125N 126H C N 1010 1012 -121.95 -63.20 79.86 9.13 -63.20 79.86 9.13
15 126H 126H N CA 1012 1013 11.78 -42.30 -42.30
16 3935 126H 127C C N 1020 1022 -124.74 -63.00 61.76 10.38 -63.00 61.76 10.38
16 127C 127C N CA 1022 1023 -42.77 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 14 8 54 88 112 127 147 169 196 211
<< 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: -91.5388
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 197899
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11697.8926
<< end of ENERGY.
DOPE score : -11697.892578
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.175230
Native energy (pair) : 2.789933
Native energy (surface) : 2.054288
Native energy (combined) : 0.682808
Z score (pair) : -3.657796
Z score (surface) : -2.662854
Z score (combined) : -3.932639
GA341 score : 0.901239
>> 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): 2404
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 : 1074.1337
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 31.491 1.000
2 Bond angle potential : 1504 1 10 2.361 2.361 169.11 1.000
3 Stereochemical cosine torsion poten: 713 0 31 47.756 47.756 255.21 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.447 1.447 20.664 1.000
5 Soft-sphere overlap restraints : 2404 2 2 0.008 0.008 18.175 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 0.298 0.298 96.645 1.000
10 Distance restraints 2 (N-O) : 2371 0 10 0.350 0.350 154.55 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 4.687 4.687 35.239 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 1 74.866 74.866 35.380 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 75.559 75.559 37.833 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 81.331 81.331 24.331 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 72.410 72.410 11.829 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.28460 1.000
19 Disulfide angle restraints : 6 0 1 5.610 5.610 4.1693 1.000
20 Disulfide dihedral angle restraints: 3 0 0 23.669 23.669 1.7403 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 1316 0 0 0.315 0.315 22.727 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 16 27.244 61.220 92.463 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.706 0.706 41.559 1.000
27 Distance restraints 5 (X-Y) : 1389 0 0 0.041 0.041 20.735 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.V99990007
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15661.7686
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 697 698 129.96 107.00 22.96 6.60 107.00 22.96 6.60
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3810 1M 2Q C N 7 9 -78.26 -73.00 16.00 0.95 -63.80 164.52 24.96
1 2Q 2Q N CA 9 10 155.82 140.70 -40.30
2 3811 2Q 3K C N 16 18 -70.68 -70.20 15.07 1.08 -62.90 163.92 21.72
2 3K 3K N CA 18 19 155.46 140.40 -40.80
3 3812 3K 4L C N 25 27 -72.67 -70.70 27.64 2.17 -63.50 155.50 21.08
3 4L 4L N CA 27 28 114.03 141.60 -41.20
4 3815 6I 7F C N 49 51 -144.24 -124.20 21.59 0.62 -63.20 -176.72 30.67
4 7F 7F N CA 51 52 151.31 143.30 -44.30
5 3816 7F 8A C N 60 62 -117.44 -134.00 16.58 0.52 -62.50 -178.56 32.66
5 8A 8A N CA 62 63 146.17 147.00 -40.90
6 3817 8A 9L C N 65 67 -67.15 -70.70 3.86 0.29 -63.50 178.76 25.03
6 9L 9L N CA 67 68 140.08 141.60 -41.20
7 3820 11V 12L C N 87 89 -70.47 -70.70 11.63 0.87 -63.50 171.31 23.40
7 12L 12L N CA 89 90 129.97 141.60 -41.20
8 3823 14V 15G C N 108 110 -129.33 -167.20 38.10 0.83 82.20 -134.09 17.07
8 15G 15G N CA 110 111 178.77 174.60 8.50
9 3824 15G 16S C N 112 114 -63.44 -72.40 28.94 1.42 -64.10 159.89 11.62
9 16S 16S N CA 114 115 124.89 152.40 -35.00
10 3844 35F 36E C N 274 276 50.46 54.60 4.79 0.63 -63.60 139.48 23.98
10 36E 36E N CA 276 277 39.98 42.40 -40.30
11 3859 50E 51S C N 405 407 -140.25 -64.10 85.68 8.82 -64.10 85.68 8.82
11 51S 51S N CA 407 408 4.28 -35.00 -35.00
12 3860 51S 52S C N 411 413 61.26 56.90 6.28 0.37 -64.10 142.09 18.81
12 52S 52S N CA 413 414 31.89 36.40 -35.00
13 3896 87K 88D C N 695 697 -143.61 -63.30 81.62 13.53 -63.30 81.62 13.53
13 88D 88D N CA 697 698 -54.51 -40.00 -40.00
14 3919 110K 111I C N 864 866 -55.34 -63.40 40.19 6.88 -63.40 40.19 6.88
14 111I 111I N CA 866 867 -4.23 -43.60 -43.60
15 3935 126H 127C C N 1020 1022 -125.36 -63.00 69.86 9.48 -63.00 69.86 9.48
15 127C 127C N CA 1022 1023 -9.59 -41.10 -41.10
16 3936 127C 128Q C N 1026 1028 -60.99 -63.80 15.11 2.08 -121.10 175.76 9.08
16 128Q 128Q N CA 1028 1029 -55.14 -40.30 139.70
17 3937 128Q 129G C N 1035 1037 -73.24 -62.40 13.40 1.97 82.20 160.97 12.03
17 129G 129G N CA 1037 1038 -33.33 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 11 14 58 75 125 122 132 168 178 183
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 196361
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11701.3447
<< end of ENERGY.
DOPE score : -11701.344727
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.204690
Native energy (pair) : -0.919580
Native energy (surface) : 0.261251
Native energy (combined) : 0.036406
Z score (pair) : -3.452739
Z score (surface) : -3.261474
Z score (combined) : -4.136772
GA341 score : 0.949526
>> 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): 2470
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 : 1094.0746
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1119 0 2 0.009 0.009 25.868 1.000
2 Bond angle potential : 1504 1 10 2.293 2.293 159.60 1.000
3 Stereochemical cosine torsion poten: 713 0 30 48.232 48.232 256.90 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.304 1.304 17.286 1.000
5 Soft-sphere overlap restraints : 2470 1 2 0.008 0.008 18.834 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 5 0.292 0.292 96.927 1.000
10 Distance restraints 2 (N-O) : 2371 0 9 0.334 0.334 147.20 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.807 4.807 37.054 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 4 83.945 83.945 47.117 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 74.187 74.187 36.866 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 76.831 76.831 24.878 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 70.049 70.049 12.161 1.000
18 Disulfide distance restraints : 3 0 0 0.023 0.023 0.28161 1.000
19 Disulfide angle restraints : 6 0 0 2.490 2.490 0.82112 1.000
20 Disulfide dihedral angle restraints: 3 0 0 21.233 21.233 1.3019 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 0.377 0.377 30.549 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 18 19 28.866 66.297 116.72 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.669 0.669 36.048 1.000
27 Distance restraints 5 (X-Y) : 1389 0 3 0.049 0.049 27.657 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.V99990008
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 16221.8418
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 697 698 128.94 107.00 21.94 6.31 107.00 21.94 6.31
-------------------------------------------------------------------------------------------------
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 -67.65 -73.00 11.55 0.86 -63.80 168.80 25.02
1 2Q 2Q N CA 9 10 150.94 140.70 -40.30
2 3811 2Q 3K C N 16 18 -66.05 -70.20 8.23 0.68 -62.90 171.72 22.47
2 3K 3K N CA 18 19 147.51 140.40 -40.80
3 3812 3K 4L C N 25 27 -68.84 -70.70 1.86 0.16 -63.50 177.39 24.94
3 4L 4L N CA 27 28 141.48 141.60 -41.20
4 3815 6I 7F C N 49 51 -73.14 -71.40 44.91 3.67 -63.20 140.48 18.84
4 7F 7F N CA 51 52 95.82 140.70 -44.30
5 3816 7F 8A C N 60 62 -164.01 -134.00 31.23 0.76 -62.50 -167.57 36.93
5 8A 8A N CA 62 63 155.63 147.00 -40.90
6 3817 8A 9L C N 65 67 -75.40 -70.70 5.64 0.39 -63.50 174.50 24.93
6 9L 9L N CA 67 68 144.71 141.60 -41.20
7 3818 9L 10V C N 73 75 -60.68 -62.40 2.25 0.38 -125.40 -172.72 10.51
7 10V 10V N CA 75 76 -40.96 -42.40 143.30
8 3820 11V 12L C N 87 89 -57.51 -70.70 16.37 1.65 -63.50 167.61 22.94
8 12L 12L N CA 89 90 151.30 141.60 -41.20
9 3821 12L 13C C N 95 97 -58.08 -63.00 7.99 0.86 -117.90 -178.37 7.87
9 13C 13C N CA 97 98 -47.40 -41.10 141.10
10 3823 14V 15G C N 108 110 -92.54 -80.20 32.53 0.78 82.20 -120.14 18.49
10 15G 15G N CA 110 111 -155.80 174.10 8.50
11 3824 15G 16S C N 112 114 -62.19 -72.40 39.99 2.02 -64.10 148.75 10.89
11 16S 16S N CA 114 115 113.74 152.40 -35.00
12 3844 35F 36E C N 274 276 51.13 54.60 5.12 0.64 -63.60 139.26 23.95
12 36E 36E N CA 276 277 38.63 42.40 -40.30
13 3859 50E 51S C N 405 407 -140.14 -64.10 88.14 8.74 -64.10 88.14 8.74
13 51S 51S N CA 407 408 9.57 -35.00 -35.00
14 3860 51S 52S C N 411 413 54.17 56.90 3.42 0.24 -64.10 139.23 18.25
14 52S 52S N CA 413 414 38.46 36.40 -35.00
15 3889 80S 81K C N 651 653 -75.49 -62.90 87.82 12.13 -62.90 87.82 12.13
15 81K 81K N CA 653 654 -127.71 -40.80 -40.80
16 3890 81K 82G C N 660 662 -103.16 -62.40 40.84 7.40 82.20 -177.69 9.95
16 82G 82G N CA 662 663 -43.81 -41.20 8.50
17 3896 87K 88D C N 695 697 172.04 -96.50 94.65 3.85 -63.30 179.99 20.17
17 88D 88D N CA 697 698 89.83 114.20 -40.00
18 3920 111I 112Y C N 872 874 -43.12 -98.40 61.38 3.75 -63.50 146.54 24.30
18 112Y 112Y N CA 874 875 101.72 128.40 -43.40
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 16 68 79 117 117 150 183 181 183
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 192650
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11540.6807
<< end of ENERGY.
DOPE score : -11540.680664
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.131893
Native energy (pair) : -24.513647
Native energy (surface) : 0.964894
Native energy (combined) : -0.814576
Z score (pair) : -4.277843
Z score (surface) : -2.888013
Z score (combined) : -4.489233
GA341 score : 0.976045
>> 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): 2391
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 : 1027.4846
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1119 0 2 0.009 0.009 27.928 1.000
2 Bond angle potential : 1504 1 12 2.258 2.258 153.87 1.000
3 Stereochemical cosine torsion poten: 713 0 29 48.825 48.825 265.04 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.313 1.313 17.089 1.000
5 Soft-sphere overlap restraints : 2391 1 2 0.008 0.008 18.032 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 5 0.290 0.290 95.115 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.332 0.332 134.35 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 4.336 4.336 30.158 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 2 79.530 79.530 40.777 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 80.044 80.044 31.051 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 85.012 85.012 24.069 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 85.930 85.930 14.041 1.000
18 Disulfide distance restraints : 3 0 0 0.031 0.031 0.49223 1.000
19 Disulfide angle restraints : 6 0 0 2.745 2.745 0.99791 1.000
20 Disulfide dihedral angle restraints: 3 0 0 22.756 22.756 1.6179 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 0.375 0.375 32.189 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 14 29.350 57.421 94.473 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.539 0.539 23.805 1.000
27 Distance restraints 5 (X-Y) : 1389 0 0 0.043 0.043 22.394 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.V99990009
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15957.3936
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 697 698 127.97 107.00 20.97 6.03 107.00 20.97 6.03
-------------------------------------------------------------------------------------------------
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 -83.56 -73.00 22.32 1.29 -63.80 160.55 24.66
1 2Q 2Q N CA 9 10 160.37 140.70 -40.30
2 3811 2Q 3K C N 16 18 -65.77 -70.20 10.37 0.84 -62.90 169.45 22.16
2 3K 3K N CA 18 19 149.77 140.40 -40.80
3 3812 3K 4L C N 25 27 -61.63 -70.70 19.15 1.19 -63.50 165.95 23.15
3 4L 4L N CA 27 28 124.74 141.60 -41.20
4 3815 6I 7F C N 49 51 -125.43 -124.20 6.74 0.34 -63.20 -170.47 30.44
4 7F 7F N CA 51 52 136.68 143.30 -44.30
5 3816 7F 8A C N 60 62 -126.17 -134.00 9.36 0.23 -62.50 -171.67 34.27
5 8A 8A N CA 62 63 141.86 147.00 -40.90
6 3817 8A 9L C N 65 67 -96.27 -108.50 32.64 1.61 -63.50 147.14 18.82
6 9L 9L N CA 67 68 102.24 132.50 -41.20
7 3820 11V 12L C N 87 89 -109.78 -108.50 4.43 0.25 -63.50 175.66 22.20
7 12L 12L N CA 89 90 128.26 132.50 -41.20
8 3823 14V 15G C N 108 110 97.07 78.70 53.49 0.86 82.20 135.97 7.34
8 15G 15G N CA 110 111 143.66 -166.10 8.50
9 3824 15G 16S C N 112 114 -139.30 -136.60 4.29 0.15 -64.10 -173.68 18.86
9 16S 16S N CA 114 115 154.53 151.20 -35.00
10 3844 35F 36E C N 274 276 53.89 54.60 5.50 0.48 -63.60 140.61 24.19
10 36E 36E N CA 276 277 36.94 42.40 -40.30
11 3859 50E 51S C N 405 407 -142.63 -64.10 91.92 9.01 -64.10 91.92 9.01
11 51S 51S N CA 407 408 12.78 -35.00 -35.00
12 3860 51S 52S C N 411 413 54.48 56.90 2.44 0.30 -64.10 138.26 18.17
12 52S 52S N CA 413 414 36.09 36.40 -35.00
13 3896 87K 88D C N 695 697 -135.92 -63.30 78.34 13.33 -63.30 78.34 13.33
13 88D 88D N CA 697 698 -69.38 -40.00 -40.00
14 3922 113K 114R C N 893 895 -62.29 -125.20 81.04 2.40 -63.00 130.61 17.69
14 114R 114R N CA 895 896 89.51 140.60 -41.10
15 3923 114R 115H C N 904 906 -176.65 -63.20 113.59 17.74 -63.20 113.59 17.74
15 115H 115H N CA 906 907 -36.74 -42.30 -42.30
16 3935 126H 127C C N 1020 1022 -125.27 -63.00 72.74 9.46 -63.00 72.74 9.46
16 127C 127C N CA 1022 1023 -3.51 -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 1 10 9 71 80 111 116 142 164 161 172
<< end of ENERGY.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: CYS:OXT CYS
>> 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): 198721
Dynamic pairs routine : 1, NATM x NATM double loop
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 : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -11385.1406
<< end of ENERGY.
DOPE score : -11385.140625
>> Model assessment by GA341 potential
Surface library : /usr/lib/modeller10.1/modlib/surf5.de
Pair library : /usr/lib/modeller10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 39.394001
Sequence length : 137
Compactness : 0.147683
Native energy (pair) : -16.243655
Native energy (surface) : 0.668470
Native energy (combined) : -0.498353
Z score (pair) : -3.419707
Z score (surface) : -2.953487
Z score (combined) : -3.992740
GA341 score : 0.903621
>> 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): 2561
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 : 1102.3550
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 1119 0 2 0.009 0.009 27.782 1.000
2 Bond angle potential : 1504 1 12 2.323 2.323 162.40 1.000
3 Stereochemical cosine torsion poten: 713 0 27 47.993 47.993 257.76 1.000
4 Stereochemical improper torsion pot: 461 0 0 1.379 1.379 18.934 1.000
5 Soft-sphere overlap restraints : 2561 1 2 0.008 0.008 18.678 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2215 0 5 0.293 0.293 97.597 1.000
10 Distance restraints 2 (N-O) : 2371 0 9 0.340 0.340 148.35 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 4.570 4.570 33.501 1.000
14 Sidechain Chi_1 dihedral restraints: 121 0 3 76.433 76.433 42.215 1.000
15 Sidechain Chi_2 dihedral restraints: 87 0 0 74.122 74.122 37.411 1.000
16 Sidechain Chi_3 dihedral restraints: 35 0 0 78.684 78.684 22.377 1.000
17 Sidechain Chi_4 dihedral restraints: 22 0 0 82.979 82.979 16.948 1.000
18 Disulfide distance restraints : 3 0 0 0.027 0.027 0.37132 1.000
19 Disulfide angle restraints : 6 0 0 2.712 2.712 0.97426 1.000
20 Disulfide dihedral angle restraints: 3 0 0 35.933 35.933 2.9700 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 0.380 0.380 33.139 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 28.909 60.951 129.53 1.000
26 Distance restraints 4 (SDCH-SDCH) : 498 0 0 0.576 0.576 26.917 1.000
27 Distance restraints 5 (X-Y) : 1389 0 2 0.045 0.045 24.496 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: sequence.V99990010
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 15641.1689
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 697 698 128.45 107.00 21.45 6.17 107.00 21.45 6.17
-------------------------------------------------------------------------------------------------
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 -77.40 -73.00 19.93 1.22 -63.80 160.14 24.27
1 2Q 2Q N CA 9 10 160.14 140.70 -40.30
2 3811 2Q 3K C N 16 18 -67.13 -70.20 5.60 0.46 -62.90 174.17 22.85
2 3K 3K N CA 18 19 145.08 140.40 -40.80
3 3812 3K 4L C N 25 27 -72.65 -70.70 4.70 0.30 -63.50 173.17 24.58
3 4L 4L N CA 27 28 145.87 141.60 -41.20
4 3815 6I 7F C N 49 51 -147.02 -124.20 28.80 0.75 -63.20 176.06 29.78
4 7F 7F N CA 51 52 160.87 143.30 -44.30
5 3816 7F 8A C N 60 62 -105.06 -134.00 33.55 0.78 -62.50 176.14 27.11
5 8A 8A N CA 62 63 130.02 147.00 -40.90
6 3817 8A 9L C N 65 67 -69.07 -70.70 6.81 0.46 -63.50 176.27 24.16
6 9L 9L N CA 67 68 134.98 141.60 -41.20
7 3820 11V 12L C N 87 89 -95.40 -63.50 70.00 8.58 -63.50 70.00 8.58
7 12L 12L N CA 89 90 21.11 -41.20 -41.20
8 3821 12L 13C C N 95 97 -66.30 -63.00 3.87 0.69 -117.90 -176.81 7.86
8 13C 13C N CA 97 98 -43.12 -41.10 141.10
9 3823 14V 15G C N 108 110 -143.27 -167.20 23.94 0.48 82.20 -145.59 16.04
9 15G 15G N CA 110 111 175.46 174.60 8.50
10 3824 15G 16S C N 112 114 -95.13 -72.40 35.18 2.76 -64.10 163.52 10.41
10 16S 16S N CA 114 115 125.55 152.40 -35.00
11 3844 35F 36E C N 274 276 51.69 54.60 5.80 0.67 -63.60 139.02 23.91
11 36E 36E N CA 276 277 37.39 42.40 -40.30
12 3859 50E 51S C N 405 407 -138.78 -64.10 86.85 8.58 -64.10 86.85 8.58
12 51S 51S N CA 407 408 9.34 -35.00 -35.00
13 3860 51S 52S C N 411 413 59.18 56.90 3.72 0.19 -64.10 141.02 18.63
13 52S 52S N CA 413 414 33.46 36.40 -35.00
14 3889 80S 81K C N 651 653 -75.77 -62.90 89.36 12.35 -62.90 89.36 12.35
14 81K 81K N CA 653 654 -129.23 -40.80 -40.80
15 3890 81K 82G C N 660 662 -102.13 -62.40 40.20 7.40 82.20 -175.68 9.91
15 82G 82G N CA 662 663 -47.33 -41.20 8.50
16 3896 87K 88D C N 695 697 -137.73 -63.30 79.60 13.52 -63.30 79.60 13.52
16 88D 88D N CA 697 698 -68.20 -40.00 -40.00
17 3920 111I 112Y C N 872 874 -33.44 -98.40 69.54 3.85 -63.50 150.01 25.35
17 112Y 112Y N CA 874 875 103.57 128.40 -43.40
18 3934 125N 126H C N 1010 1012 -116.95 -63.20 68.61 8.10 -63.20 68.61 8.10
18 126H 126H N CA 1012 1013 0.35 -42.30 -42.30
19 3935 126H 127C C N 1020 1022 -118.96 -63.00 56.13 9.12 -63.00 56.13 9.12
19 127C 127C N CA 1022 1023 -36.63 -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 1 6 16 57 92 139 135 135 168 185 207
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf DOPE score GA341 score
----------------------------------------------------------------------
sequence.B99990001.pdb 1157.54688 -11354.38281 0.96782
sequence.B99990002.pdb 1024.42957 -11830.95996 0.87179
sequence.B99990003.pdb 997.50891 -11941.00488 0.88792
sequence.B99990004.pdb 1057.10339 -11715.81836 0.89582
sequence.B99990005.pdb 1016.02600 -11733.74902 0.96813
sequence.B99990006.pdb 984.13531 -11783.32910 0.83884
sequence.B99990007.pdb 1074.13367 -11697.89258 0.90124
sequence.B99990008.pdb 1094.07458 -11701.34473 0.94953
sequence.B99990009.pdb 1027.48462 -11540.68066 0.97605
sequence.B99990010.pdb 1102.35498 -11385.14062 0.90362
GA341 score - один из скоров, позволяющих оценить качество модели. В отличие от других скоров его значения абсолютны, поэтому значения можно теоретически сравнивать при моделировании разных белков. Значения ранжируются от 0 до 1, чем ближе к 1, тем лучше.
Судя по значениям GA341 score, которые близки к 1, все полученные модели качеством не хуже среднего.
In [18]:
from IPython.display import display, Image
Для визуализации используем Pymol.
In [24]:
def show_model(pdb_1, pdb_2):
command = f"load {pdb_1}, model_1; load {pdb_2}, model_2; " \
f"util.cbag model_1; util.cbac model_2; " \
f"align model_1, model_2; " \
f"as cartoon; as sticks, hetatm; " \
f"as cartoon; as sticks, hetatm; orient; " \
f"set ray_trace_mode, 1; set antialias, 2; bg_color black" \
f"png tmp.png"
! pymol -Qcd "$command"
display(Image('tmp.png'))
In [25]:
show_model('sequence.B99990001.pdb', 'template.pdb')
<string>:1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
Зелёным показан смоделированный белок, а бирюзовым белок, на основе которого производилось моделирование. Полученная модель содержит довольно большую вставку в выравнивании и этот участок остался без какой-либо укладки, при этом остальная часть неплохо накладывается на белок-заготовку.