Гомологичное моделирование комплекса белка с лигандом
В данном занятии мы будем моделировать структуру лизоцима из одного из предложенных нами геномов на основании известной структуры.
In [1]:
import sys
sys.path.append('/usr/lib/modeller9v7/modlib/')
sys.path.append('/usr/lib/modeller9v7/lib/x86_64-intel8/python2.5/')
import modeller
import _modeller
import modeller.automodel
import nglview
import ipywidgets
In [2]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo.fbb.msu.ru 3.8-2-amd64 x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/05/05 14:02:19
In [3]:
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2017-05-05 14:02:21-- http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org... 132.249.231.77
Connecting to www.pdb.org|132.249.231.77|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2017-05-05 14:02:22-- http://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org... 132.249.231.10
Connecting to www.rcsb.org|132.249.231.10|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://files.rcsb.org/view/1lmp.pdb [following]
--2017-05-05 14:02:22-- http://files.rcsb.org/view/1lmp.pdb
Resolving files.rcsb.org... 132.249.213.140
Connecting to files.rcsb.org|132.249.213.140|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: `1lmp.pdb.4'
[ <=> ] 131,301 130K/s in 1.0s
2017-05-05 14:02:24 (130 KB/s) - `1lmp.pdb.4' saved [131301]
In [4]:
! wget http://www.uniprot.org/uniprot/P62693.fasta
--2017-05-05 14:02:24-- http://www.uniprot.org/uniprot/P62693.fasta Resolving www.uniprot.org... 193.62.193.81, 128.175.240.211 Connecting to www.uniprot.org|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 305 [text/plain] Saving to: `P62693.fasta.4' 100%[======================================>] 305 --.-K/s in 0s 2017-05-05 14:02:24 (28.9 MB/s) - `P62693.fasta.4' saved [305/305]
In [5]:
alignm=modeller.alignment(env)
In [6]:
alignm.append(file='P62693.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
read_pd_459W> Residue type NAG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NDG not recognized. 'automodel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
In [7]:
alignm.append_sequence("".join(x.code for x in alignm[0].residues) + "...")
In [8]:
alignm.salign()
alignm[2].code = "red"
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [9]:
!cat all_in_one.ali
>P1;sp|P62693|LYS_BPPHV sequence:: : : : :::-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASG-- -EVK* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGI-FQINSRY------------ ------------------WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQ- --------------------------------------------------------------DLRSYVAGCGV-- -...* >P1;red sequence::1 : :+229 : :undefined:undefined:-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGEV K...*
In [10]:
s = alignm[2]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
red 1lmp
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16102 14513
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4026
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 : 2024.6575
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 : 1824 0 0 0.007 0.007 26.394 1.000
2 Bond angle potential : 2468 9 22 3.416 3.416 378.11 1.000
3 Stereochemical cosine torsion poten: 1168 0 61 50.456 50.456 457.99 1.000
4 Stereochemical improper torsion pot: 773 0 2 1.432 1.432 33.313 1.000
5 Soft-sphere overlap restraints : 4026 1 3 0.010 0.010 43.991 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) : 2407 4 9 0.400 0.400 169.52 1.000
10 Distance restraints 2 (N-O) : 2568 4 21 0.532 0.532 289.27 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 225 2 6 5.012 5.012 66.644 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 5 84.570 84.570 76.143 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 86.008 86.008 82.263 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 98.562 98.562 46.829 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 63.551 63.551 13.140 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 905 0 0 0.423 0.423 15.376 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: 224 98 33 34.886 109.860 245.43 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 1 0.963 0.963 11.870 1.000
27 Distance restraints 5 (X-Y) : 1401 0 5 0.080 0.080 68.370 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: red.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: 36915.0352
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 2840 93V 94F C N 728 730 146.72 120.00 26.72 6.07 120.00 26.72 6.07
2 2855 94F 94F C CA 739 731 131.81 108.00 23.81 5.52 108.00 23.81 5.52
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8938 95V 105A CA CA 742 819 7.26 4.31 2.95 6.67 4.31 2.95 6.67
2 8965 96A 105A CA CA 749 819 8.79 5.45 3.35 5.38 5.45 3.35 5.38
3 9049 105A 109S CA CA 819 847 9.58 6.73 2.85 5.34 6.73 2.85 5.34
4 9051 105A 111I CA CA 819 861 12.13 9.10 3.03 4.68 9.10 3.03 4.68
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11085 106Y 63Y N O 823 506 5.91 2.86 3.05 6.07 2.86 3.05 6.07
2 11086 106Y 94F N O 823 740 6.21 3.61 2.59 5.15 3.61 2.59 5.15
3 11104 107C 94F N O 835 740 4.66 2.92 1.74 5.05 2.92 1.74 5.05
-------------------------------------------------------------------------------------------------
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 6251 18R 19L C N 141 143 75.21 60.20 28.32 1.06 -63.50 146.38 26.78
1 19L 19L N CA 143 144 5.58 29.60 -41.20
2 6253 20T 21A C N 156 158 53.36 55.40 3.15 0.34 -62.50 138.94 28.22
2 21A 21A N CA 158 159 35.80 38.20 -40.90
3 6254 21A 22Y C N 161 163 65.06 55.90 13.47 0.77 -63.50 147.86 27.90
3 22Y 22Y N CA 163 164 29.63 39.50 -43.40
4 6270 37H 38Y C N 302 304 61.24 55.90 7.98 0.45 -63.50 146.57 27.71
4 38Y 38Y N CA 304 305 33.57 39.50 -43.40
5 6281 48Q 49A C N 385 387 83.38 55.40 36.58 2.18 -62.50 156.09 31.60
5 49A 49A N CA 387 388 14.63 38.20 -40.90
6 6287 54Q 55L C N 427 429 -65.67 -63.50 48.42 6.60 -63.50 48.42 6.60
6 55L 55L N CA 429 430 7.17 -41.20 -41.20
7 6288 55L 56E C N 435 437 47.08 -63.60 142.72 24.44 -63.60 142.72 24.44
7 56E 56E N CA 437 438 49.82 -40.30 -40.30
8 6295 62K 63Y C N 493 495 -65.93 -98.40 39.58 2.84 -63.50 149.19 23.55
8 63Y 63Y N CA 495 496 105.77 128.40 -43.40
9 6296 63Y 64A C N 505 507 -154.91 -134.00 43.81 1.80 -62.50 162.45 31.51
9 64A 64A N CA 507 508 -174.50 147.00 -40.90
10 6298 65P 66M C N 517 519 -116.45 -125.60 9.44 0.32 -63.40 -173.61 24.26
10 66M 66M N CA 519 520 138.18 140.50 -40.50
11 6300 67V 68D C N 532 534 -113.44 -63.30 50.54 8.28 -63.30 50.54 8.28
11 68D 68D N CA 534 535 -46.29 -40.00 -40.00
12 6301 68D 69A C N 540 542 -109.91 -134.00 24.09 0.80 -62.50 178.50 31.77
12 69A 69A N CA 542 543 147.01 147.00 -40.90
13 6302 69A 70Y C N 545 547 -120.55 -124.30 4.27 0.36 -63.50 -172.00 32.72
13 70Y 70Y N CA 547 548 137.46 135.40 -43.40
14 6304 71V 72K C N 564 566 -133.11 -118.00 17.75 0.59 -62.90 -175.36 28.18
14 72K 72K N CA 566 567 148.43 139.10 -40.80
15 6305 72K 73G C N 573 575 89.52 78.70 38.77 0.69 82.20 148.35 7.57
15 73G 73G N CA 575 576 156.67 -166.10 8.50
16 6306 73G 74K C N 577 579 -134.47 -118.00 17.66 0.59 -62.90 -172.12 28.68
16 74K 74K N CA 579 580 145.48 139.10 -40.80
17 6307 74K 75A C N 586 588 -139.32 -134.00 6.01 0.14 -62.50 -174.08 34.59
17 75A 75A N CA 588 589 149.79 147.00 -40.90
18 6308 75A 76N C N 591 593 -126.99 -119.90 9.29 0.27 -63.20 -172.88 27.02
18 76N 76N N CA 593 594 143.00 137.00 -41.10
19 6309 76N 77Q C N 599 601 -127.19 -121.10 35.81 1.59 -63.80 157.98 26.56
19 77Q 77Q N CA 601 602 174.99 139.70 -40.30
20 6311 78N 79E C N 616 618 -78.97 -69.30 11.22 0.66 -63.60 172.20 23.81
20 79E 79E N CA 618 619 148.19 142.50 -40.30
21 6312 79E 80F C N 625 627 -82.46 -71.40 19.33 1.20 -63.20 160.30 23.56
21 80F 80F N CA 627 628 156.56 140.70 -44.30
22 6313 80F 81D C N 636 638 56.13 54.50 2.28 0.14 -63.30 143.36 24.41
22 81D 81D N CA 638 639 39.31 40.90 -40.00
23 6315 82A 83L C N 649 651 -64.42 -70.70 6.68 0.52 -63.50 179.49 24.97
23 83L 83L N CA 651 652 139.32 141.60 -41.20
24 6317 84V 85S C N 664 666 -136.87 -136.60 6.54 0.33 -64.10 -177.59 18.40
24 85S 85S N CA 666 667 157.73 151.20 -35.00
25 6318 85S 86L C N 670 672 -77.56 -70.70 21.46 1.40 -63.50 157.49 22.70
25 86L 86L N CA 672 673 161.94 141.60 -41.20
26 6319 86L 87A C N 678 680 -59.65 -68.20 9.36 0.90 -62.50 170.03 27.73
26 87A 87A N CA 680 681 149.10 145.30 -40.90
27 6320 87A 88Y C N 683 685 -107.27 -98.40 9.10 0.38 -63.50 175.32 25.73
27 88Y 88Y N CA 685 686 126.37 128.40 -43.40
28 6321 88Y 89N C N 695 697 -98.16 -119.90 31.41 0.92 -63.20 159.31 18.21
28 89N 89N N CA 697 698 114.33 137.00 -41.10
29 6324 91G 92N C N 713 715 -73.33 -71.20 23.71 1.58 -63.20 160.60 19.54
29 92N 92N N CA 715 716 119.19 142.80 -41.10
30 6329 96A 97D C N 751 753 -115.69 -63.30 66.23 7.91 -63.30 66.23 7.91
30 97D 97D N CA 753 754 0.51 -40.00 -40.00
31 6331 98G 99W C N 763 765 -128.58 -124.90 73.06 3.63 -63.00 132.06 14.56
31 99W 99W N CA 765 766 70.43 143.40 -44.20
32 6333 100A 101P C N 782 784 -54.32 -58.70 37.53 2.76 -64.50 145.38 11.39
32 101P 101P N CA 784 785 -67.77 -30.50 147.20
33 6334 101P 102F C N 789 791 -104.80 -124.20 50.93 1.84 58.10 174.77 19.06
33 102F 102F N CA 791 792 96.22 143.30 32.90
34 6336 103S 104H C N 806 808 -159.32 -63.20 114.81 14.17 -63.20 114.81 14.17
34 104H 104H N CA 808 809 20.49 -42.30 -42.30
35 6337 104H 105A C N 816 818 -78.43 -68.20 68.12 5.13 -62.50 107.63 18.46
35 105A 105A N CA 818 819 -147.35 145.30 -40.90
36 6338 105A 106Y C N 821 823 -136.00 -63.50 100.35 13.99 -63.50 100.35 13.99
36 106Y 106Y N CA 823 824 25.99 -43.40 -43.40
37 6340 107C 108A C N 839 841 68.87 55.40 18.85 1.01 -62.50 146.98 29.88
37 108A 108A N CA 841 842 25.01 38.20 -40.90
38 6349 116N 117A C N 913 915 -67.24 -68.20 6.60 0.57 -62.50 167.33 27.66
38 117A 117A N CA 915 916 151.83 145.30 -40.90
39 6350 117A 118G C N 918 920 100.10 82.20 88.37 5.17 -80.20 -163.68 14.48
39 118G 118G N CA 920 921 95.04 8.50 174.10
40 6366 133L 134N C N 1042 1044 -91.60 -119.90 51.91 1.65 -63.20 137.54 15.79
40 134N 134N N CA 1044 1045 93.48 137.00 -41.10
41 6367 134N 135L C N 1050 1052 -50.19 -63.50 74.35 9.64 -108.50 127.29 7.25
41 135L 135L N CA 1052 1053 -114.35 -41.20 132.50
42 6376 143N 144S C N 1120 1122 -81.74 -72.40 22.60 1.06 -64.10 153.03 12.22
42 144S 144S N CA 1122 1123 172.98 152.40 -35.00
43 6377 144S 145N C N 1126 1128 64.56 55.90 96.53 6.12 -63.20 128.70 18.74
43 145N 145N N CA 1128 1129 -56.64 39.50 -41.10
44 6379 146Q 147N C N 1143 1145 42.18 -71.20 123.16 9.82 -119.90 170.80 8.33
44 147N 147N N CA 1145 1146 -169.11 142.80 137.00
45 6380 147N 148N C N 1151 1153 -58.69 -63.20 14.16 1.57 55.90 148.22 17.92
45 148N 148N N CA 1153 1154 -54.52 -41.10 39.50
46 6382 149Q 150T C N 1168 1170 -69.14 -78.10 15.11 0.51 -63.20 179.83 22.68
46 150T 150T N CA 1170 1171 137.63 149.80 -42.10
47 6383 150T 151G C N 1175 1177 -67.53 -62.40 6.87 0.98 82.20 156.38 11.78
47 151G 151G N CA 1177 1178 -36.63 -41.20 8.50
48 6384 151G 152G C N 1179 1181 -66.23 -80.20 19.97 0.63 82.20 -148.03 6.56
48 152G 152G N CA 1181 1182 159.82 174.10 8.50
49 6385 152G 153M C N 1183 1185 -74.85 -73.00 18.07 1.19 -63.40 158.94 24.63
49 153M 153M N CA 1185 1186 160.97 143.00 -40.50
50 6387 154I 155K C N 1199 1201 -58.04 -70.20 25.01 1.54 -62.90 159.41 20.97
50 155K 155K N CA 1201 1202 118.54 140.40 -40.80
51 6388 155K 156M C N 1208 1210 -153.74 -125.60 43.62 1.39 -63.40 171.41 32.53
51 156M 156M N CA 1210 1211 173.83 140.50 -40.50
52 6389 156M 157Y C N 1216 1218 -106.30 -98.40 21.45 2.11 -63.50 157.78 23.01
52 157Y 157Y N CA 1218 1219 108.46 128.40 -43.40
53 6390 157Y 158L C N 1228 1230 -123.94 -108.50 27.35 1.28 -63.50 174.52 27.97
53 158L 158L N CA 1230 1231 155.08 132.50 -41.20
54 6393 160I 161G C N 1252 1254 -175.57 -167.20 10.07 0.34 82.20 -169.71 13.72
54 161G 161G N CA 1254 1255 168.99 174.60 8.50
55 6394 161G 162L C N 1256 1258 -101.67 -108.50 7.33 0.38 -63.50 -179.56 23.15
55 162L 162L N CA 1258 1259 135.16 132.50 -41.20
56 6395 162L 163D C N 1264 1266 -88.65 -96.50 9.79 0.40 -63.30 162.06 18.60
56 163D 163D N CA 1266 1267 120.06 114.20 -40.00
57 6396 163D 164N C N 1272 1274 -121.06 -119.90 11.49 0.49 -63.20 -179.98 25.80
57 164N 164N N CA 1274 1275 148.43 137.00 -41.10
58 6397 164N 165S C N 1280 1282 -123.34 -136.60 13.31 0.50 -64.10 -175.26 17.53
58 165S 165S N CA 1282 1283 150.01 151.20 -35.00
59 6398 165S 166G C N 1286 1288 95.65 78.70 59.97 1.06 82.20 128.57 6.91
59 166G 166G N CA 1288 1289 136.37 -166.10 8.50
60 6399 166G 167K C N 1290 1292 -137.07 -118.00 20.22 0.89 -62.90 -171.58 21.72
60 167K 167K N CA 1292 1293 132.40 139.10 -40.80
61 6400 167K 168A C N 1299 1301 -85.41 -68.20 17.78 1.35 -62.50 170.90 29.19
61 168A 168A N CA 1301 1302 149.75 145.30 -40.90
62 6401 168A 169K C N 1304 1306 -124.99 -118.00 8.80 0.30 -62.90 -174.56 27.79
62 169K 169K N CA 1306 1307 144.46 139.10 -40.80
63 6402 169K 170H C N 1313 1315 -104.58 -63.20 84.64 9.00 -63.20 84.64 9.00
63 170H 170H N CA 1315 1316 31.54 -42.30 -42.30
64 6403 170H 171W C N 1323 1325 -117.00 -124.90 40.09 1.75 -63.00 157.81 17.45
64 171W 171W N CA 1325 1326 104.09 143.40 -44.20
65 6404 171W 172Y C N 1337 1339 -130.93 -124.30 15.52 1.11 -63.50 178.03 25.26
65 172Y 172Y N CA 1339 1340 121.37 135.40 -43.40
66 6406 173V 174S C N 1356 1358 -159.26 -136.60 24.81 1.24 -64.10 -159.84 12.96
66 174S 174S N CA 1358 1359 141.09 151.20 -35.00
67 6407 174S 175D C N 1362 1364 -91.18 -70.90 35.02 1.22 -63.30 143.88 19.54
67 175D 175D N CA 1364 1365 178.85 150.30 -40.00
68 6410 177V 178S C N 1381 1383 -67.53 -72.40 14.96 0.73 -64.10 173.28 12.35
68 178S 178S N CA 1383 1384 138.25 152.40 -35.00
69 6412 179V 180R C N 1394 1396 -148.79 -125.20 38.80 1.26 -63.00 170.63 28.81
69 180R 180R N CA 1396 1397 171.40 140.60 -41.10
70 6413 180R 181H C N 1405 1407 56.16 56.30 4.66 0.40 -63.20 148.15 25.33
70 181H 181H N CA 1407 1408 45.46 40.80 -42.30
71 6415 182V 183R C N 1422 1424 -93.13 -72.10 31.93 2.07 -63.00 155.91 23.14
71 183R 183R N CA 1424 1425 165.93 141.90 -41.10
72 6416 183R 184T C N 1433 1435 -102.34 -124.80 28.27 0.99 -63.20 172.92 19.84
72 184T 184T N CA 1435 1436 126.33 143.50 -42.10
73 6418 185I 186R C N 1448 1450 -70.00 -72.10 38.04 2.97 -63.00 139.20 19.28
73 186R 186R N CA 1450 1451 179.88 141.90 -41.10
74 6419 186R 187M C N 1459 1461 -59.84 -73.00 21.65 1.35 -63.40 166.35 25.11
74 187M 187M N CA 1461 1462 125.81 143.00 -40.50
75 6420 187M 188L C N 1467 1469 -144.40 -108.50 35.96 1.69 -63.50 -166.44 23.77
75 188L 188L N CA 1469 1470 134.64 132.50 -41.20
76 6421 188L 189E C N 1475 1477 -152.28 -117.80 100.11 4.25 -63.60 125.57 21.28
76 189E 189E N CA 1477 1478 -129.21 136.80 -40.30
77 6422 189E 190N C N 1484 1486 -57.36 -71.20 18.41 1.01 -63.20 171.86 21.81
77 190N 190N N CA 1486 1487 130.66 142.80 -41.10
78 6424 191Y 192Q C N 1504 1506 67.45 -73.00 145.63 11.02 -63.80 -167.70 24.94
78 192Q 192Q N CA 1506 1507 179.16 140.70 -40.30
79 6425 192Q 193N C N 1513 1515 -67.57 -71.20 11.33 0.83 -63.20 165.43 20.92
79 193N 193N N CA 1515 1516 153.53 142.80 -41.10
80 6426 193N 194K C N 1521 1523 -82.11 -70.20 20.17 1.22 -62.90 163.66 22.35
80 194K 194K N CA 1523 1524 156.67 140.40 -40.80
81 6427 194K 195W C N 1530 1532 -74.86 -71.30 11.92 0.80 -63.00 165.86 21.47
81 195W 195W N CA 1532 1533 150.37 139.00 -44.20
82 6428 195W 196A C N 1544 1546 -74.38 -68.20 18.06 1.24 -62.50 157.28 26.38
82 196A 196A N CA 1546 1547 162.27 145.30 -40.90
83 6429 196A 197K C N 1549 1551 -78.62 -70.20 13.67 0.82 -62.90 168.77 22.81
83 197K 197K N CA 1551 1552 151.16 140.40 -40.80
84 6430 197K 198L C N 1558 1560 -82.60 -70.70 21.82 1.35 -63.50 160.06 23.36
84 198L 198L N CA 1560 1561 159.89 141.60 -41.20
85 6431 198L 199N C N 1566 1568 -63.52 -71.20 9.00 0.52 -63.20 179.21 22.39
85 199N 199N N CA 1568 1569 138.11 142.80 -41.10
86 6432 199N 200L C N 1574 1576 -72.99 -70.70 4.47 0.42 -63.50 179.22 24.36
86 200L 200L N CA 1576 1577 137.76 141.60 -41.20
87 6436 203D 204T C N 1604 1606 -130.92 -124.80 14.15 0.78 -63.20 -174.37 20.18
87 204T 204T N CA 1606 1607 130.74 143.50 -42.10
88 6437 204T 205M C N 1611 1613 175.98 -125.60 89.07 2.81 -63.40 164.44 33.02
88 205M 205M N CA 1613 1614 -152.26 140.50 -40.50
89 6440 207I 208A C N 1638 1640 -77.33 -68.20 9.24 0.73 -62.50 173.06 29.11
89 208A 208A N CA 1640 1641 146.68 145.30 -40.90
90 6441 208A 209E C N 1643 1645 -130.90 -117.80 16.18 0.48 -63.60 -174.00 28.60
90 209E 209E N CA 1645 1646 146.30 136.80 -40.30
91 6443 210I 211E C N 1660 1662 -72.39 -69.30 53.91 4.22 -63.60 129.28 16.77
91 211E 211E N CA 1662 1663 88.68 142.50 -40.30
92 6444 211E 212A C N 1669 1671 -154.10 -134.00 25.18 0.65 -62.50 -178.27 34.67
92 212A 212A N CA 1671 1672 162.15 147.00 -40.90
93 6447 214F 215G C N 1694 1696 58.68 78.70 33.32 0.59 -62.40 155.94 22.61
93 215G 215G N CA 1696 1697 -139.47 -166.10 -41.20
94 6448 215G 216R C N 1698 1700 -87.10 -63.00 82.60 9.78 -63.00 82.60 9.78
94 216R 216R N CA 1700 1701 37.90 -41.10 -41.10
95 6451 218I 219D C N 1726 1728 42.26 54.50 27.22 1.33 -70.90 141.58 6.61
95 219D 219D N CA 1728 1729 65.21 40.90 150.30
96 6454 221A 222S C N 1747 1749 65.56 56.90 12.33 0.73 -64.10 143.99 19.15
96 222S 222S N CA 1749 1750 27.61 36.40 -35.00
97 6455 222S 223G C N 1753 1755 -65.93 -80.20 53.47 1.45 82.20 -173.04 6.83
97 223G 223G N CA 1755 1756 122.57 174.10 8.50
98 6456 223G 224E C N 1757 1759 -64.16 -69.30 8.11 0.46 -63.60 176.53 23.51
98 224E 224E N CA 1759 1760 136.23 142.50 -40.30
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 22 47 192 149 237 228 209 280 287 282
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3752
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 : 1945.0626
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 : 1824 2 5 0.010 0.010 53.584 1.000
2 Bond angle potential : 2468 6 25 2.568 2.568 303.16 1.000
3 Stereochemical cosine torsion poten: 1168 0 56 50.752 50.752 463.05 1.000
4 Stereochemical improper torsion pot: 773 3 3 1.893 1.893 52.827 1.000
5 Soft-sphere overlap restraints : 3752 2 9 0.012 0.012 61.729 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) : 2407 1 2 0.384 0.384 127.22 1.000
10 Distance restraints 2 (N-O) : 2568 1 20 0.552 0.552 266.62 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: 225 1 7 5.147 5.147 70.287 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 1 87.455 87.455 63.730 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 84.608 84.608 74.121 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 96.513 96.513 45.779 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 100.754 100.754 15.434 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 905 0 0 0.475 0.475 11.772 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: 224 98 38 30.402 110.872 224.07 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 0 0.934 0.934 11.882 1.000
27 Distance restraints 5 (X-Y) : 1401 3 16 0.097 0.097 99.796 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: red.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: 36954.0234
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 741 93V 93V CB CA 725 724 1.67 1.50 0.17 4.60 1.50 0.17 4.60
2 746 93V 93V C CA 728 724 1.68 1.49 0.19 5.46 1.49 0.19 5.46
-------------------------------------------------------------------------------------------------
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 2534 64A 64A N CA 507 508 125.10 107.00 18.10 5.20 107.00 18.10 5.20
2 2837 93V 93V CA C 724 728 135.46 116.50 18.96 5.45 116.50 18.96 5.45
3 2839 93V 93V C CA 728 724 141.78 108.00 33.77 7.83 108.00 33.77 7.83
4 2977 105A 106Y C N 821 823 140.10 120.00 20.10 4.57 120.00 20.10 4.57
5 2980 106Y 106Y N CA 823 824 127.65 107.00 20.65 5.94 107.00 20.65 5.94
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 5788 94F 94F CA N 731 730 58.27 35.27 23.00 5.48 35.27 23.00 5.48
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8938 95V 105A CA CA 742 819 6.47 4.31 2.16 4.89 4.31 2.16 4.89
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11130 108A 105A N O 841 822 5.81 3.15 2.66 5.07 3.15 2.66 5.07
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6251 18R 19L C N 141 143 74.39 60.20 30.00 1.06 -63.50 144.86 26.47
1 19L 19L N CA 143 144 3.17 29.60 -41.20
2 6253 20T 21A C N 156 158 54.82 55.40 4.17 0.30 -62.50 139.22 28.29
2 21A 21A N CA 158 159 34.07 38.20 -40.90
3 6254 21A 22Y C N 161 163 64.78 55.90 13.07 0.75 -63.50 147.75 27.88
3 22Y 22Y N CA 163 164 29.91 39.50 -43.40
4 6270 37H 38Y C N 302 304 64.49 55.90 14.75 0.75 -63.50 146.32 27.59
4 38Y 38Y N CA 304 305 27.51 39.50 -43.40
5 6281 48Q 49A C N 385 387 86.26 55.40 41.19 2.37 -62.50 157.53 31.83
5 49A 49A N CA 387 388 10.93 38.20 -40.90
6 6289 56E 57I C N 444 446 -161.02 -120.60 46.51 3.71 -63.40 179.72 27.32
6 57I 57I N CA 446 447 107.29 130.30 -43.60
7 6290 57I 58D C N 452 454 -47.16 -96.50 50.71 2.08 54.50 118.85 9.47
7 58D 58D N CA 454 455 102.48 114.20 40.90
8 6295 62K 63Y C N 493 495 -85.39 -98.40 67.78 7.15 -63.50 107.53 16.00
8 63Y 63Y N CA 495 496 61.88 128.40 -43.40
9 6296 63Y 64A C N 505 507 -126.48 -134.00 44.01 2.64 -62.50 143.77 26.99
9 64A 64A N CA 507 508 -169.64 147.00 -40.90
10 6298 65P 66M C N 517 519 -132.44 -125.60 23.72 1.25 -63.40 172.69 21.65
10 66M 66M N CA 519 520 117.78 140.50 -40.50
11 6300 67V 68D C N 532 534 -124.24 -96.50 55.93 2.31 -63.30 121.95 12.95
11 68D 68D N CA 534 535 65.63 114.20 -40.00
12 6301 68D 69A C N 540 542 -128.50 -134.00 11.97 0.50 -62.50 -170.85 28.59
12 69A 69A N CA 542 543 136.36 147.00 -40.90
13 6302 69A 70Y C N 545 547 -127.09 -124.30 12.16 0.77 -63.50 178.67 25.49
13 70Y 70Y N CA 547 548 123.57 135.40 -43.40
14 6304 71V 72K C N 564 566 -162.54 -118.00 47.60 1.59 -62.90 -168.69 30.77
14 72K 72K N CA 566 567 155.89 139.10 -40.80
15 6305 72K 73G C N 573 575 137.97 -167.20 56.29 1.40 82.20 163.18 10.55
15 73G 73G N CA 575 576 161.86 174.60 8.50
16 6306 73G 74K C N 577 579 -125.13 -118.00 7.14 0.27 -62.90 -169.69 28.43
16 74K 74K N CA 579 580 139.35 139.10 -40.80
17 6307 74K 75A C N 586 588 -144.90 -134.00 15.15 0.45 -62.50 -178.62 34.14
17 75A 75A N CA 588 589 157.52 147.00 -40.90
18 6308 75A 76N C N 591 593 -74.62 -71.20 8.56 0.47 -63.20 168.65 21.72
18 76N 76N N CA 593 594 150.64 142.80 -41.10
19 6309 76N 77Q C N 599 601 -108.64 -121.10 12.65 0.43 -63.80 -176.61 24.84
19 77Q 77Q N CA 601 602 137.52 139.70 -40.30
20 6310 77Q 78N C N 608 610 -82.40 -71.20 22.09 1.18 -63.20 158.23 20.86
20 78N 78N N CA 610 611 161.84 142.80 -41.10
21 6311 78N 79E C N 616 618 -84.14 -69.30 62.81 5.27 -63.60 123.49 15.43
21 79E 79E N CA 618 619 81.47 142.50 -40.30
22 6312 79E 80F C N 625 627 -158.89 -124.20 44.11 1.15 -63.20 173.85 30.06
22 80F 80F N CA 627 628 170.56 143.30 -44.30
23 6313 80F 81D C N 636 638 -88.62 -63.30 70.49 7.57 -63.30 70.49 7.57
23 81D 81D N CA 638 639 25.79 -40.00 -40.00
24 6315 82A 83L C N 649 651 -70.13 -70.70 7.91 0.58 -63.50 175.04 23.93
24 83L 83L N CA 651 652 133.71 141.60 -41.20
25 6317 84V 85S C N 664 666 -66.68 -72.40 6.95 0.36 -64.10 176.55 12.95
25 85S 85S N CA 666 667 148.47 152.40 -35.00
26 6318 85S 86L C N 670 672 -70.72 -70.70 9.30 0.71 -63.50 173.66 23.71
26 86L 86L N CA 672 673 132.30 141.60 -41.20
27 6319 86L 87A C N 678 680 -135.26 -134.00 5.64 0.34 -62.50 -168.07 35.35
27 87A 87A N CA 680 681 141.50 147.00 -40.90
28 6320 87A 88Y C N 683 685 -134.34 -124.30 19.00 0.75 -63.50 179.63 32.02
28 88Y 88Y N CA 685 686 151.53 135.40 -43.40
29 6321 88Y 89N C N 695 697 -92.93 -119.90 38.46 1.13 -63.20 153.58 17.72
29 89N 89N N CA 697 698 109.58 137.00 -41.10
30 6323 90C 91G C N 709 711 -102.65 -80.20 64.51 3.65 82.20 -155.73 15.95
30 91G 91G N CA 711 712 113.61 174.10 8.50
31 6324 91G 92N C N 713 715 -124.46 -119.90 25.22 1.24 -63.20 165.09 18.04
31 92N 92N N CA 715 716 112.20 137.00 -41.10
32 6325 92N 93V C N 721 723 -148.87 -62.40 90.30 15.23 -125.40 150.12 6.84
32 93V 93V N CA 723 724 -68.42 -42.40 143.30
33 6326 93V 94F C N 728 730 3.44 -63.20 103.10 11.71 -63.20 103.10 11.71
33 94F 94F N CA 730 731 -122.96 -44.30 -44.30
34 6329 96A 97D C N 751 753 -112.75 -63.30 49.71 7.63 -63.30 49.71 7.63
34 97D 97D N CA 753 754 -34.89 -40.00 -40.00
35 6333 100A 101P C N 782 784 -64.73 -58.70 19.12 2.08 -64.50 164.15 12.24
35 101P 101P N CA 784 785 -48.65 -30.50 147.20
36 6334 101P 102F C N 789 791 -68.39 -63.20 15.20 1.80 58.10 141.27 21.72
36 102F 102F N CA 791 792 -30.02 -44.30 32.90
37 6337 104H 105A C N 816 818 58.07 55.40 47.63 3.09 -62.50 174.87 34.82
37 105A 105A N CA 818 819 85.76 38.20 -40.90
38 6340 107C 108A C N 839 841 76.42 55.40 21.48 2.49 -62.50 162.10 32.96
38 108A 108A N CA 841 842 42.64 38.20 -40.90
39 6349 116N 117A C N 913 915 -66.98 -68.20 6.65 0.58 -62.50 167.32 27.64
39 117A 117A N CA 915 916 151.84 145.30 -40.90
40 6350 117A 118G C N 918 920 99.89 82.20 87.52 5.11 -80.20 -163.16 14.52
40 118G 118G N CA 920 921 94.22 8.50 174.10
41 6366 133L 134N C N 1042 1044 -92.29 -119.90 61.67 2.10 -63.20 126.34 14.38
41 134N 134N N CA 1044 1045 81.85 137.00 -41.10
42 6367 134N 135L C N 1050 1052 -36.21 -63.50 79.19 9.82 -108.50 133.26 7.59
42 135L 135L N CA 1052 1053 -115.55 -41.20 132.50
43 6379 146Q 147N C N 1143 1145 -59.75 -63.20 11.04 1.58 -119.90 178.08 6.58
43 147N 147N N CA 1145 1146 -30.61 -41.10 137.00
44 6380 147N 148N C N 1151 1153 -64.02 -71.20 10.44 0.56 55.90 153.44 10.35
44 148N 148N N CA 1153 1154 135.22 142.80 39.50
45 6381 148N 149Q C N 1159 1161 61.13 55.10 10.87 0.54 -121.10 -151.77 10.07
45 149Q 149Q N CA 1161 1162 31.26 40.30 139.70
46 6384 151G 152G C N 1179 1181 -63.19 -62.40 5.99 0.93 82.20 155.67 11.92
46 152G 152G N CA 1181 1182 -47.14 -41.20 8.50
47 6385 152G 153M C N 1183 1185 -139.75 -125.60 16.13 0.82 -63.40 -170.65 23.72
47 153M 153M N CA 1185 1186 132.77 140.50 -40.50
48 6387 154I 155K C N 1199 1201 -84.02 -70.20 13.86 0.99 -62.90 179.00 24.45
48 155K 155K N CA 1201 1202 141.45 140.40 -40.80
49 6388 155K 156M C N 1208 1210 -130.93 -125.60 5.78 0.28 -63.40 -168.88 24.27
49 156M 156M N CA 1210 1211 138.29 140.50 -40.50
50 6389 156M 157Y C N 1216 1218 -120.00 -124.30 18.85 0.83 -63.50 170.11 24.41
50 157Y 157Y N CA 1218 1219 117.05 135.40 -43.40
51 6390 157Y 158L C N 1228 1230 -140.93 -108.50 45.78 2.06 -63.50 172.35 28.72
51 158L 158L N CA 1230 1231 164.81 132.50 -41.20
52 6393 160I 161G C N 1252 1254 163.21 -167.20 29.60 0.55 82.20 -174.53 12.71
52 161G 161G N CA 1254 1255 175.34 174.60 8.50
53 6394 161G 162L C N 1256 1258 -99.99 -108.50 8.62 0.43 -63.50 178.85 23.00
53 162L 162L N CA 1258 1259 133.89 132.50 -41.20
54 6395 162L 163D C N 1264 1266 -93.79 -96.50 14.81 0.62 -63.30 142.93 16.03
54 163D 163D N CA 1266 1267 99.65 114.20 -40.00
55 6396 163D 164N C N 1272 1274 -117.79 -119.90 3.97 0.21 -63.20 -173.30 26.45
55 164N 164N N CA 1274 1275 140.36 137.00 -41.10
56 6397 164N 165S C N 1280 1282 -125.22 -136.60 13.89 0.42 -64.10 -171.58 11.61
56 165S 165S N CA 1282 1283 143.23 151.20 -35.00
57 6398 165S 166G C N 1286 1288 87.13 78.70 40.42 0.82 82.20 145.94 7.33
57 166G 166G N CA 1288 1289 154.36 -166.10 8.50
58 6399 166G 167K C N 1290 1292 -137.76 -118.00 26.69 0.93 -62.90 178.59 27.67
58 167K 167K N CA 1292 1293 157.05 139.10 -40.80
59 6400 167K 168A C N 1299 1301 -108.05 -134.00 31.17 0.76 -62.50 176.59 27.09
59 168A 168A N CA 1301 1302 129.72 147.00 -40.90
60 6401 168A 169K C N 1304 1306 -123.64 -118.00 5.87 0.20 -62.90 -171.48 28.10
60 169K 169K N CA 1306 1307 140.73 139.10 -40.80
61 6402 169K 170H C N 1313 1315 -112.85 -125.60 27.22 0.77 -63.20 164.72 18.07
61 170H 170H N CA 1315 1316 114.75 138.80 -42.30
62 6403 170H 171W C N 1323 1325 -127.77 -124.90 10.01 0.54 -63.00 -170.57 20.95
62 171W 171W N CA 1325 1326 133.81 143.40 -44.20
63 6404 171W 172Y C N 1337 1339 -123.65 -124.30 8.25 0.41 -63.50 -179.13 25.95
63 172Y 172Y N CA 1339 1340 127.18 135.40 -43.40
64 6406 173V 174S C N 1356 1358 -151.21 -136.60 16.23 0.50 -64.10 -171.89 19.88
64 174S 174S N CA 1358 1359 158.27 151.20 -35.00
65 6407 174S 175D C N 1362 1364 -94.33 -96.50 6.56 0.27 -63.30 163.37 18.50
65 175D 175D N CA 1364 1365 120.40 114.20 -40.00
66 6408 175D 176G C N 1370 1372 -62.75 -80.20 49.56 1.21 82.20 -172.32 6.59
66 176G 176G N CA 1372 1373 127.72 174.10 8.50
67 6410 177V 178S C N 1381 1383 -103.94 -136.60 48.32 1.60 -64.10 155.77 9.68
67 178S 178S N CA 1383 1384 115.59 151.20 -35.00
68 6412 179V 180R C N 1394 1396 -119.15 -125.20 26.37 1.13 -63.00 165.82 19.33
68 180R 180R N CA 1396 1397 114.93 140.60 -41.10
69 6413 180R 181H C N 1405 1407 -148.66 -125.60 25.63 0.68 -63.20 -171.77 29.08
69 181H 181H N CA 1407 1408 149.99 138.80 -42.30
70 6415 182V 183R C N 1422 1424 51.30 57.30 21.40 1.07 -63.00 151.64 27.39
70 183R 183R N CA 1424 1425 58.54 38.00 -41.10
71 6416 183R 184T C N 1433 1435 -63.63 -78.10 17.19 1.14 -63.20 158.83 20.40
71 184T 184T N CA 1435 1436 159.07 149.80 -42.10
72 6418 185I 186R C N 1448 1450 -120.64 -125.20 7.53 0.42 -63.00 -178.30 28.52
72 186R 186R N CA 1450 1451 146.59 140.60 -41.10
73 6419 186R 187M C N 1459 1461 -70.17 -73.00 13.27 0.85 -63.40 170.67 24.96
73 187M 187M N CA 1461 1462 130.04 143.00 -40.50
74 6420 187M 188L C N 1467 1469 -124.24 -108.50 33.84 1.63 -63.50 167.73 27.05
74 188L 188L N CA 1469 1470 162.46 132.50 -41.20
75 6421 188L 189E C N 1475 1477 -69.53 -69.30 2.99 0.22 -63.60 174.31 23.57
75 189E 189E N CA 1477 1478 145.49 142.50 -40.30
76 6422 189E 190N C N 1484 1486 -100.02 -119.90 27.08 1.46 -63.20 167.60 23.05
76 190N 190N N CA 1486 1487 155.40 137.00 -41.10
77 6423 190N 191Y C N 1492 1494 -107.62 -98.40 11.18 0.72 -63.50 171.25 25.07
77 191Y 191Y N CA 1494 1495 122.07 128.40 -43.40
78 6424 191Y 192Q C N 1504 1506 -102.64 -121.10 22.23 1.09 -63.80 172.06 27.38
78 192Q 192Q N CA 1506 1507 152.08 139.70 -40.30
79 6425 192Q 193N C N 1513 1515 -98.34 -119.90 36.40 1.12 -63.20 152.86 17.40
79 193N 193N N CA 1515 1516 107.66 137.00 -41.10
80 6426 193N 194K C N 1521 1523 -123.25 -118.00 9.55 0.49 -62.90 -177.79 21.20
80 194K 194K N CA 1523 1524 131.12 139.10 -40.80
81 6427 194K 195W C N 1530 1532 -128.91 -124.90 22.02 1.15 -63.00 178.55 19.67
81 195W 195W N CA 1532 1533 121.74 143.40 -44.20
82 6428 195W 196A C N 1544 1546 -162.06 -134.00 30.50 0.69 -62.50 -171.42 36.20
82 196A 196A N CA 1546 1547 158.95 147.00 -40.90
83 6429 196A 197K C N 1549 1551 -136.04 -118.00 18.79 0.81 -62.90 -170.63 21.85
83 197K 197K N CA 1551 1552 133.87 139.10 -40.80
84 6430 197K 198L C N 1558 1560 -102.43 -108.50 21.22 1.07 -63.50 158.24 20.10
84 198L 198L N CA 1560 1561 112.17 132.50 -41.20
85 6431 198L 199N C N 1566 1568 -164.28 -119.90 80.26 2.54 -63.20 153.13 24.50
85 199N 199N N CA 1568 1569 -156.13 137.00 -41.10
86 6432 199N 200L C N 1574 1576 -70.15 -70.70 38.71 2.95 -63.50 138.65 19.64
86 200L 200L N CA 1576 1577 -179.69 141.60 -41.20
87 6435 202V 203D C N 1596 1598 -91.07 -70.90 43.78 1.47 -63.30 133.76 18.29
87 203D 203D N CA 1598 1599 -170.84 150.30 -40.00
88 6436 203D 204T C N 1604 1606 -85.64 -78.10 8.53 0.39 -63.20 165.62 22.73
88 204T 204T N CA 1606 1607 153.80 149.80 -42.10
89 6441 208A 209E C N 1643 1645 176.86 -117.80 67.22 2.12 -63.60 -154.55 33.85
89 209E 209E N CA 1645 1646 152.61 136.80 -40.30
90 6444 211E 212A C N 1669 1671 -76.56 -68.20 37.30 3.29 -62.50 150.50 24.01
90 212A 212A N CA 1671 1672 108.95 145.30 -40.90
91 6446 213E 214F C N 1683 1685 -115.45 -124.20 73.79 3.25 -63.20 125.71 14.55
91 214F 214F N CA 1685 1686 70.04 143.30 -44.30
92 6448 215G 216R C N 1698 1700 -116.74 -125.20 77.13 3.53 -63.00 117.98 13.40
92 216R 216R N CA 1700 1701 63.93 140.60 -41.10
93 6449 216R 217K C N 1709 1711 -117.57 -62.90 55.41 8.64 -62.90 55.41 8.64
93 217K 217K N CA 1711 1712 -31.74 -40.80 -40.80
94 6451 218I 219D C N 1726 1728 -47.72 -63.30 25.73 2.78 -70.90 151.02 8.61
94 219D 219D N CA 1728 1729 -60.47 -40.00 150.30
95 6452 219D 220M C N 1734 1736 -66.47 -63.40 8.78 1.12 56.30 139.90 25.78
95 220M 220M N CA 1736 1737 -32.28 -40.50 34.80
96 6454 221A 222S C N 1747 1749 55.80 56.90 2.20 0.09 -64.10 140.53 18.44
96 222S 222S N CA 1749 1750 38.31 36.40 -35.00
97 6455 222S 223G C N 1753 1755 -69.48 -80.20 39.88 1.08 82.20 -162.05 6.87
97 223G 223G N CA 1755 1756 135.69 174.10 8.50
98 6456 223G 224E C N 1757 1759 -61.76 -69.30 7.55 0.58 -63.60 176.95 23.49
98 224E 224E N CA 1759 1760 142.75 142.50 -40.30
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 21 28 154 174 203 218 205 239 263 265
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
red.B99990001.pdb 2024.65747
red.B99990002.pdb 1945.06262
Получаем достаточно странную модель, явно биологического смысла у нее нет
In [49]:
from IPython.display import Image
Image(filename='red.png')
Out[49]:
Добавим специальные условия моделирования, может, качество улучшится.
In [13]:
from modeller import *
from modeller.automodel import *
In [23]:
class MyModel(model):
def select_atoms(self):
return selection(self) - selection(self.residue_range('213', '223'))# remove loop from refining
def special_restraints(self, aln):
rsr = self.restraints
for ids in (('OH:31', '06:229'),
('O:138', 'N2:228'),
('OD2:52', 'O1L:229')):
atoms = [self.atoms[i] for i in ids]
rsr.add(forms.upper_bound(group=physical.upper_distance,
feature=features.distance(*atoms),
mean=3.5, stdev=0.1))
class LoopModel(loopmodel):
def select_loop_atoms(self):
return selection(self.residue_range('213', '223'))
In [24]:
alignm=modeller.alignment(env)
In [25]:
alignm.append(file='P62693.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = MyModel(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
In [26]:
new_seq = "".join(x.code for x in alignm[0].residues) + "..."
alignm.append_sequence(new_seq)
In [27]:
alignm.salign()
alignm[2].code ="red1"
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1 SALIGN_____> adding the next group to the alignment; iteration 2
In [28]:
!cat all_in_one.ali
>P1;sp|P62693|LYS_BPPHV sequence:: : : : :::-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASG-- -EVK* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGI-FQINSRY------------ ------------------WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQ- --------------------------------------------------------------DLRSYVAGCGV-- -...* >P1;red1 sequence::1 : :+229 : :undefined:undefined:-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGEV K...*
In [30]:
s = alignm[2]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = LoopModel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code,
loop_assess_methods=assess.DOPE)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
red1 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16102 14513
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3785
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 : 1925.4180
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 : 1824 0 2 0.008 0.008 32.350 1.000
2 Bond angle potential : 2468 8 19 2.444 2.444 276.84 1.000
3 Stereochemical cosine torsion poten: 1168 0 63 52.247 52.247 489.34 1.000
4 Stereochemical improper torsion pot: 773 0 3 1.445 1.445 33.859 1.000
5 Soft-sphere overlap restraints : 3785 1 7 0.011 0.011 51.143 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) : 2407 1 6 0.409 0.409 157.12 1.000
10 Distance restraints 2 (N-O) : 2568 2 17 0.553 0.553 274.85 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: 225 3 10 5.156 5.156 70.541 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 6 84.089 84.089 66.216 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 0 83.811 83.811 72.665 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 90.566 90.566 44.689 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 90.232 90.232 14.101 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 905 0 0 0.482 0.482 12.547 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: 224 105 28 36.821 115.725 232.28 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 0 0.923 0.923 9.8616 1.000
27 Distance restraints 5 (X-Y) : 1401 2 8 0.090 0.090 87.009 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: red1.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: 37771.4609
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 2531 63Y 64A C N 505 507 141.93 120.00 21.93 4.98 120.00 21.93 4.98
2 2534 64A 64A N CA 507 508 123.19 107.00 16.19 4.66 107.00 16.19 4.66
3 2837 93V 93V CA C 724 728 133.60 116.50 17.10 4.92 116.50 17.10 4.92
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8938 95V 105A CA CA 742 819 6.83 4.31 2.52 5.70 4.31 2.52 5.70
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11130 108A 105A N O 841 822 5.77 3.15 2.62 4.99 3.15 2.62 4.99
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6520 63Y 63Y CA C 496 505 -156.72 -180.00 23.28 4.65 -180.00 23.28 4.65
-------------------------------------------------------------------------------------------------
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 6251 18R 19L C N 141 143 59.48 60.20 5.86 0.29 -63.50 144.90 26.69
1 19L 19L N CA 143 144 35.41 29.60 -41.20
2 6253 20T 21A C N 156 158 54.72 55.40 3.28 0.25 -62.50 139.64 28.37
2 21A 21A N CA 158 159 34.99 38.20 -40.90
3 6254 21A 22Y C N 161 163 64.75 55.90 12.24 0.75 -63.50 148.29 28.00
3 22Y 22Y N CA 163 164 31.05 39.50 -43.40
4 6270 37H 38Y C N 302 304 64.14 55.90 16.93 0.81 -63.50 144.67 27.25
4 38Y 38Y N CA 304 305 24.71 39.50 -43.40
5 6281 48Q 49A C N 385 387 82.74 55.40 35.84 2.12 -62.50 155.64 31.52
5 49A 49A N CA 387 388 15.03 38.20 -40.90
6 6288 55L 56E C N 435 437 110.92 -117.80 -179.38 9.56 -63.60 -177.60 30.84
6 56E 56E N CA 437 438 12.75 136.80 -40.30
7 6295 62K 63Y C N 493 495 -81.06 -98.40 66.96 6.99 -63.50 108.56 16.36
7 63Y 63Y N CA 495 496 63.73 128.40 -43.40
8 6296 63Y 64A C N 505 507 -86.22 -68.20 29.92 1.89 -62.50 151.78 26.10
8 64A 64A N CA 507 508 169.18 145.30 -40.90
9 6298 65P 66M C N 517 519 -134.10 -125.60 12.09 0.65 -63.40 -173.67 23.48
9 66M 66M N CA 519 520 131.90 140.50 -40.50
10 6300 67V 68D C N 532 534 -129.65 -96.50 58.85 2.43 -63.30 124.70 13.28
10 68D 68D N CA 534 535 65.58 114.20 -40.00
11 6301 68D 69A C N 540 542 -154.17 -134.00 21.16 0.50 -62.50 -170.60 35.94
11 69A 69A N CA 542 543 153.37 147.00 -40.90
12 6302 69A 70Y C N 545 547 -127.96 -124.30 6.67 0.27 -63.50 -172.92 32.92
12 70Y 70Y N CA 547 548 140.97 135.40 -43.40
13 6304 71V 72K C N 564 566 -140.55 -118.00 27.86 0.94 -62.90 -178.79 28.18
13 72K 72K N CA 566 567 155.47 139.10 -40.80
14 6305 72K 73G C N 573 575 -169.99 -167.20 28.52 1.15 82.20 174.89 13.03
14 73G 73G N CA 575 576 146.22 174.60 8.50
15 6306 73G 74K C N 577 579 -127.73 -118.00 9.75 0.38 -62.90 -169.38 22.14
15 74K 74K N CA 579 580 138.45 139.10 -40.80
16 6307 74K 75A C N 586 588 -106.15 -134.00 32.92 0.79 -62.50 175.84 27.03
16 75A 75A N CA 588 589 129.44 147.00 -40.90
17 6308 75A 76N C N 591 593 -129.91 -119.90 11.64 0.35 -63.20 -171.80 27.32
17 76N 76N N CA 593 594 142.93 137.00 -41.10
18 6309 76N 77Q C N 599 601 -86.72 -73.00 29.74 2.21 -63.80 156.31 21.84
18 77Q 77Q N CA 601 602 114.31 140.70 -40.30
19 6310 77Q 78N C N 608 610 -142.59 -119.90 31.71 0.92 -63.20 178.40 26.77
19 78N 78N N CA 610 611 159.14 137.00 -41.10
20 6311 78N 79E C N 616 618 -91.74 -117.80 45.76 1.65 -63.60 142.30 17.58
20 79E 79E N CA 618 619 99.19 136.80 -40.30
21 6312 79E 80F C N 625 627 -156.25 -124.20 36.54 0.98 -63.20 -179.34 30.92
21 80F 80F N CA 627 628 160.85 143.30 -44.30
22 6313 80F 81D C N 636 638 -105.98 -96.50 24.14 1.00 -63.30 138.72 15.08
22 81D 81D N CA 638 639 92.00 114.20 -40.00
23 6314 81D 82A C N 644 646 -134.17 -134.00 1.54 0.09 -62.50 -172.15 34.62
23 82A 82A N CA 646 647 145.47 147.00 -40.90
24 6315 82A 83L C N 649 651 -114.97 -108.50 7.10 0.38 -63.50 178.38 22.40
24 83L 83L N CA 651 652 129.59 132.50 -41.20
25 6317 84V 85S C N 664 666 -135.52 -136.60 2.56 0.14 -64.10 -174.24 18.53
25 85S 85S N CA 666 667 153.52 151.20 -35.00
26 6318 85S 86L C N 670 672 -104.86 -108.50 4.13 0.22 -63.50 -179.55 23.03
26 86L 86L N CA 672 673 134.44 132.50 -41.20
27 6319 86L 87A C N 678 680 -126.22 -134.00 7.83 0.22 -62.50 -175.58 33.63
27 87A 87A N CA 680 681 146.04 147.00 -40.90
28 6320 87A 88Y C N 683 685 -121.78 -124.30 3.85 0.30 -63.50 -172.43 32.71
28 88Y 88Y N CA 685 686 138.31 135.40 -43.40
29 6321 88Y 89N C N 695 697 -109.22 -119.90 10.69 0.43 -63.20 -176.48 20.75
29 89N 89N N CA 697 698 136.55 137.00 -41.10
30 6323 90C 91G C N 709 711 -104.54 -80.20 76.07 4.20 82.20 -163.11 15.34
30 91G 91G N CA 711 712 102.02 174.10 8.50
31 6324 91G 92N C N 713 715 -139.86 -119.90 26.08 1.40 -63.20 178.60 19.31
31 92N 92N N CA 715 716 120.21 137.00 -41.10
32 6326 93V 94F C N 728 730 91.04 -124.20 158.96 4.44 -63.20 -172.44 23.06
32 94F 94F N CA 730 731 -151.01 143.30 -44.30
33 6329 96A 97D C N 751 753 -109.54 -63.30 48.84 6.84 -63.30 48.84 6.84
33 97D 97D N CA 753 754 -24.27 -40.00 -40.00
34 6331 98G 99W C N 763 765 -122.28 -124.90 83.65 4.00 -63.00 119.70 13.20
34 99W 99W N CA 765 766 59.79 143.40 -44.20
35 6333 100A 101P C N 782 784 -47.54 -58.70 41.09 2.61 -64.50 143.76 11.64
35 101P 101P N CA 784 785 -70.05 -30.50 147.20
36 6334 101P 102F C N 789 791 -92.79 -71.40 32.90 2.91 58.10 172.12 16.53
36 102F 102F N CA 791 792 115.71 140.70 32.90
37 6336 103S 104H C N 806 808 -123.93 -63.20 64.95 8.91 -63.20 64.95 8.91
37 104H 104H N CA 808 809 -19.27 -42.30 -42.30
38 6337 104H 105A C N 816 818 58.43 55.40 47.42 3.11 -62.50 174.94 34.85
38 105A 105A N CA 818 819 85.52 38.20 -40.90
39 6338 105A 106Y C N 821 823 -137.57 -124.30 18.44 1.49 -63.50 -178.22 25.64
39 106Y 106Y N CA 823 824 122.60 135.40 -43.40
40 6339 106Y 107C C N 833 835 161.87 -63.00 138.13 21.32 -63.00 138.13 21.32
40 107C 107C N CA 835 836 -12.46 -41.10 -41.10
41 6340 107C 108A C N 839 841 56.20 55.40 7.01 0.49 -62.50 146.61 29.72
41 108A 108A N CA 841 842 45.17 38.20 -40.90
42 6366 133L 134N C N 1042 1044 -88.87 -119.90 56.07 1.77 -63.20 133.88 15.46
42 134N 134N N CA 1044 1045 90.30 137.00 -41.10
43 6367 134N 135L C N 1050 1052 -49.57 -63.50 73.32 9.47 -108.50 128.61 7.32
43 135L 135L N CA 1052 1053 -113.18 -41.20 132.50
44 6376 143N 144S C N 1120 1122 -111.76 -136.60 45.38 1.66 -64.10 155.70 9.59
44 144S 144S N CA 1122 1123 113.22 151.20 -35.00
45 6377 144S 145N C N 1126 1128 94.27 55.90 76.67 3.70 -63.20 158.11 24.55
45 145N 145N N CA 1128 1129 -26.88 39.50 -41.10
46 6379 146Q 147N C N 1143 1145 -63.07 -63.20 6.77 0.85 -119.90 -179.49 6.78
46 147N 147N N CA 1145 1146 -34.33 -41.10 137.00
47 6380 147N 148N C N 1151 1153 -55.12 -63.20 10.11 1.19 55.90 140.85 17.10
47 148N 148N N CA 1153 1154 -47.18 -41.10 39.50
48 6382 149Q 150T C N 1168 1170 -152.49 -124.80 28.20 1.61 -63.20 -159.27 31.55
48 150T 150T N CA 1170 1171 138.12 143.50 -42.10
49 6384 151G 152G C N 1179 1181 81.60 78.70 4.99 0.08 82.20 178.67 8.70
49 152G 152G N CA 1181 1182 -170.17 -166.10 8.50
50 6385 152G 153M C N 1183 1185 -131.72 -125.60 29.74 1.28 -63.40 164.73 29.98
50 153M 153M N CA 1185 1186 169.60 140.50 -40.50
51 6387 154I 155K C N 1199 1201 56.49 56.60 1.10 0.09 -62.90 142.78 24.87
51 155K 155K N CA 1201 1202 37.51 38.60 -40.80
52 6388 155K 156M C N 1208 1210 -84.43 -73.00 12.52 0.86 -63.40 172.69 27.45
52 156M 156M N CA 1210 1211 148.10 143.00 -40.50
53 6389 156M 157Y C N 1216 1218 -105.12 -98.40 15.18 1.44 -63.50 163.57 23.97
53 157Y 157Y N CA 1218 1219 114.79 128.40 -43.40
54 6390 157Y 158L C N 1228 1230 -126.22 -108.50 32.79 1.54 -63.50 170.65 27.58
54 158L 158L N CA 1230 1231 160.09 132.50 -41.20
55 6393 160I 161G C N 1252 1254 148.70 -167.20 44.70 0.70 82.20 -174.26 12.14
55 161G 161G N CA 1254 1255 -178.07 174.60 8.50
56 6394 161G 162L C N 1256 1258 -100.76 -108.50 11.79 0.67 -63.50 -178.73 27.44
56 162L 162L N CA 1258 1259 141.40 132.50 -41.20
57 6395 162L 163D C N 1264 1266 -90.84 -96.50 20.28 0.85 -63.30 137.51 15.50
57 163D 163D N CA 1266 1267 94.73 114.20 -40.00
58 6396 163D 164N C N 1272 1274 -117.83 -119.90 4.14 0.14 -63.20 -177.14 20.36
58 164N 164N N CA 1274 1275 133.41 137.00 -41.10
59 6397 164N 165S C N 1280 1282 -145.20 -136.60 9.66 0.30 -64.10 -172.20 19.41
59 165S 165S N CA 1282 1283 155.61 151.20 -35.00
60 6398 165S 166G C N 1286 1288 90.14 78.70 40.40 0.71 82.20 146.86 7.53
60 166G 166G N CA 1288 1289 155.15 -166.10 8.50
61 6399 166G 167K C N 1290 1292 -136.51 -118.00 21.61 0.72 -62.90 -175.70 28.34
61 167K 167K N CA 1292 1293 150.24 139.10 -40.80
62 6400 167K 168A C N 1299 1301 -123.28 -134.00 12.20 0.28 -62.50 -171.97 34.06
62 168A 168A N CA 1301 1302 141.16 147.00 -40.90
63 6401 168A 169K C N 1304 1306 -125.48 -118.00 8.97 0.43 -62.90 -174.19 21.59
63 169K 169K N CA 1306 1307 134.15 139.10 -40.80
64 6402 169K 170H C N 1313 1315 -129.99 -125.60 17.00 0.72 -63.20 177.71 19.12
64 170H 170H N CA 1315 1316 122.37 138.80 -42.30
65 6403 170H 171W C N 1323 1325 -136.17 -124.90 18.21 1.04 -63.00 -171.90 20.68
65 171W 171W N CA 1325 1326 129.09 143.40 -44.20
66 6404 171W 172Y C N 1337 1339 -125.76 -124.30 17.78 1.00 -63.50 172.70 24.61
66 172Y 172Y N CA 1339 1340 117.68 135.40 -43.40
67 6406 173V 174S C N 1356 1358 -116.77 -136.60 24.50 0.75 -64.10 179.70 11.09
67 174S 174S N CA 1358 1359 136.80 151.20 -35.00
68 6407 174S 175D C N 1362 1364 -110.06 -96.50 16.66 0.68 -63.30 151.90 16.51
68 175D 175D N CA 1364 1365 104.52 114.20 -40.00
69 6408 175D 176G C N 1370 1372 83.63 78.70 31.65 0.70 82.20 154.14 7.56
69 176G 176G N CA 1372 1373 162.64 -166.10 8.50
70 6410 177V 178S C N 1381 1383 -76.20 -72.40 11.69 0.57 -64.10 161.99 12.50
70 178S 178S N CA 1383 1384 163.46 152.40 -35.00
71 6412 179V 180R C N 1394 1396 -135.49 -125.20 22.40 0.82 -63.00 174.20 28.49
71 180R 180R N CA 1396 1397 160.50 140.60 -41.10
72 6413 180R 181H C N 1405 1407 -87.42 -67.60 52.80 4.56 -63.20 135.55 15.58
72 181H 181H N CA 1407 1408 91.06 140.00 -42.30
73 6416 183R 184T C N 1433 1435 -139.85 -124.80 15.57 0.71 -63.20 -173.15 28.98
73 184T 184T N CA 1435 1436 147.50 143.50 -42.10
74 6417 184T 185I C N 1440 1442 -64.24 -63.40 5.61 0.95 -120.60 -171.90 8.69
74 185I 185I N CA 1442 1443 -49.15 -43.60 130.30
75 6418 185I 186R C N 1448 1450 47.65 57.30 14.57 0.88 -63.00 142.63 25.85
75 186R 186R N CA 1450 1451 48.91 38.00 -41.10
76 6419 186R 187M C N 1459 1461 -67.25 -73.00 5.94 0.42 -63.40 178.04 26.88
76 187M 187M N CA 1461 1462 141.50 143.00 -40.50
77 6420 187M 188L C N 1467 1469 -101.59 -108.50 21.33 1.21 -63.50 170.43 25.99
77 188L 188L N CA 1469 1470 152.68 132.50 -41.20
78 6421 188L 189E C N 1475 1477 -69.10 -69.30 12.55 0.96 -63.60 164.74 22.27
78 189E 189E N CA 1477 1478 155.05 142.50 -40.30
79 6422 189E 190N C N 1484 1486 -60.42 -71.20 11.21 0.88 -63.20 173.03 21.48
79 190N 190N N CA 1486 1487 145.89 142.80 -41.10
80 6423 190N 191Y C N 1492 1494 -95.88 -98.40 3.53 0.29 -63.50 172.40 25.77
80 191Y 191Y N CA 1494 1495 125.93 128.40 -43.40
81 6424 191Y 192Q C N 1504 1506 -143.47 -121.10 25.25 0.78 -63.80 -173.80 31.54
81 192Q 192Q N CA 1506 1507 151.41 139.70 -40.30
82 6425 192Q 193N C N 1513 1515 -80.02 -71.20 15.83 0.84 -63.20 163.82 21.42
82 193N 193N N CA 1515 1516 155.95 142.80 -41.10
83 6426 193N 194K C N 1521 1523 -66.90 -70.20 9.61 0.77 -62.90 169.82 22.27
83 194K 194K N CA 1523 1524 149.42 140.40 -40.80
84 6427 194K 195W C N 1530 1532 -60.48 -71.30 11.17 0.72 -63.00 179.57 22.30
84 195W 195W N CA 1532 1533 136.25 139.00 -44.20
85 6428 195W 196A C N 1544 1546 -66.86 -68.20 2.66 0.25 -62.50 171.56 28.33
85 196A 196A N CA 1546 1547 147.60 145.30 -40.90
86 6429 196A 197K C N 1549 1551 -85.56 -70.20 36.26 2.94 -62.90 150.07 18.37
86 197K 197K N CA 1551 1552 107.55 140.40 -40.80
87 6430 197K 198L C N 1558 1560 -116.91 -108.50 22.54 1.11 -63.50 173.79 27.43
87 198L 198L N CA 1560 1561 153.42 132.50 -41.20
88 6431 198L 199N C N 1566 1568 -107.67 -119.90 19.19 0.58 -63.20 169.25 19.06
88 199N 199N N CA 1568 1569 122.20 137.00 -41.10
89 6432 199N 200L C N 1574 1576 -108.26 -108.50 21.30 1.15 -63.50 158.84 19.98
89 200L 200L N CA 1576 1577 111.20 132.50 -41.20
90 6434 201P 202V C N 1589 1591 -67.08 -62.40 5.13 0.87 -125.40 -178.19 10.15
90 202V 202V N CA 1591 1592 -44.50 -42.40 143.30
91 6435 202V 203D C N 1596 1598 -109.86 -96.50 20.03 0.84 -63.30 175.41 19.31
91 203D 203D N CA 1598 1599 129.12 114.20 -40.00
92 6437 204T 205M C N 1611 1613 -70.09 -73.00 15.54 1.10 -63.40 161.38 24.62
92 205M 205M N CA 1613 1614 158.26 143.00 -40.50
93 6438 205M 206F C N 1619 1621 -63.77 -71.40 23.09 1.62 -63.20 163.21 22.62
93 206F 206F N CA 1621 1622 118.91 140.70 -44.30
94 6439 206F 207I C N 1630 1632 -66.13 -63.40 3.07 0.50 -120.60 -179.10 8.35
94 207I 207I N CA 1632 1633 -42.20 -43.60 130.30
95 6440 207I 208A C N 1638 1640 -58.86 -68.20 12.84 0.81 -62.50 177.42 29.26
95 208A 208A N CA 1640 1641 136.49 145.30 -40.90
96 6441 208A 209E C N 1643 1645 -123.06 -117.80 24.96 1.14 -63.60 169.28 25.93
96 209E 209E N CA 1645 1646 161.20 136.80 -40.30
97 6443 210I 211E C N 1660 1662 -89.98 -69.30 21.85 1.88 -63.60 177.70 22.35
97 211E 211E N CA 1662 1663 135.43 142.50 -40.30
98 6444 211E 212A C N 1669 1671 76.00 -68.20 144.73 11.84 -62.50 -137.68 43.66
98 212A 212A N CA 1671 1672 133.00 145.30 -40.90
99 6446 213E 214F C N 1683 1685 -98.00 -63.20 85.54 9.92 -63.20 85.54 9.92
99 214F 214F N CA 1685 1686 33.84 -44.30 -44.30
100 6447 214F 215G C N 1694 1696 22.77 78.70 92.68 1.64 -62.40 99.27 15.06
100 215G 215G N CA 1696 1697 -92.21 -166.10 -41.20
101 6451 218I 219D C N 1726 1728 51.01 -70.90 130.56 10.89 -70.90 130.56 10.89
101 219D 219D N CA 1728 1729 -162.95 150.30 150.30
102 6452 219D 220M C N 1734 1736 -84.61 -73.00 79.92 5.60 56.30 143.89 23.55
102 220M 220M N CA 1736 1737 63.93 143.00 34.80
103 6454 221A 222S C N 1747 1749 65.78 56.90 9.99 0.86 -64.10 146.07 19.37
103 222S 222S N CA 1749 1750 31.83 36.40 -35.00
104 6455 222S 223G C N 1753 1755 -81.07 -80.20 101.59 4.04 82.20 175.37 8.86
104 223G 223G N CA 1755 1756 72.51 174.10 8.50
105 6457 224E 225V C N 1766 1768 -58.38 -62.40 4.13 0.61 -125.40 -174.13 10.47
105 225V 225V N CA 1768 1769 -43.33 -42.40 143.30
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 22 35 143 168 215 205 216 260 261 266
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 1827
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 14513 14513
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3831
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 : 2252.3091
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 : 1824 0 1 0.007 0.007 23.584 1.000
2 Bond angle potential : 2468 2 23 2.205 2.205 235.46 1.000
3 Stereochemical cosine torsion poten: 1168 0 51 51.865 51.865 485.35 1.000
4 Stereochemical improper torsion pot: 773 0 2 1.587 1.587 39.283 1.000
5 Soft-sphere overlap restraints : 3831 2 4 0.009 0.009 38.312 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) : 2407 9 27 0.551 0.551 288.53 1.000
10 Distance restraints 2 (N-O) : 2568 9 45 0.680 0.680 427.36 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: 225 2 5 4.888 4.888 63.408 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 6 89.748 89.748 85.608 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 3 88.617 88.617 83.788 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 98.620 98.620 46.828 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 78.759 78.759 13.648 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 905 0 0 0.450 0.450 13.701 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: 224 100 34 40.379 116.150 311.01 1.000
26 Distance restraints 4 (SDCH-SDCH) : 130 0 1 1.081 1.081 15.119 1.000
27 Distance restraints 5 (X-Y) : 1401 1 9 0.087 0.087 81.323 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: red1.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: 39051.0312
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 2516 63Y 63Y N CA 495 496 125.21 107.00 18.21 5.24 107.00 18.21 5.24
2 2995 106Y 107C C N 833 835 139.99 120.00 19.99 4.54 120.00 19.99 4.54
-------------------------------------------------------------------------------------------------
Feature 9 : Distance restraints 1 (CA-CA)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 8944 95V 111I CA CA 742 861 6.44 4.98 1.46 4.82 4.98 1.46 4.82
2 9048 105A 108A CA CA 819 842 7.54 5.15 2.39 4.76 5.15 2.39 4.76
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 11085 106Y 63Y N O 823 506 5.52 2.86 2.66 5.30 2.86 2.66 5.30
2 11130 108A 105A N O 841 822 6.80 3.15 3.65 6.96 3.15 3.65 6.96
3 11148 109S 105A N O 846 822 8.08 5.07 3.00 5.25 5.07 3.00 5.25
-------------------------------------------------------------------------------------------------
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 6251 18R 19L C N 141 143 64.37 60.20 8.82 0.31 -63.50 142.56 26.28
1 19L 19L N CA 143 144 21.83 29.60 -41.20
2 6253 20T 21A C N 156 158 54.61 55.40 2.70 0.23 -62.50 139.89 28.41
2 21A 21A N CA 158 159 35.62 38.20 -40.90
3 6254 21A 22Y C N 161 163 65.59 55.90 15.11 0.82 -63.50 147.48 27.81
3 22Y 22Y N CA 163 164 27.91 39.50 -43.40
4 6265 32T 33I C N 262 264 -85.97 -120.60 64.78 4.90 -63.40 133.28 22.67
4 33I 33I N CA 264 265 -174.95 130.30 -43.60
5 6266 33I 34G C N 270 272 79.13 78.70 67.24 1.93 -62.40 152.83 24.40
5 34G 34G N CA 272 273 -98.86 -166.10 -41.20
6 6270 37H 38Y C N 302 304 63.19 55.90 14.82 0.71 -63.50 144.74 27.29
6 38Y 38Y N CA 304 305 26.59 39.50 -43.40
7 6281 48Q 49A C N 385 387 142.76 55.40 98.07 7.67 -62.50 158.55 28.83
7 49A 49A N CA 387 388 -6.37 38.20 -40.90
8 6288 55L 56E C N 435 437 154.38 -63.60 144.67 21.55 -63.60 144.67 21.55
8 56E 56E N CA 437 438 -12.74 -40.30 -40.30
9 6295 62K 63Y C N 493 495 -67.46 -98.40 41.67 3.33 -63.50 143.94 22.64
9 63Y 63Y N CA 495 496 100.48 128.40 -43.40
10 6296 63Y 64A C N 505 507 130.23 -134.00 97.04 2.66 -62.50 -130.95 45.94
10 64A 64A N CA 507 508 162.63 147.00 -40.90
11 6298 65P 66M C N 517 519 -126.99 -125.60 4.61 0.24 -63.40 -172.30 23.95
11 66M 66M N CA 519 520 136.10 140.50 -40.50
12 6300 67V 68D C N 532 534 -74.17 -70.90 8.63 0.59 -63.30 178.02 22.64
12 68D 68D N CA 534 535 142.31 150.30 -40.00
13 6301 68D 69A C N 540 542 -117.09 -134.00 22.45 0.63 -62.50 -178.48 27.64
13 69A 69A N CA 542 543 132.22 147.00 -40.90
14 6302 69A 70Y C N 545 547 -131.09 -124.30 8.19 0.42 -63.50 -170.89 33.39
14 70Y 70Y N CA 547 548 139.98 135.40 -43.40
15 6304 71V 72K C N 564 566 -132.06 -118.00 20.67 0.74 -62.90 178.85 27.36
15 72K 72K N CA 566 567 154.26 139.10 -40.80
16 6305 72K 73G C N 573 575 -179.95 -167.20 24.53 0.99 82.20 175.04 12.74
16 73G 73G N CA 575 576 153.64 174.60 8.50
17 6306 73G 74K C N 577 579 -119.96 -118.00 6.79 0.30 -62.90 -177.27 27.13
17 74K 74K N CA 579 580 145.61 139.10 -40.80
18 6307 74K 75A C N 586 588 -120.70 -134.00 15.74 0.38 -62.50 -171.33 28.69
18 75A 75A N CA 588 589 138.57 147.00 -40.90
19 6308 75A 76N C N 591 593 -128.91 -119.90 13.13 0.39 -63.20 -175.54 26.80
19 76N 76N N CA 593 594 146.55 137.00 -41.10
20 6309 76N 77Q C N 599 601 -75.93 -73.00 21.31 1.45 -63.80 160.35 22.96
20 77Q 77Q N CA 601 602 119.59 140.70 -40.30
21 6310 77Q 78N C N 608 610 -158.39 -119.90 43.80 1.33 -63.20 -172.96 28.68
21 78N 78N N CA 610 611 157.89 137.00 -41.10
22 6311 78N 79E C N 616 618 -95.80 -117.80 42.88 1.62 -63.60 143.95 17.62
22 79E 79E N CA 618 619 100.00 136.80 -40.30
23 6312 79E 80F C N 625 627 -151.35 -124.20 30.00 0.83 -63.20 -177.65 30.92
23 80F 80F N CA 627 628 156.07 143.30 -44.30
24 6313 80F 81D C N 636 638 -110.63 -96.50 29.85 1.24 -63.30 136.39 14.68
24 81D 81D N CA 638 639 87.91 114.20 -40.00
25 6314 81D 82A C N 644 646 -135.44 -134.00 7.14 0.43 -62.50 -166.62 35.60
25 82A 82A N CA 646 647 140.01 147.00 -40.90
26 6315 82A 83L C N 649 651 -126.24 -108.50 17.81 0.83 -63.50 -173.77 23.13
26 83L 83L N CA 651 652 134.14 132.50 -41.20
27 6317 84V 85S C N 664 666 -137.97 -136.60 6.88 0.37 -64.10 -165.93 12.04
27 85S 85S N CA 666 667 144.45 151.20 -35.00
28 6318 85S 86L C N 670 672 -121.13 -108.50 13.42 0.70 -63.50 178.71 22.27
28 86L 86L N CA 672 673 127.97 132.50 -41.20
29 6319 86L 87A C N 678 680 -146.54 -134.00 12.88 0.33 -62.50 -171.08 35.46
29 87A 87A N CA 680 681 149.91 147.00 -40.90
30 6320 87A 88Y C N 683 685 -124.35 -124.30 5.86 0.31 -63.50 -176.66 26.31
30 88Y 88Y N CA 685 686 129.54 135.40 -43.40
31 6321 88Y 89N C N 695 697 -124.30 -119.90 14.65 0.75 -63.20 175.13 19.23
31 89N 89N N CA 697 698 123.02 137.00 -41.10
32 6323 90C 91G C N 709 711 -79.04 -80.20 24.19 0.89 82.20 -145.52 7.24
32 91G 91G N CA 711 712 149.94 174.10 8.50
33 6324 91G 92N C N 713 715 -129.60 -119.90 10.98 0.57 -63.20 -174.72 20.30
33 92N 92N N CA 715 716 131.88 137.00 -41.10
34 6325 92N 93V C N 721 723 -114.29 -62.40 66.82 8.01 -125.40 144.03 6.88
34 93V 93V N CA 723 724 -0.29 -42.40 143.30
35 6326 93V 94F C N 728 730 -133.47 -124.20 22.61 0.80 -63.20 167.25 27.78
35 94F 94F N CA 730 731 163.93 143.30 -44.30
36 6331 98G 99W C N 763 765 -120.37 -124.90 101.36 4.81 -63.00 103.66 11.56
36 99W 99W N CA 765 766 42.14 143.40 -44.20
37 6336 103S 104H C N 806 808 -118.66 -125.60 78.27 3.10 -63.20 115.17 17.99
37 104H 104H N CA 808 809 -143.24 138.80 -42.30
38 6337 104H 105A C N 816 818 -179.26 -134.00 126.66 5.83 -62.50 128.56 26.11
38 105A 105A N CA 818 819 -94.70 147.00 -40.90
39 6338 105A 106Y C N 821 823 -125.50 -124.30 15.83 0.89 -63.50 174.41 24.88
39 106Y 106Y N CA 823 824 119.61 135.40 -43.40
40 6339 106Y 107C C N 833 835 41.13 -63.00 149.88 25.74 -63.00 149.88 25.74
40 107C 107C N CA 835 836 66.70 -41.10 -41.10
41 6340 107C 108A C N 839 841 47.65 55.40 12.18 0.56 -62.50 141.30 28.54
41 108A 108A N CA 841 842 47.60 38.20 -40.90
42 6366 133L 134N C N 1042 1044 -89.55 -119.90 55.66 1.77 -63.20 134.05 15.45
42 134N 134N N CA 1044 1045 90.34 137.00 -41.10
43 6367 134N 135L C N 1050 1052 -46.60 -63.50 75.41 9.64 -108.50 128.67 7.33
43 135L 135L N CA 1052 1053 -114.69 -41.20 132.50
44 6379 146Q 147N C N 1143 1145 -61.68 -63.20 1.95 0.32 -119.90 -173.79 7.00
44 147N 147N N CA 1145 1146 -39.87 -41.10 137.00
45 6380 147N 148N C N 1151 1153 -62.77 -63.20 5.07 0.61 55.90 146.35 17.87
45 148N 148N N CA 1153 1154 -46.15 -41.10 39.50
46 6382 149Q 150T C N 1168 1170 -160.31 -124.80 67.57 2.10 -63.20 151.98 25.40
46 150T 150T N CA 1170 1171 -159.01 143.50 -42.10
47 6383 150T 151G C N 1175 1177 -78.94 -80.20 4.30 0.23 82.20 -125.97 7.12
47 151G 151G N CA 1177 1178 178.21 174.10 8.50
48 6384 151G 152G C N 1179 1181 99.61 78.70 28.20 0.69 82.20 167.38 8.99
48 152G 152G N CA 1181 1182 174.97 -166.10 8.50
49 6385 152G 153M C N 1183 1185 -71.01 -73.00 6.16 0.45 -63.40 170.84 26.10
49 153M 153M N CA 1185 1186 148.83 143.00 -40.50
50 6387 154I 155K C N 1199 1201 -135.40 -118.00 53.42 2.75 -62.90 148.32 17.05
50 155K 155K N CA 1201 1202 88.59 139.10 -40.80
51 6388 155K 156M C N 1208 1210 -144.93 -125.60 29.86 0.95 -63.40 176.23 32.68
51 156M 156M N CA 1210 1211 163.26 140.50 -40.50
52 6389 156M 157Y C N 1216 1218 -106.22 -98.40 30.55 3.12 -63.50 148.55 21.57
52 157Y 157Y N CA 1218 1219 98.87 128.40 -43.40
53 6390 157Y 158L C N 1228 1230 -133.09 -108.50 28.30 1.25 -63.50 -174.18 30.11
53 158L 158L N CA 1230 1231 146.50 132.50 -41.20
54 6393 160I 161G C N 1252 1254 -178.24 -167.20 26.42 1.08 82.20 173.50 12.71
54 161G 161G N CA 1254 1255 150.59 174.60 8.50
55 6394 161G 162L C N 1256 1258 -76.83 -70.70 6.14 0.55 -63.50 177.36 25.41
55 162L 162L N CA 1258 1259 141.94 141.60 -41.20
56 6395 162L 163D C N 1264 1266 -102.44 -96.50 16.00 0.67 -63.30 144.74 15.91
56 163D 163D N CA 1266 1267 99.35 114.20 -40.00
57 6396 163D 164N C N 1272 1274 -126.46 -119.90 8.18 0.44 -63.20 -175.58 20.28
57 164N 164N N CA 1274 1275 132.13 137.00 -41.10
58 6397 164N 165S C N 1280 1282 -144.20 -136.60 7.81 0.27 -64.10 -170.27 19.47
58 165S 165S N CA 1282 1283 153.00 151.20 -35.00
59 6398 165S 166G C N 1286 1288 89.92 78.70 44.23 0.82 82.20 142.82 7.32
59 166G 166G N CA 1288 1289 151.12 -166.10 8.50
60 6399 166G 167K C N 1290 1292 -133.19 -118.00 19.05 0.64 -62.90 -177.33 27.93
60 167K 167K N CA 1292 1293 150.60 139.10 -40.80
61 6400 167K 168A C N 1299 1301 -117.41 -134.00 22.33 0.63 -62.50 -178.54 27.62
61 168A 168A N CA 1301 1302 132.05 147.00 -40.90
62 6401 168A 169K C N 1304 1306 -135.17 -118.00 17.19 0.64 -62.90 -166.67 29.43
62 169K 169K N CA 1306 1307 139.89 139.10 -40.80
63 6402 169K 170H C N 1313 1315 -139.70 -125.60 18.80 0.85 -63.20 -174.80 19.80
63 170H 170H N CA 1315 1316 126.36 138.80 -42.30
64 6403 170H 171W C N 1323 1325 -132.49 -124.90 15.25 0.87 -63.00 -172.30 20.68
64 171W 171W N CA 1325 1326 130.17 143.40 -44.20
65 6404 171W 172Y C N 1337 1339 -129.41 -124.30 8.01 0.63 -63.50 -175.22 26.36
65 172Y 172Y N CA 1339 1340 129.23 135.40 -43.40
66 6406 173V 174S C N 1356 1358 -136.59 -136.60 13.16 0.67 -64.10 -172.39 11.66
66 174S 174S N CA 1358 1359 138.03 151.20 -35.00
67 6407 174S 175D C N 1362 1364 -136.18 -96.50 43.04 1.78 -63.30 -174.25 19.83
67 175D 175D N CA 1364 1365 130.86 114.20 -40.00
68 6408 175D 176G C N 1370 1372 134.52 -167.20 61.15 1.65 82.20 156.56 10.07
68 176G 176G N CA 1372 1373 156.07 174.60 8.50
69 6410 177V 178S C N 1381 1383 -125.28 -136.60 17.28 0.58 -64.10 -176.36 11.31
69 178S 178S N CA 1383 1384 138.14 151.20 -35.00
70 6412 179V 180R C N 1394 1396 -107.32 -125.20 18.36 0.63 -63.00 -177.03 22.08
70 180R 180R N CA 1396 1397 136.42 140.60 -41.10
71 6413 180R 181H C N 1405 1407 -99.33 -125.60 63.81 1.88 -63.20 128.15 14.15
71 181H 181H N CA 1407 1408 80.65 138.80 -42.30
72 6415 182V 183R C N 1422 1424 -126.06 -125.20 45.79 2.23 -63.00 149.83 17.11
72 183R 183R N CA 1424 1425 94.82 140.60 -41.10
73 6418 185I 186R C N 1448 1450 -60.04 -72.10 12.30 0.99 -63.00 174.61 23.39
73 186R 186R N CA 1450 1451 144.32 141.90 -41.10
74 6419 186R 187M C N 1459 1461 -69.47 -73.00 3.54 0.27 -63.40 176.38 26.81
74 187M 187M N CA 1461 1462 143.23 143.00 -40.50
75 6420 187M 188L C N 1467 1469 -78.37 -70.70 13.78 0.85 -63.50 166.42 23.99
75 188L 188L N CA 1469 1470 153.05 141.60 -41.20
76 6421 188L 189E C N 1475 1477 -72.34 -69.30 4.88 0.28 -63.60 173.60 23.63
76 189E 189E N CA 1477 1478 146.31 142.50 -40.30
77 6422 189E 190N C N 1484 1486 -134.02 -119.90 17.84 0.52 -63.20 -174.90 27.16
77 190N 190N N CA 1486 1487 147.89 137.00 -41.10
78 6423 190N 191Y C N 1492 1494 -123.90 -124.30 11.41 0.62 -63.50 -179.78 31.64
78 191Y 191Y N CA 1494 1495 146.80 135.40 -43.40
79 6424 191Y 192Q C N 1504 1506 -73.26 -73.00 0.67 0.05 -63.80 179.86 26.95
79 192Q 192Q N CA 1506 1507 140.09 140.70 -40.30
80 6425 192Q 193N C N 1513 1515 -79.06 -71.20 8.26 0.65 -63.20 179.34 23.31
80 193N 193N N CA 1515 1516 140.27 142.80 -41.10
81 6426 193N 194K C N 1521 1523 -125.84 -118.00 24.56 1.06 -62.90 168.98 25.71
81 194K 194K N CA 1523 1524 162.38 139.10 -40.80
82 6427 194K 195W C N 1530 1532 83.74 -124.90 151.42 6.56 -63.00 -136.85 25.88
82 195W 195W N CA 1532 1533 147.68 143.40 -44.20
83 6428 195W 196A C N 1544 1546 -171.18 -134.00 40.49 0.92 -62.50 -169.81 36.91
83 196A 196A N CA 1546 1547 163.02 147.00 -40.90
84 6429 196A 197K C N 1549 1551 -69.34 -70.20 16.81 1.20 -62.90 164.53 21.02
84 197K 197K N CA 1551 1552 123.61 140.40 -40.80
85 6430 197K 198L C N 1558 1560 -117.89 -108.50 11.30 0.62 -63.50 176.02 21.99
85 198L 198L N CA 1560 1561 126.21 132.50 -41.20
86 6431 198L 199N C N 1566 1568 -113.44 -119.90 11.79 0.37 -63.20 175.58 19.62
86 199N 199N N CA 1568 1569 127.14 137.00 -41.10
87 6432 199N 200L C N 1574 1576 -90.81 -108.50 17.72 0.83 -63.50 174.84 22.85
87 200L 200L N CA 1576 1577 131.49 132.50 -41.20
88 6435 202V 203D C N 1596 1598 -81.10 -70.90 26.83 0.92 -63.30 145.98 19.14
88 203D 203D N CA 1598 1599 175.11 150.30 -40.00
89 6436 203D 204T C N 1604 1606 -85.05 -78.10 58.28 2.72 -63.20 135.80 16.06
89 204T 204T N CA 1606 1607 91.93 149.80 -42.10
90 6437 204T 205M C N 1611 1613 -136.59 -125.60 24.76 1.34 -63.40 174.87 21.83
90 205M 205M N CA 1613 1614 118.32 140.50 -40.50
91 6438 205M 206F C N 1619 1621 -171.62 -63.20 113.66 16.10 -63.20 113.66 16.10
91 206F 206F N CA 1621 1622 -10.18 -44.30 -44.30
92 6440 207I 208A C N 1638 1640 -69.88 -68.20 7.25 0.64 -62.50 179.30 29.03
92 208A 208A N CA 1640 1641 138.25 145.30 -40.90
93 6443 210I 211E C N 1660 1662 -128.62 -63.60 69.17 11.77 -63.60 69.17 11.77
93 211E 211E N CA 1662 1663 -63.90 -40.30 -40.30
94 6444 211E 212A C N 1669 1671 105.47 -134.00 127.11 3.00 -62.50 -146.53 33.97
94 212A 212A N CA 1671 1672 -172.64 147.00 -40.90
95 6445 212A 213E C N 1674 1676 150.62 -63.60 145.90 23.41 -117.80 -160.60 7.82
95 213E 213E N CA 1676 1677 -46.08 -40.30 136.80
96 6446 213E 214F C N 1683 1685 130.71 -124.20 134.41 7.26 -63.20 -164.13 24.58
96 214F 214F N CA 1685 1686 59.51 143.30 -44.30
97 6451 218I 219D C N 1726 1728 45.48 -70.90 127.68 10.70 -70.90 127.68 10.70
97 219D 219D N CA 1728 1729 -157.19 150.30 150.30
98 6452 219D 220M C N 1734 1736 -84.39 -73.00 86.34 6.03 56.30 142.49 23.87
98 220M 220M N CA 1736 1737 57.41 143.00 34.80
99 6454 221A 222S C N 1747 1749 157.29 -136.60 122.11 4.47 -64.10 155.79 20.67
99 222S 222S N CA 1749 1750 -106.13 151.20 -35.00
100 6456 223G 224E C N 1757 1759 -122.73 -117.80 16.91 0.74 -63.60 176.90 26.93
100 224E 224E N CA 1759 1760 152.97 136.80 -40.30
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 13422 94F 229. CA O4 731 1823 10.12 9.21 0.92 4.58 9.21 0.92 4.58
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 2 19 40 159 156 213 237 222 248 207 253
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
# ALGNMT CODE
1 red1
2 red1
83 atoms selected for loop refinement
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.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 399 330
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2208
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 212.1127
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 : 85 0 0 0.004 0.004 0.42863 1.000
2 Bond angle potential : 113 0 1 2.395 2.395 12.097 1.000
3 Stereochemical cosine torsion poten: 55 0 6 56.831 56.831 25.937 1.000
4 Stereochemical improper torsion pot: 31 0 0 1.343 1.343 1.0142 1.000
5 Soft-sphere overlap restraints : 2208 0 0 0.001 0.001 0.20957 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 12 0 1 5.841 5.841 4.8319 1.000
14 Sidechain Chi_1 dihedral restraints: 8 0 0 92.836 92.836 3.6353 1.000
15 Sidechain Chi_2 dihedral restraints: 7 0 0 76.324 76.324 4.5729 1.000
16 Sidechain Chi_3 dihedral restraints: 4 0 0 140.105 140.105 3.8788 1.000
17 Sidechain Chi_4 dihedral restraints: 2 0 0 58.398 58.398 1.0524 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 13 9 8 87.185 136.772 64.439 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 2208 0 20 1.904 1.904 90.016 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 285 211E 212A C N 1669 1671 76.00 -68.20 144.72 11.84 -62.50 -137.70 43.68
1 212A 212A N CA 1671 1672 132.99 145.30 -40.90
2 286 212A 213E C N 1674 1676 162.91 -117.80 79.87 2.70 -63.60 -141.26 36.31
2 213E 213E N CA 1676 1677 146.42 136.80 -40.30
3 287 213E 214F C N 1683 1685 -97.97 -63.20 85.55 9.93 -63.20 85.55 9.93
3 214F 214F N CA 1685 1686 33.86 -44.30 -44.30
4 288 214F 215G C N 1694 1696 22.68 78.70 92.75 1.65 82.20 116.95 8.32
4 215G 215G N CA 1696 1697 -92.18 -166.10 8.50
5 291 217K 218I C N 1718 1720 -68.36 -63.40 4.97 0.88 -120.60 -178.73 8.44
5 218I 218I N CA 1720 1721 -43.28 -43.60 130.30
6 292 218I 219D C N 1726 1728 50.99 -70.90 130.55 10.89 -63.30 167.86 18.71
6 219D 219D N CA 1728 1729 -162.94 150.30 -40.00
7 293 219D 220M C N 1734 1736 -84.61 -73.00 79.91 5.60 -63.40 106.57 14.39
7 220M 220M N CA 1736 1737 63.93 143.00 -40.50
8 295 221A 222S C N 1747 1749 65.79 -64.10 146.05 19.37 -64.10 146.05 19.37
8 222S 222S N CA 1749 1750 31.78 -35.00 -35.00
9 296 222S 223G C N 1753 1755 -81.02 -80.20 101.59 4.04 82.20 175.32 8.86
9 223G 223G N CA 1755 1756 72.51 174.10 8.50
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 1785 1809 1.523
serious non-bonded atom clash: 1796 1809 2.252
serious non-bonded atom clash: 1799 1816 2.150
serious non-bonded atom clash: 1799 1823 1.402
serious non-bonded atom clash: 1800 1823 2.289
serious non-bonded atom clash: 1810 1823 2.107
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: 2 2 2 0 0 22 35 143 168 215 205 215 260 262 266
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2199
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 8.0191
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 : 85 0 0 0.009 0.009 2.0908 1.000
2 Bond angle potential : 113 0 1 2.411 2.411 12.580 1.000
3 Stereochemical cosine torsion poten: 55 0 2 40.257 40.257 15.422 1.000
4 Stereochemical improper torsion pot: 31 0 0 1.582 1.582 2.2584 1.000
5 Soft-sphere overlap restraints : 2199 0 0 0.000 0.000 0.0000 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 12 0 0 4.694 4.694 3.1202 1.000
14 Sidechain Chi_1 dihedral restraints: 8 0 0 90.060 90.060 2.2619 1.000
15 Sidechain Chi_2 dihedral restraints: 7 0 0 38.715 38.715 2.3371 1.000
16 Sidechain Chi_3 dihedral restraints: 4 0 0 127.486 127.486 4.1637 1.000
17 Sidechain Chi_4 dihedral restraints: 2 0 0 62.197 62.197 1.5094 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 13 8 4 49.902 132.709 28.868 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 2199 0 2 1.833 1.833 -66.594 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 285 211E 212A C N 1669 1671 76.00 -68.20 144.23 12.12 -62.50 -135.39 34.02
1 212A 212A N CA 1671 1672 142.28 145.30 -40.90
2 287 213E 214F C N 1683 1685 -55.28 -71.40 30.43 1.93 -63.20 159.39 22.67
2 214F 214F N CA 1685 1686 114.89 140.70 -44.30
3 289 215G 216R C N 1698 1700 -86.31 -72.10 14.35 1.05 -63.00 176.57 25.46
3 216R 216R N CA 1700 1701 143.87 141.90 -41.10
4 292 218I 219D C N 1726 1728 -109.08 -63.30 63.63 10.62 -63.30 63.63 10.62
4 219D 219D N CA 1728 1729 -84.19 -40.00 -40.00
5 293 219D 220M C N 1734 1736 -84.24 -73.00 29.75 1.87 -63.40 150.40 24.11
5 220M 220M N CA 1736 1737 170.55 143.00 -40.50
6 294 220M 221A C N 1742 1744 -55.55 -68.20 37.37 2.58 -62.50 151.19 25.13
6 221A 221A N CA 1744 1745 110.13 145.30 -40.90
7 295 221A 222S C N 1747 1749 -131.31 -136.60 31.80 1.71 -64.10 157.50 16.22
7 222S 222S N CA 1749 1750 -177.44 151.20 -35.00
8 296 222S 223G C N 1753 1755 -91.30 -80.20 40.54 2.15 82.20 -145.22 8.10
8 223G 223G N CA 1755 1756 135.11 174.10 8.50
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 1785 1809 1.523
serious non-bonded atom clash: 1796 1809 2.252
serious non-bonded atom clash: 1799 1816 2.150
serious non-bonded atom clash: 1799 1823 1.402
serious non-bonded atom clash: 1800 1823 2.289
serious non-bonded atom clash: 1810 1823 2.107
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: 2 2 2 0 0 23 32 145 166 207 206 212 258 262 277
<< 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: LYS:OXT LYS
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 21866
Dynamic pairs routine : 5, NATM_SEL 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 : -960.6663
<< end of ENERGY.
DOPE score : -960.666321
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C +N
atom indices : 1782 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 9 226
atom names : C CA +N O
atom indices : 1782 1776 0 1783
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
# ALGNMT CODE
1 red1
2 red1
83 atoms selected for loop refinement
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.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 399 330
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2199
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 185.4746
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 : 85 0 0 0.006 0.006 0.76081 1.000
2 Bond angle potential : 113 0 0 2.062 2.062 8.6176 1.000
3 Stereochemical cosine torsion poten: 55 0 6 60.713 60.713 27.535 1.000
4 Stereochemical improper torsion pot: 31 0 0 2.053 2.053 2.3463 1.000
5 Soft-sphere overlap restraints : 2199 0 0 0.001 0.001 0.30765 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 12 0 0 3.297 3.297 1.5391 1.000
14 Sidechain Chi_1 dihedral restraints: 8 0 1 89.546 89.546 10.408 1.000
15 Sidechain Chi_2 dihedral restraints: 7 0 0 52.177 52.177 3.6795 1.000
16 Sidechain Chi_3 dihedral restraints: 4 0 0 109.590 109.590 2.7984 1.000
17 Sidechain Chi_4 dihedral restraints: 2 0 0 69.872 69.872 1.6343 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 13 9 6 85.956 150.082 63.762 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 2199 0 13 1.891 1.891 62.086 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 285 211E 212A C N 1669 1671 105.49 -134.00 127.09 3.00 -62.50 -146.51 33.99
1 212A 212A N CA 1671 1672 -172.66 147.00 -40.90
2 286 212A 213E C N 1674 1676 150.62 -63.60 145.89 23.42 -63.60 145.89 23.42
2 213E 213E N CA 1676 1677 -46.10 -40.30 -40.30
3 287 213E 214F C N 1683 1685 130.71 -124.20 134.38 7.26 -63.20 -164.11 24.57
3 214F 214F N CA 1685 1686 59.56 143.30 -44.30
4 288 214F 215G C N 1694 1696 -68.88 -62.40 6.87 1.11 82.20 158.35 11.97
4 215G 215G N CA 1696 1697 -38.93 -41.20 8.50
5 291 217K 218I C N 1718 1720 -72.50 -63.40 9.10 1.62 -120.60 -179.77 8.52
5 218I 218I N CA 1720 1721 -43.40 -43.60 130.30
6 292 218I 219D C N 1726 1728 45.46 -70.90 127.64 10.70 -63.30 159.91 17.82
6 219D 219D N CA 1728 1729 -157.23 150.30 -40.00
7 293 219D 220M C N 1734 1736 -84.38 -73.00 86.29 6.03 -63.40 100.18 13.46
7 220M 220M N CA 1736 1737 57.46 143.00 -40.50
8 295 221A 222S C N 1747 1749 157.32 -136.60 122.08 4.47 -64.10 155.78 20.66
8 222S 222S N CA 1749 1750 -106.15 151.20 -35.00
9 297 223G 224E C N 1757 1759 -122.71 -117.80 16.94 0.74 -63.60 176.86 26.92
9 224E 224E N CA 1759 1760 153.01 136.80 -40.30
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 1785 1809 1.496
serious non-bonded atom clash: 1796 1809 2.233
serious non-bonded atom clash: 1799 1816 2.138
serious non-bonded atom clash: 1799 1823 1.379
serious non-bonded atom clash: 1800 1823 2.291
serious non-bonded atom clash: 1810 1823 2.097
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: 3 1 2 0 2 19 40 159 156 213 236 222 249 208 253
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4831
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2473.6514
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 : 85 12 17 0.113 0.113 308.13 1.000
2 Bond angle potential : 113 16 32 12.551 12.551 318.21 1.000
3 Stereochemical cosine torsion poten: 55 0 8 59.141 59.141 37.233 1.000
4 Stereochemical improper torsion pot: 31 4 7 13.465 13.465 97.535 1.000
5 Soft-sphere overlap restraints : 4831 41 56 0.038 0.038 838.52 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 12 1 3 20.558 20.558 59.855 1.000
14 Sidechain Chi_1 dihedral restraints: 8 0 0 113.065 113.065 5.7725 1.000
15 Sidechain Chi_2 dihedral restraints: 7 0 0 73.205 73.205 6.9463 1.000
16 Sidechain Chi_3 dihedral restraints: 4 0 0 113.065 113.065 4.0293 1.000
17 Sidechain Chi_4 dihedral restraints: 2 0 0 89.837 89.837 1.6875 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 13 11 7 84.796 171.301 62.545 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 4830 0 157 1.913 1.913 733.19 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 26 215G 216R C N 1698 1700 1.49 1.35 0.14 5.07 1.35 0.14 5.07
2 34 216R 216R N CA 1700 1701 1.71 1.43 0.28 9.28 1.43 0.28 9.28
3 36 216R 216R C CA 1709 1701 2.07 1.49 0.58 16.93 1.49 0.58 16.93
4 37 216R 217K C N 1709 1711 1.64 1.35 0.30 10.49 1.35 0.30 10.49
5 38 217K 217K CB CA 1713 1712 1.72 1.54 0.18 4.94 1.54 0.18 4.94
6 43 217K 217K N CA 1711 1712 1.70 1.43 0.27 8.97 1.43 0.27 8.97
7 47 218I 218I CB CA 1722 1721 1.76 1.50 0.26 7.11 1.50 0.26 7.11
8 53 218I 218I C CA 1726 1721 1.78 1.49 0.29 8.30 1.49 0.29 8.30
9 54 218I 219D C N 1726 1728 1.47 1.35 0.13 4.60 1.35 0.13 4.60
10 61 219D 219D C CA 1734 1729 1.82 1.49 0.33 9.73 1.49 0.33 9.73
11 62 219D 220M C N 1734 1736 1.52 1.35 0.18 6.32 1.35 0.18 6.32
12 67 220M 220M N CA 1736 1737 1.61 1.43 0.18 5.98 1.43 0.18 5.98
-------------------------------------------------------------------------------------------------
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
1 120 215G 216R C N 1698 1700 158.94 120.00 38.94 8.85 120.00 38.94 8.85
2 127 216R 216R CB CG 1702 1703 134.72 113.60 21.12 5.18 113.60 21.12 5.18
3 134 216R 217K C N 1709 1711 157.91 120.00 37.91 8.61 120.00 37.91 8.61
4 136 217K 217K N CA 1711 1712 136.95 113.50 23.45 6.30 113.50 23.45 6.30
5 138 217K 217K CA CB 1712 1713 138.10 113.50 24.60 6.04 113.50 24.60 6.04
6 149 218I 218I CA CB 1721 1722 136.72 111.00 25.72 6.04 111.00 25.72 6.04
7 150 218I 218I CA CB 1721 1722 128.46 108.50 19.96 4.68 108.50 19.96 4.68
8 156 218I 219D C N 1726 1728 154.33 120.00 34.33 7.80 120.00 34.33 7.80
9 159 219D 219D N CA 1728 1729 136.28 107.00 29.28 8.41 107.00 29.28 8.41
10 167 219D 220M C N 1734 1736 177.04 120.00 57.04 12.96 120.00 57.04 12.96
11 169 220M 220M N CA 1736 1737 132.79 113.50 19.29 5.18 113.50 19.29 5.18
12 170 220M 220M N CA 1736 1737 124.21 107.00 17.21 4.94 107.00 17.21 4.94
13 171 220M 220M CA CB 1737 1738 134.35 113.50 20.85 5.12 113.50 20.85 5.12
-------------------------------------------------------------------------------------------------
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
1 303 217K 217K CA C 1712 1718 -116.49 180.00 63.51 12.70 180.00 63.51 12.70
-------------------------------------------------------------------------------------------------
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
1 285 211E 212A C N 1669 1671 105.49 -134.00 123.96 3.14 -62.50 -139.33 34.77
1 212A 212A N CA 1671 1672 176.01 147.00 -40.90
2 286 212A 213E C N 1674 1676 156.34 -117.80 109.19 5.64 -63.60 177.87 22.03
2 213E 213E N CA 1676 1677 69.35 136.80 -40.30
3 287 213E 214F C N 1683 1685 -138.78 -124.20 32.34 1.77 -63.20 175.81 20.27
3 214F 214F N CA 1685 1686 114.43 143.30 -44.30
4 288 214F 215G C N 1694 1696 -101.48 -80.20 26.83 1.02 82.20 -109.41 7.80
4 215G 215G N CA 1696 1697 -169.56 174.10 8.50
5 290 216R 217K C N 1709 1711 -98.49 -118.00 21.96 1.02 -62.90 173.71 24.64
5 217K 217K N CA 1711 1712 149.18 139.10 -40.80
6 292 218I 219D C N 1726 1728 99.50 54.50 143.63 7.50 -63.30 172.00 24.09
6 219D 219D N CA 1728 1729 -95.50 40.90 -40.00
7 293 219D 220M C N 1734 1736 131.69 -125.60 130.67 3.88 -63.40 -168.05 39.02
7 220M 220M N CA 1736 1737 -138.72 140.50 -40.50
8 294 220M 221A C N 1742 1744 -70.86 -68.20 44.50 3.49 -62.50 129.65 21.67
8 221A 221A N CA 1744 1745 -170.28 145.30 -40.90
9 295 221A 222S C N 1747 1749 59.46 -72.40 140.72 8.41 -64.10 -174.59 22.31
9 222S 222S N CA 1749 1750 103.24 152.40 -35.00
10 296 222S 223G C N 1753 1755 96.17 78.70 41.65 0.62 82.20 148.26 7.89
10 223G 223G N CA 1755 1756 156.10 -166.10 8.50
11 297 223G 224E C N 1757 1759 -134.66 -117.80 23.39 0.74 -63.60 -178.80 28.16
11 224E 224E N CA 1759 1760 153.01 136.80 -40.30
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 190 1719 2.152
serious non-bonded atom clash: 194 1736 2.290
serious non-bonded atom clash: 218 1700 2.200
serious non-bonded atom clash: 218 1701 1.849
serious non-bonded atom clash: 218 1709 2.052
serious non-bonded atom clash: 1785 1809 1.496
serious non-bonded atom clash: 1796 1809 2.233
serious non-bonded atom clash: 1799 1816 2.138
serious non-bonded atom clash: 1799 1823 1.379
serious non-bonded atom clash: 1800 1823 2.291
serious non-bonded atom clash: 1810 1823 2.097
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: 5 2 4 5 10 42 66 173 181 238 260 253 270 251 291
<< end of ENERGY.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: LYS:OXT LYS
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1827 83
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 330 330
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 34566
Dynamic pairs routine : 5, NATM_SEL 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 : 555.3052
<< end of ENERGY.
DOPE score : 555.305237
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
red1.B99990001.pdb 1925.41797
red1.B99990002.pdb 2252.30908
>> Summary of successfully produced loop models:
Filename molpdf DOPE score
-------------------------------------------------------
red1.BL00010001.pdb 8.01915 -960.66632
red1.BL00010002.pdb 2473.65137 555.30524
In [50]:
Image(filename='red1.png')
Out[50]:
Уберем из выравнивания длинную петлю в конце, в BLAST она маппится только на геном вируса и его других штаммов. Не совсем понятно, зачем вирусу такой хвост. Потому попробуем его просто обрезать по какой-нибкдь аминокислоте, в которой, возможно, из-за ошибки секвенирования, появился стоп-кодон - например, по G151
In [37]:
alignm=modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
new_seq1 = new_seq[:151] + "..."
alignm.append_sequence(new_seq1)
In [38]:
alignm.salign()
alignm[1].code ="red2"
alignm.write(file='all_in_one.ali', alignment_format='PIR')
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.)
SALIGN_____> adding the next group to the alignment; iteration 1
In [39]:
!cat all_in_one.ali
>P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00:-1.00 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV CGIRCSQLLT----------------------DDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCG V...* >P1;red2 sequence::1 : :+154 : :undefined:undefined:-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT G...*
Сделаем LoopModel, и укажем ей моделировать петлю в нашем белке
In [40]:
class LoopModel1(loopmodel):
def select_loop_atoms(self):
return selection(self.residue_range('86', '107'))
In [41]:
s = alignm[1]
pdb = alignm[0]
print s.code, pdb.code
## Создаем объект automodel
a = LoopModel1(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code, loop_assess_methods=assess.DOPE)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
red2 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C +N
atom indices : 1179 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C CA +N O
atom indices : 1179 1178 0 1180
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13042 11987
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 1224
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11987 11987
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2974
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 : 1253.1537
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 : 1209 0 0 0.006 0.006 12.065 1.000
2 Bond angle potential : 1642 1 8 2.425 2.425 183.92 1.000
3 Stereochemical cosine torsion poten: 785 0 37 49.116 49.116 287.56 1.000
4 Stereochemical improper torsion pot: 524 0 1 1.424 1.424 21.850 1.000
5 Soft-sphere overlap restraints : 2974 1 2 0.008 0.008 21.447 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.229 0.229 52.352 1.000
10 Distance restraints 2 (N-O) : 2564 3 25 0.464 0.464 252.98 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: 150 0 4 4.877 4.877 42.081 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 4 86.219 86.219 56.660 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 2 82.202 82.202 55.333 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 0 75.752 75.752 29.873 1.000
17 Sidechain Chi_4 dihedral restraints: 13 0 0 102.236 102.236 9.8859 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 786 0 0 0.399 0.399 12.498 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: 149 35 29 39.549 83.639 189.94 1.000
26 Distance restraints 4 (SDCH-SDCH) : 102 0 0 0.668 0.668 3.4893 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.043 0.043 21.217 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: red2.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: 20577.4336
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 1857 59I 59I N CA 462 463 126.16 107.00 19.16 5.51 107.00 19.16 5.51
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 7891 37H 33I N O 294 271 5.62 3.00 2.62 4.57 3.00 2.62 4.57
2 8490 63Y 59I N O 495 469 5.51 3.13 2.38 5.96 3.13 2.38 5.96
3 8515 64A 59I N O 507 469 6.12 4.01 2.11 4.77 4.01 2.11 4.77
-------------------------------------------------------------------------------------------------
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 4165 5Q 6N C N 38 40 -82.00 -119.90 62.97 3.42 -63.20 132.95 17.68
1 6N 6N N CA 40 41 -172.71 137.00 -41.10
2 4166 6N 7G C N 46 48 78.68 78.70 87.25 2.48 -62.40 146.02 24.29
2 7G 7G N CA 48 49 -78.85 -166.10 -41.20
3 4178 18R 19L C N 141 143 53.96 60.20 22.63 0.87 -63.50 149.54 27.35
3 19L 19L N CA 143 144 51.35 29.60 -41.20
4 4180 20T 21A C N 156 158 -82.40 -68.20 64.43 5.68 -62.50 124.95 19.60
4 21A 21A N CA 158 159 82.46 145.30 -40.90
5 4181 21A 22Y C N 161 163 60.51 55.90 11.09 0.53 -63.50 143.81 27.16
5 22Y 22Y N CA 163 164 29.41 39.50 -43.40
6 4192 32T 33I C N 262 264 -93.74 -120.60 33.81 1.55 -63.40 156.35 24.65
6 33I 33I N CA 264 265 109.77 130.30 -43.60
7 4193 33I 34G C N 270 272 136.08 82.20 75.74 2.38 -62.40 161.56 29.00
7 34G 34G N CA 272 273 -44.74 8.50 -41.20
8 4195 35W 36G C N 288 290 -173.56 82.20 104.27 6.91 -62.40 120.82 19.19
8 36G 36G N CA 290 291 6.15 8.50 -41.20
9 4197 37H 38Y C N 302 304 60.51 55.90 7.88 0.40 -63.50 145.72 27.55
9 38Y 38Y N CA 304 305 33.11 39.50 -43.40
10 4207 47T 48Q C N 376 378 -86.30 -63.80 83.73 11.26 -63.80 83.73 11.26
10 48Q 48Q N CA 378 379 40.34 -40.30 -40.30
11 4208 48Q 49A C N 385 387 66.04 55.40 27.66 1.01 -62.50 139.25 28.24
11 49A 49A N CA 387 388 12.67 38.20 -40.90
12 4216 56E 57I C N 444 446 29.07 -97.30 132.72 7.15 -63.40 159.71 29.44
12 57I 57I N CA 446 447 86.62 127.20 -43.60
13 4218 58D 59I C N 460 462 -70.92 -63.40 22.68 3.50 -120.60 160.40 7.36
13 59I 59I N CA 462 463 -22.21 -43.60 130.30
14 4219 59I 60N C N 468 470 76.43 55.90 85.03 4.58 -63.20 139.64 21.07
14 60N 60N N CA 470 471 -43.02 39.50 -41.10
15 4221 61N 62K C N 484 486 -115.40 -62.90 53.29 9.07 -62.90 53.29 9.07
15 62K 62K N CA 486 487 -49.94 -40.80 -40.80
16 4227 67V 68D C N 532 534 74.72 54.50 27.09 1.77 -63.30 151.67 25.87
16 68D 68D N CA 534 535 22.88 40.90 -40.00
17 4230 70Y 71V C N 557 559 61.28 55.90 6.03 0.74 -125.40 -159.36 10.67
17 71V 71V N CA 559 560 42.22 39.50 143.30
18 4232 72K 73G C N 573 575 172.27 82.20 106.24 8.30 -62.40 164.19 23.67
18 73G 73G N CA 575 576 64.86 8.50 -41.20
19 4233 73G 74K C N 577 579 -22.37 -70.20 81.27 4.91 56.60 86.82 7.88
19 74K 74K N CA 579 580 74.69 140.40 38.60
20 4236 76N 77Q C N 599 601 65.01 55.10 9.93 1.18 -121.10 -159.43 9.62
20 77Q 77Q N CA 601 602 39.75 40.30 139.70
21 4245 85S 86L C N 670 672 -116.70 -108.50 8.23 0.40 -63.50 -179.06 22.69
21 86L 86L N CA 672 673 131.74 132.50 -41.20
22 4246 86L 87A C N 678 680 -72.79 -68.20 4.87 0.46 -62.50 175.74 29.32
22 87A 87A N CA 680 681 143.66 145.30 -40.90
23 4247 87A 88Y C N 683 685 -49.43 -98.40 48.98 1.89 -63.50 172.82 28.15
23 88Y 88Y N CA 685 686 128.84 128.40 -43.40
24 4248 88Y 89N C N 695 697 -139.55 -119.90 29.22 0.86 -63.20 177.54 26.50
24 89N 89N N CA 697 698 158.62 137.00 -41.10
25 4250 90C 91G C N 709 711 99.00 78.70 47.91 0.71 82.20 142.99 7.78
25 91G 91G N CA 711 712 150.50 -166.10 8.50
26 4251 91G 92N C N 713 715 -87.69 -71.20 31.94 1.70 -63.20 150.76 20.23
26 92N 92N N CA 715 716 170.15 142.80 -41.10
27 4253 93V 94F C N 728 730 -120.47 -124.20 10.78 0.58 -63.20 172.09 27.68
27 94F 94F N CA 730 731 153.42 143.30 -44.30
28 4255 95V 96A C N 746 748 -104.80 -134.00 39.67 1.14 -62.50 166.50 25.56
28 96A 96A N CA 748 749 120.14 147.00 -40.90
29 4256 96A 97D C N 751 753 -96.37 -70.90 29.35 1.55 -63.30 158.62 21.69
29 97D 97D N CA 753 754 164.87 150.30 -40.00
30 4259 99W 100A C N 777 779 -72.84 -68.20 9.85 0.94 -62.50 177.81 28.65
30 100A 100A N CA 779 780 136.61 145.30 -40.90
31 4261 101P 102F C N 789 791 -62.59 -71.40 19.63 1.30 -63.20 167.46 23.29
31 102F 102F N CA 791 792 123.16 140.70 -44.30
32 4263 103S 104H C N 806 808 -145.98 -125.60 60.05 1.86 -63.20 147.77 23.75
32 104H 104H N CA 808 809 -164.71 138.80 -42.30
33 4264 104H 105A C N 816 818 -138.43 -134.00 22.82 1.18 -62.50 167.87 31.58
33 105A 105A N CA 818 819 169.38 147.00 -40.90
34 4283 123Q 124G C N 959 961 29.07 -62.40 97.73 15.75 -62.40 97.73 15.75
34 124G 124G N CA 961 962 -75.61 -41.20 -41.20
35 4309 149Q 150T C N 1168 1170 51.76 55.90 9.37 0.45 -63.20 146.00 25.08
35 150T 150T N CA 1170 1171 47.90 39.50 -42.10
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 15 31 100 115 181 174 205 210 181 237
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 1224
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11987 11987
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2842
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 : 1180.2064
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 : 1209 0 0 0.005 0.005 9.3759 1.000
2 Bond angle potential : 1642 0 5 2.177 2.177 148.04 1.000
3 Stereochemical cosine torsion poten: 785 0 36 49.120 49.120 289.34 1.000
4 Stereochemical improper torsion pot: 524 0 1 1.364 1.364 20.509 1.000
5 Soft-sphere overlap restraints : 2842 1 2 0.008 0.008 21.409 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.297 0.297 69.288 1.000
10 Distance restraints 2 (N-O) : 2564 0 18 0.449 0.449 209.42 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 150 0 4 5.121 5.121 46.392 1.000
14 Sidechain Chi_1 dihedral restraints: 123 0 3 88.767 88.767 49.554 1.000
15 Sidechain Chi_2 dihedral restraints: 94 0 1 77.882 77.882 45.115 1.000
16 Sidechain Chi_3 dihedral restraints: 40 0 0 82.704 82.704 30.650 1.000
17 Sidechain Chi_4 dihedral restraints: 13 0 0 87.126 87.126 10.155 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 786 0 0 0.416 0.416 14.696 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: 149 38 31 39.658 86.841 196.64 1.000
26 Distance restraints 4 (SDCH-SDCH) : 102 0 1 1.046 1.046 6.5973 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.033 0.033 13.025 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: red2.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: 20008.0684
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 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 4177 17C 18R C N 130 132 -50.91 -63.00 13.12 2.38 -125.20 -168.39 7.37
1 18R 18R N CA 132 133 -36.02 -41.10 140.60
2 4178 18R 19L C N 141 143 -147.89 -108.50 86.02 4.90 -63.50 128.74 16.24
2 19L 19L N CA 143 144 56.03 132.50 -41.20
3 4179 19L 20T C N 149 151 -57.91 -63.20 27.20 3.17 -78.10 142.85 6.79
3 20T 20T N CA 151 152 -68.78 -42.10 149.80
4 4180 20T 21A C N 156 158 -83.70 -62.50 85.43 15.12 -62.50 85.43 15.12
4 21A 21A N CA 158 159 -123.66 -40.90 -40.90
5 4181 21A 22Y C N 161 163 -103.07 -98.40 69.58 7.36 -63.50 109.76 15.64
5 22Y 22Y N CA 163 164 58.97 128.40 -43.40
6 4195 35W 36G C N 288 290 179.56 82.20 117.23 9.16 -62.40 164.80 23.31
6 36G 36G N CA 290 291 73.80 8.50 -41.20
7 4196 36G 37H C N 292 294 -10.97 56.30 72.84 9.46 56.30 72.84 9.46
7 37H 37H N CA 294 295 68.74 40.80 40.80
8 4197 37H 38Y C N 302 304 56.18 55.90 5.65 0.37 -63.50 142.45 26.95
8 38Y 38Y N CA 304 305 33.86 39.50 -43.40
9 4208 48Q 49A C N 385 387 83.64 55.40 38.06 2.16 -62.50 155.65 31.49
9 49A 49A N CA 387 388 12.68 38.20 -40.90
10 4216 56E 57I C N 444 446 54.19 -97.30 160.36 8.85 -63.40 166.74 31.25
10 57I 57I N CA 446 447 74.62 127.20 -43.60
11 4221 61N 62K C N 484 486 -117.31 -62.90 55.17 8.60 -62.90 55.17 8.60
11 62K 62K N CA 486 487 -31.69 -40.80 -40.80
12 4222 62K 63Y C N 493 495 -115.95 -63.50 73.00 10.17 -63.50 73.00 10.17
12 63Y 63Y N CA 495 496 7.37 -43.40 -43.40
13 4226 66M 67V C N 525 527 70.47 55.90 23.31 1.24 -125.40 -155.50 11.26
13 67V 67V N CA 527 528 21.30 39.50 143.30
14 4227 67V 68D C N 532 534 -140.07 -63.30 96.32 11.55 -63.30 96.32 11.55
14 68D 68D N CA 534 535 18.18 -40.00 -40.00
15 4230 70Y 71V C N 557 559 59.81 55.90 14.30 1.30 -125.40 -163.38 10.25
15 71V 71V N CA 559 560 53.25 39.50 143.30
16 4232 72K 73G C N 573 575 153.54 82.20 84.42 3.45 -62.40 144.13 25.56
16 73G 73G N CA 575 576 -36.63 8.50 -41.20
17 4234 74K 75A C N 586 588 -72.41 -68.20 19.66 1.44 -62.50 154.92 25.89
17 75A 75A N CA 588 589 164.50 145.30 -40.90
18 4235 75A 76N C N 591 593 75.96 55.90 59.63 2.96 -63.20 141.29 22.37
18 76N 76N N CA 593 594 -16.65 39.50 -41.10
19 4245 85S 86L C N 670 672 135.03 -108.50 116.52 5.51 -63.50 -120.43 30.43
19 86L 86L N CA 672 673 135.78 132.50 -41.20
20 4246 86L 87A C N 678 680 -80.25 -68.20 23.55 1.52 -62.50 154.58 26.24
20 87A 87A N CA 680 681 165.54 145.30 -40.90
21 4247 87A 88Y C N 683 685 -71.09 -98.40 27.41 1.05 -63.50 174.27 27.26
21 88Y 88Y N CA 685 686 130.70 128.40 -43.40
22 4248 88Y 89N C N 695 697 -141.62 -119.90 32.48 0.96 -63.20 176.18 26.44
22 89N 89N N CA 697 698 161.14 137.00 -41.10
23 4249 89N 90C C N 703 705 -63.08 -63.00 1.12 0.14 -117.90 -175.01 7.96
23 90C 90C N CA 705 706 -42.22 -41.10 141.10
24 4250 90C 91G C N 709 711 101.18 78.70 50.37 0.75 82.20 141.60 7.82
24 91G 91G N CA 711 712 148.82 -166.10 8.50
25 4251 91G 92N C N 713 715 -119.36 -119.90 0.78 0.02 -63.20 -173.79 20.71
25 92N 92N N CA 715 716 136.44 137.00 -41.10
26 4252 92N 93V C N 721 723 -64.14 -62.40 4.40 0.66 -125.40 -179.05 10.14
26 93V 93V N CA 723 724 -46.44 -42.40 143.30
27 4253 93V 94F C N 728 730 -132.46 -124.20 18.25 0.62 -63.20 170.80 28.22
27 94F 94F N CA 730 731 159.58 143.30 -44.30
28 4255 95V 96A C N 746 748 -66.58 -68.20 7.03 0.51 -62.50 179.41 29.20
28 96A 96A N CA 748 749 138.47 145.30 -40.90
29 4256 96A 97D C N 751 753 -90.32 -70.90 30.47 1.12 -63.30 148.70 20.07
29 97D 97D N CA 753 754 173.78 150.30 -40.00
30 4258 98G 99W C N 763 765 -140.77 -124.90 15.98 0.66 -63.00 -172.54 28.67
30 99W 99W N CA 765 766 145.24 143.40 -44.20
31 4259 99W 100A C N 777 779 -142.62 -134.00 12.81 0.41 -62.50 -178.70 34.00
31 100A 100A N CA 779 780 156.47 147.00 -40.90
32 4262 102F 103S C N 800 802 -61.77 -72.40 12.98 1.04 -64.10 165.15 11.83
32 103S 103S N CA 802 803 159.86 152.40 -35.00
33 4264 104H 105A C N 816 818 179.57 -134.00 46.44 1.50 -62.50 -152.23 40.28
33 105A 105A N CA 818 819 148.04 147.00 -40.90
34 4265 105A 106Y C N 821 823 -157.12 -124.30 61.46 2.43 -63.50 159.59 29.63
34 106Y 106Y N CA 823 824 -172.64 135.40 -43.40
35 4266 106Y 107C C N 833 835 -55.65 -63.00 14.46 1.51 -117.90 176.67 7.69
35 107C 107C N CA 835 836 -53.55 -41.10 141.10
36 4297 137N 138K C N 1077 1079 -55.84 -62.90 30.28 3.61 -118.00 162.97 8.43
36 138K 138K N CA 1079 1080 -70.25 -40.80 139.10
37 4305 145N 146Q C N 1134 1136 -111.32 -63.80 82.95 10.63 -63.80 82.95 10.63
37 146Q 146Q N CA 1136 1137 27.69 -40.30 -40.30
38 4308 148N 149Q C N 1159 1161 -117.44 -121.10 20.22 0.90 -63.80 168.86 22.41
38 149Q 149Q N CA 1161 1162 119.81 139.70 -40.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 16 22 119 111 156 149 162 180 196 221
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C +N
atom indices : 1179 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C CA +N O
atom indices : 1179 1178 0 1180
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
# ALGNMT CODE
1 red2
2 red2
169 atoms selected for loop refinement
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.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 883 756
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3098
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 260.4635
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 : 178 0 0 0.003 0.003 0.38405 1.000
2 Bond angle potential : 247 0 0 1.583 1.583 11.537 1.000
3 Stereochemical cosine torsion poten: 164 0 1 38.649 38.649 38.288 1.000
4 Stereochemical improper torsion pot: 92 0 0 0.722 0.722 1.0886 1.000
5 Soft-sphere overlap restraints : 3098 0 0 0.001 0.001 0.11939 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 23 0 0 3.000 3.000 2.4426 1.000
14 Sidechain Chi_1 dihedral restraints: 16 0 0 87.939 87.939 4.2690 1.000
15 Sidechain Chi_2 dihedral restraints: 11 0 1 102.707 102.707 7.1026 1.000
16 Sidechain Chi_3 dihedral restraints: 1 0 0 51.982 51.982 0.41909 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 24 14 3 32.064 135.246 21.747 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 3098 0 27 1.867 1.867 173.07 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 682 84V 85S C N 664 666 -101.72 -72.40 76.14 3.62 -64.10 109.03 10.55
1 85S 85S N CA 666 667 -137.34 152.40 -35.00
2 683 85S 86L C N 670 672 -116.73 -108.50 8.27 0.40 -63.50 -179.10 22.69
2 86L 86L N CA 672 673 131.69 132.50 -41.20
3 684 86L 87A C N 678 680 -72.76 -68.20 4.84 0.46 -62.50 175.73 29.32
3 87A 87A N CA 680 681 143.67 145.30 -40.90
4 685 87A 88Y C N 683 685 -49.39 -98.40 49.01 1.89 -63.50 172.84 28.16
4 88Y 88Y N CA 685 686 128.87 128.40 -43.40
5 686 88Y 89N C N 695 697 -139.57 -119.90 29.24 0.86 -63.20 177.53 26.50
5 89N 89N N CA 697 698 158.63 137.00 -41.10
6 688 90C 91G C N 709 711 98.96 78.70 47.90 0.71 82.20 142.98 7.77
6 91G 91G N CA 711 712 150.49 -166.10 8.50
7 689 91G 92N C N 713 715 -87.72 -71.20 31.97 1.70 -63.20 150.74 20.23
7 92N 92N N CA 715 716 170.17 142.80 -41.10
8 691 93V 94F C N 728 730 -120.46 -124.20 10.79 0.58 -63.20 172.08 27.69
8 94F 94F N CA 730 731 153.42 143.30 -44.30
9 693 95V 96A C N 746 748 -104.86 -134.00 39.61 1.14 -62.50 166.54 25.58
9 96A 96A N CA 748 749 120.16 147.00 -40.90
10 694 96A 97D C N 751 753 -96.38 -70.90 29.36 1.55 -63.30 158.60 21.70
10 97D 97D N CA 753 754 164.88 150.30 -40.00
11 697 99W 100A C N 777 779 -72.79 -68.20 9.81 0.93 -62.50 177.83 28.66
11 100A 100A N CA 779 780 136.63 145.30 -40.90
12 699 101P 102F C N 789 791 -62.56 -71.40 19.63 1.30 -63.20 167.48 23.30
12 102F 102F N CA 791 792 123.18 140.70 -44.30
13 701 103S 104H C N 806 808 -145.97 -125.60 60.07 1.86 -63.20 147.75 23.74
13 104H 104H N CA 808 809 -164.69 138.80 -42.30
14 702 104H 105A C N 816 818 -138.46 -134.00 22.82 1.18 -62.50 167.89 31.59
14 105A 105A N CA 818 819 169.38 147.00 -40.90
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 1182 1206 1.552
serious non-bonded atom clash: 1193 1206 2.274
serious non-bonded atom clash: 1196 1213 2.151
serious non-bonded atom clash: 1196 1220 1.404
serious non-bonded atom clash: 1197 1220 2.278
serious non-bonded atom clash: 1207 1220 2.101
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: 2 2 2 0 0 15 31 100 115 181 174 205 210 179 237
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6265
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2591.1199
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 : 178 10 30 0.072 0.072 262.08 1.000
2 Bond angle potential : 247 19 49 10.945 10.945 544.05 1.000
3 Stereochemical cosine torsion poten: 164 3 22 52.703 52.703 111.80 1.000
4 Stereochemical improper torsion pot: 92 4 7 7.621 7.621 82.038 1.000
5 Soft-sphere overlap restraints : 6265 27 45 0.031 0.031 692.56 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 23 3 7 17.011 17.011 78.545 1.000
14 Sidechain Chi_1 dihedral restraints: 16 0 6 88.828 88.828 29.875 1.000
15 Sidechain Chi_2 dihedral restraints: 11 0 2 115.750 115.750 14.613 1.000
16 Sidechain Chi_3 dihedral restraints: 1 0 0 7.397 7.397 -0.11882 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 24 19 18 80.661 150.465 150.53 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 6265 0 143 1.859 1.859 625.15 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 109 99W 100A C N 777 779 1.52 1.35 0.17 6.09 1.35 0.17 6.09
2 120 101P 102F C N 789 791 1.52 1.35 0.17 6.09 1.35 0.17 6.09
3 134 102F 102F N CA 791 792 1.63 1.43 0.20 6.47 1.43 0.20 6.47
4 136 102F 102F C CA 800 792 1.91 1.49 0.42 12.10 1.49 0.42 12.10
5 137 102F 103S C N 800 802 1.52 1.35 0.17 6.07 1.35 0.17 6.07
6 140 103S 103S N CA 802 803 1.61 1.43 0.18 5.91 1.43 0.18 5.91
7 142 103S 103S C CA 806 803 1.91 1.49 0.42 12.10 1.49 0.42 12.10
8 150 104H 104H N CA 808 809 1.59 1.43 0.16 5.42 1.43 0.16 5.42
9 152 104H 104H C CA 816 809 1.65 1.49 0.16 4.66 1.49 0.16 4.66
-------------------------------------------------------------------------------------------------
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
1 277 94F 95V C N 739 741 140.80 120.00 20.80 4.72 120.00 20.80 4.72
2 310 98G 99W C N 763 765 151.38 120.00 31.38 7.13 120.00 31.38 7.13
3 312 99W 99W N CA 765 766 130.36 113.50 16.86 4.53 113.50 16.86 4.53
4 327 99W 99W NE1 CE2 771 772 151.66 130.60 21.06 8.56 130.60 21.06 8.56
5 333 99W 100A C N 777 779 155.65 120.00 35.65 8.10 120.00 35.65 8.10
6 336 100A 100A N CA 779 780 142.32 107.00 35.32 10.15 107.00 35.32 10.15
7 340 100A 101P C N 782 784 136.22 117.00 19.22 4.78 117.00 19.22 4.78
8 352 101P 102F C N 789 791 152.04 120.00 32.04 7.28 120.00 32.04 7.28
9 355 102F 102F N CA 791 792 128.72 107.00 21.72 6.24 107.00 21.72 6.24
10 368 102F 103S C N 800 802 179.97 120.00 59.97 13.63 120.00 59.97 13.63
11 374 103S 103S CA C 803 806 145.53 116.50 29.03 8.34 116.50 29.03 8.34
12 375 103S 103S C CA 806 803 133.01 108.00 25.01 5.79 108.00 25.01 5.79
13 379 104H 104H N CA 808 809 126.09 107.00 19.09 5.49 107.00 19.09 5.49
14 422 107C 107C CA C 836 839 133.75 116.50 17.25 4.96 116.50 17.25 4.96
-------------------------------------------------------------------------------------------------
Feature 3 : Stereochemical cosine torsion potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 593 99W 99W NE1 CD1 771 770 -124.09 180.00 55.91 4.80 180.00 55.91 4.80
2 599 99W 99W CE2 NE1 772 771 -42.50 0.00 -42.50 4.57 0.00 -42.50 4.57
3 615 99W 99W CD1 NE1 770 771 62.41 0.00 62.41 4.71 0.00 62.41 4.71
-------------------------------------------------------------------------------------------------
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
1 728 107C 107C CA C 836 839 -126.87 180.00 53.13 10.63 180.00 53.13 10.63
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 682 84V 85S C N 664 666 -101.72 -72.40 74.70 3.54 -64.10 110.49 10.65
1 85S 85S N CA 666 667 -138.89 152.40 -35.00
2 683 85S 86L C N 670 672 -127.49 -108.50 29.78 1.69 -63.50 163.78 20.18
2 86L 86L N CA 672 673 109.56 132.50 -41.20
3 685 87A 88Y C N 683 685 40.48 -98.40 138.92 5.41 -63.50 -161.97 36.35
3 88Y 88Y N CA 685 686 125.13 128.40 -43.40
4 686 88Y 89N C N 695 697 -157.05 -63.20 106.55 17.51 -63.20 106.55 17.51
4 89N 89N N CA 697 698 -91.54 -41.10 -41.10
5 688 90C 91G C N 709 711 150.78 -167.20 78.25 3.14 82.20 121.33 8.86
5 91G 91G N CA 711 712 108.59 174.60 8.50
6 689 91G 92N C N 713 715 -100.04 -119.90 22.59 1.17 -63.20 175.04 23.97
6 92N 92N N CA 715 716 147.78 137.00 -41.10
7 691 93V 94F C N 728 730 -25.14 -71.40 65.88 3.83 -63.20 143.24 22.44
7 94F 94F N CA 730 731 93.79 140.70 -44.30
8 692 94F 95V C N 739 741 48.60 -62.40 137.02 16.83 -125.40 -162.25 10.39
8 95V 95V N CA 741 742 -122.74 -42.40 143.30
9 693 95V 96A C N 746 748 -106.90 -134.00 27.84 1.17 -62.50 171.59 30.48
9 96A 96A N CA 748 749 153.35 147.00 -40.90
10 694 96A 97D C N 751 753 142.52 54.50 116.57 14.77 -63.30 -139.72 24.79
10 97D 97D N CA 753 754 117.33 40.90 -40.00
11 696 98G 99W C N 763 765 149.18 -124.90 85.97 3.86 -63.00 -130.65 38.42
11 99W 99W N CA 765 766 140.44 143.40 -44.20
12 697 99W 100A C N 777 779 -32.55 -68.20 47.63 3.03 -62.50 157.49 27.38
12 100A 100A N CA 779 780 113.72 145.30 -40.90
13 698 100A 101P C N 782 784 -75.92 -58.70 19.57 1.82 -64.50 168.78 13.21
13 101P 101P N CA 784 785 -21.20 -30.50 147.20
14 699 101P 102F C N 789 791 -60.37 -71.40 40.97 2.97 -63.20 145.57 20.41
14 102F 102F N CA 791 792 101.24 140.70 -44.30
15 700 102F 103S C N 800 802 -130.31 -136.60 83.94 4.38 -64.10 111.81 12.88
15 103S 103S N CA 802 803 -125.10 151.20 -35.00
16 701 103S 104H C N 806 808 -138.81 -125.60 70.36 2.90 -63.20 135.13 14.45
16 104H 104H N CA 808 809 69.69 138.80 -42.30
17 702 104H 105A C N 816 818 75.46 -68.20 150.30 11.16 -62.50 -161.98 39.50
17 105A 105A N CA 818 819 101.14 145.30 -40.90
18 703 105A 106Y C N 821 823 -143.21 -63.50 99.44 18.84 -63.50 99.44 18.84
18 106Y 106Y N CA 823 824 -102.85 -43.40 -43.40
19 705 107C 108A C N 839 841 -136.82 -62.50 74.98 13.97 -62.50 74.98 13.97
19 108A 108A N CA 841 842 -30.97 -40.90 -40.90
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 293 807 2.116
serious non-bonded atom clash: 316 802 2.277
serious non-bonded atom clash: 319 802 2.100
serious non-bonded atom clash: 431 791 2.056
serious non-bonded atom clash: 443 777 1.878
serious non-bonded atom clash: 443 778 2.170
serious non-bonded atom clash: 443 779 1.976
serious non-bonded atom clash: 778 885 2.257
serious non-bonded atom clash: 1182 1206 1.552
serious non-bonded atom clash: 1193 1206 2.274
serious non-bonded atom clash: 1196 1213 2.151
serious non-bonded atom clash: 1196 1220 1.404
serious non-bonded atom clash: 1197 1220 2.278
serious non-bonded atom clash: 1207 1220 2.101
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: 5 5 4 1 5 26 47 124 136 190 202 220 233 206 264
<< 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.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: GLY:OXT GLY
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 51893
Dynamic pairs routine : 5, NATM_SEL 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 : -1439.0332
<< end of ENERGY.
DOPE score : -1439.033203
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C +N
atom indices : 1179 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 151
atom names : C CA +N O
atom indices : 1179 1178 0 1180
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
# ALGNMT CODE
1 red2
2 red2
169 atoms selected for loop refinement
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.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 883 756
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2345
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 239.2606
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 : 178 0 0 0.004 0.004 0.86355 1.000
2 Bond angle potential : 247 0 2 2.024 2.024 18.984 1.000
3 Stereochemical cosine torsion poten: 164 0 4 41.664 41.664 45.883 1.000
4 Stereochemical improper torsion pot: 92 0 1 1.502 1.502 3.8475 1.000
5 Soft-sphere overlap restraints : 2345 0 0 0.001 0.001 0.13236 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 23 0 1 4.687 4.687 5.9641 1.000
14 Sidechain Chi_1 dihedral restraints: 16 0 1 89.838 89.838 5.8588 1.000
15 Sidechain Chi_2 dihedral restraints: 11 0 0 85.872 85.872 6.1867 1.000
16 Sidechain Chi_3 dihedral restraints: 1 0 0 50.804 50.804 0.50067 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 24 18 3 37.255 155.138 30.592 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 2345 0 20 1.833 1.833 120.45 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 682 84V 85S C N 664 666 -49.09 -72.40 30.10 1.49 -64.10 169.02 13.20
1 85S 85S N CA 666 667 133.35 152.40 -35.00
2 683 85S 86L C N 670 672 135.01 -108.50 116.54 5.51 -63.50 -120.42 30.43
2 86L 86L N CA 672 673 135.77 132.50 -41.20
3 684 86L 87A C N 678 680 -80.21 -68.20 23.50 1.52 -62.50 154.61 26.25
3 87A 87A N CA 680 681 165.50 145.30 -40.90
4 685 87A 88Y C N 683 685 -71.01 -98.40 27.49 1.06 -63.50 174.25 27.28
4 88Y 88Y N CA 685 686 130.69 128.40 -43.40
5 686 88Y 89N C N 695 697 -141.65 -119.90 32.50 0.96 -63.20 176.19 26.44
5 89N 89N N CA 697 698 161.14 137.00 -41.10
6 687 89N 90C C N 703 705 -63.12 -63.00 1.08 0.14 -117.90 -174.97 7.96
6 90C 90C N CA 705 706 -42.17 -41.10 141.10
7 688 90C 91G C N 709 711 101.15 78.70 50.40 0.75 82.20 141.55 7.81
7 91G 91G N CA 711 712 148.78 -166.10 8.50
8 689 91G 92N C N 713 715 -119.35 -119.90 0.77 0.02 -63.20 -173.78 20.71
8 92N 92N N CA 715 716 136.46 137.00 -41.10
9 690 92N 93V C N 721 723 -64.10 -62.40 4.42 0.66 -125.40 -179.08 10.14
9 93V 93V N CA 723 724 -46.48 -42.40 143.30
10 691 93V 94F C N 728 730 -132.43 -124.20 18.28 0.62 -63.20 170.74 28.22
10 94F 94F N CA 730 731 159.62 143.30 -44.30
11 693 95V 96A C N 746 748 -66.63 -68.20 6.96 0.51 -62.50 179.46 29.22
11 96A 96A N CA 748 749 138.52 145.30 -40.90
12 694 96A 97D C N 751 753 -90.39 -70.90 30.52 1.13 -63.30 148.70 20.08
12 97D 97D N CA 753 754 173.79 150.30 -40.00
13 696 98G 99W C N 763 765 -140.75 -124.90 15.95 0.66 -63.00 -172.56 28.66
13 99W 99W N CA 765 766 145.25 143.40 -44.20
14 697 99W 100A C N 777 779 -142.61 -134.00 12.81 0.41 -62.50 -178.72 34.01
14 100A 100A N CA 779 780 156.48 147.00 -40.90
15 700 102F 103S C N 800 802 -61.79 -72.40 12.97 1.04 -64.10 165.15 11.83
15 103S 103S N CA 802 803 159.86 152.40 -35.00
16 702 104H 105A C N 816 818 179.58 -134.00 46.43 1.50 -62.50 -152.25 40.29
16 105A 105A N CA 818 819 148.06 147.00 -40.90
17 703 105A 106Y C N 821 823 -157.10 -124.30 61.45 2.43 -63.50 159.57 29.63
17 106Y 106Y N CA 823 824 -172.63 135.40 -43.40
18 704 106Y 107C C N 833 835 -55.70 -63.00 14.42 1.50 -117.90 176.68 7.69
18 107C 107C N CA 835 836 -53.53 -41.10 141.10
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 1182 1206 1.546
serious non-bonded atom clash: 1193 1206 2.273
serious non-bonded atom clash: 1196 1213 2.142
serious non-bonded atom clash: 1196 1220 1.403
serious non-bonded atom clash: 1197 1220 2.283
serious non-bonded atom clash: 1207 1220 2.102
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: 2 2 2 0 0 16 22 119 111 156 150 161 180 196 220
<< end of ENERGY.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NAG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
read_pd_403W> Treating residue type NDG as a BLK (rigid body)
even though topology information appears to be at least
partially available. To treat this residue flexibly
instead, remove the corresponding 'MODELLER BLK RESIDUE'
REMARK from the input PDB file.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
preppdf_457W> Both soft sphere and statistical potential terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5364
Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 7.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 3435.4692
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 : 178 11 19 0.079 0.079 344.00 1.000
2 Bond angle potential : 247 18 34 10.315 10.315 455.96 1.000
3 Stereochemical cosine torsion poten: 164 7 18 49.753 49.753 119.69 1.000
4 Stereochemical improper torsion pot: 92 1 3 3.898 3.898 30.145 1.000
5 Soft-sphere overlap restraints : 5364 56 70 0.052 0.052 1696.1 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) : 0 0 0 0.000 0.000 0.0000 1.000
10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 23 0 2 7.372 7.372 14.752 1.000
14 Sidechain Chi_1 dihedral restraints: 16 0 1 81.961 81.961 14.110 1.000
15 Sidechain Chi_2 dihedral restraints: 11 0 1 116.829 116.829 9.6981 1.000
16 Sidechain Chi_3 dihedral restraints: 1 0 0 12.840 12.840 0.53429 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 24 19 10 53.390 147.181 65.703 1.000
26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 5316 0 157 1.870 1.870 684.79 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
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 84 96A 97D C N 751 753 1.56 1.35 0.21 7.50 1.35 0.21 7.50
2 89 97D 97D N CA 753 754 1.72 1.43 0.29 9.56 1.43 0.29 9.56
3 92 97D 98G C N 759 761 1.55 1.35 0.21 7.31 1.35 0.21 7.31
4 93 98G 98G N CA 761 762 2.00 1.43 0.57 18.63 1.43 0.57 18.63
5 95 98G 98G C CA 763 762 1.81 1.49 0.32 9.26 1.49 0.32 9.26
6 96 98G 99W C N 763 765 1.48 1.35 0.13 4.74 1.35 0.13 4.74
7 106 99W 99W N CA 765 766 1.87 1.43 0.44 14.44 1.43 0.44 14.44
8 108 99W 99W C CA 777 766 1.70 1.49 0.21 6.09 1.49 0.21 6.09
9 116 100A 100A C CA 782 780 1.66 1.49 0.17 4.81 1.49 0.17 4.81
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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
1 294 96A 97D C N 751 753 170.22 120.00 50.22 11.41 120.00 50.22 11.41
2 297 97D 97D N CA 753 754 135.16 107.00 28.16 8.09 107.00 28.16 8.09
3 298 97D 97D CA CB 754 755 141.88 108.00 33.88 7.85 108.00 33.88 7.85
4 305 97D 98G C N 759 761 169.22 120.00 49.22 11.18 120.00 49.22 11.18
5 307 98G 98G N CA 761 762 127.11 107.00 20.11 5.78 107.00 20.11 5.78
6 309 98G 98G CA C 762 763 135.69 116.50 19.19 5.52 116.50 19.19 5.52
7 310 98G 99W C N 763 765 143.84 120.00 23.84 5.42 120.00 23.84 5.42
8 313 99W 99W N CA 765 766 125.77 107.00 18.77 5.39 107.00 18.77 5.39
9 314 99W 99W CA CB 766 767 143.45 114.00 29.45 7.23 114.00 29.45 7.23
10 336 100A 100A N CA 779 780 128.22 107.00 21.22 6.10 107.00 21.22 6.10
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Feature 3 : Stereochemical cosine torsion potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 597 99W 99W CE3 CD2 773 769 77.06 0.00 77.06 5.70 0.00 77.06 5.70
2 598 99W 99W CE3 CD2 773 769 -88.56 0.00 -88.56 6.00 0.00 -88.56 6.00
3 600 99W 99W CZ2 CE2 774 772 -130.84 180.00 49.16 11.45 180.00 49.16 11.45
4 603 99W 99W NE1 CE2 771 772 135.18 180.00 -44.82 9.94 180.00 -44.82 9.94
5 604 99W 99W CH2 CZ2 776 774 -92.46 180.00 87.54 6.19 180.00 87.54 6.19
6 613 99W 99W CE2 CD2 772 769 88.97 0.00 88.97 6.20 0.00 88.97 6.20
7 615 99W 99W CD1 NE1 770 771 107.01 180.00 -72.99 5.49 180.00 -72.99 5.49
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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
1 682 84V 85S C N 664 666 -49.09 -72.40 31.05 1.51 -64.10 167.56 13.09
1 85S 85S N CA 666 667 131.89 152.40 -35.00
2 683 85S 86L C N 670 672 -89.01 -70.70 33.14 2.05 -63.50 151.74 22.62
2 86L 86L N CA 672 673 169.22 141.60 -41.20
3 684 86L 87A C N 678 680 -125.18 -134.00 29.09 1.40 -62.50 172.01 25.96
3 87A 87A N CA 680 681 119.28 147.00 -40.90
4 685 87A 88Y C N 683 685 77.13 -124.30 158.74 11.71 -63.50 -136.37 30.86
4 88Y 88Y N CA 685 686 142.73 135.40 -43.40
5 686 88Y 89N C N 695 697 54.69 55.90 33.06 2.22 -63.20 163.74 26.53
5 89N 89N N CA 697 698 72.54 39.50 -41.10
6 688 90C 91G C N 709 711 -126.87 -167.20 54.53 2.00 82.20 -142.07 6.67
6 91G 91G N CA 711 712 -148.71 174.60 8.50
7 689 91G 92N C N 713 715 -113.19 -63.20 69.22 11.22 -63.20 69.22 11.22
7 92N 92N N CA 715 716 -88.98 -41.10 -41.10
8 691 93V 94F C N 728 730 -145.33 -124.20 26.18 0.68 -63.20 177.13 29.85
8 94F 94F N CA 730 731 158.76 143.30 -44.30
9 693 95V 96A C N 746 748 -157.50 -134.00 27.29 1.43 -62.50 -161.74 29.71
9 96A 96A N CA 748 749 133.12 147.00 -40.90
10 694 96A 97D C N 751 753 -50.41 -63.30 80.40 10.74 -63.30 80.40 10.74
10 97D 97D N CA 753 754 39.36 -40.00 -40.00
11 695 97D 98G C N 759 761 178.25 -167.20 77.31 3.15 82.20 131.74 10.16
11 98G 98G N CA 761 762 98.67 174.60 8.50
12 696 98G 99W C N 763 765 -14.56 -71.30 63.46 3.83 -63.00 162.18 23.49
12 99W 99W N CA 765 766 110.58 139.00 -44.20
13 697 99W 100A C N 777 779 -154.25 -134.00 70.07 4.29 -62.50 151.72 22.94
13 100A 100A N CA 779 780 79.93 147.00 -40.90
14 699 101P 102F C N 789 791 -143.65 -124.20 32.71 0.97 -63.20 166.78 28.27
14 102F 102F N CA 791 792 169.60 143.30 -44.30
15 700 102F 103S C N 800 802 -131.20 -136.60 40.31 2.15 -64.10 149.73 15.66
15 103S 103S N CA 802 803 -168.85 151.20 -35.00
16 701 103S 104H C N 806 808 -61.63 -67.60 27.87 1.96 -63.20 155.09 19.48
16 104H 104H N CA 808 809 112.78 140.00 -42.30
17 702 104H 105A C N 816 818 -151.17 -134.00 40.21 1.74 -62.50 162.14 31.29
17 105A 105A N CA 818 819 -176.64 147.00 -40.90
18 703 105A 106Y C N 821 823 -113.61 -124.30 15.48 1.24 -63.50 177.24 30.68
18 106Y 106Y N CA 823 824 146.59 135.40 -43.40
19 704 106Y 107C C N 833 835 -52.79 -63.00 16.85 1.81 -117.90 176.81 7.71
19 107C 107C N CA 835 836 -54.51 -41.10 141.10
report______> Distribution of short non-bonded contacts:
serious non-bonded atom clash: 338 753 1.946
serious non-bonded atom clash: 413 753 2.092
serious non-bonded atom clash: 418 761 2.002
serious non-bonded atom clash: 419 761 1.949
serious non-bonded atom clash: 419 762 1.803
serious non-bonded atom clash: 419 763 1.961
serious non-bonded atom clash: 422 764 2.242
serious non-bonded atom clash: 428 759 2.285
serious non-bonded atom clash: 428 761 2.016
serious non-bonded atom clash: 446 761 2.254
serious non-bonded atom clash: 446 762 1.986
serious non-bonded atom clash: 447 761 2.140
serious non-bonded atom clash: 456 765 2.052
serious non-bonded atom clash: 458 768 2.279
serious non-bonded atom clash: 458 771 2.132
serious non-bonded atom clash: 656 766 2.178
serious non-bonded atom clash: 765 880 1.944
serious non-bonded atom clash: 767 881 2.224
serious non-bonded atom clash: 771 933 2.155
serious non-bonded atom clash: 775 914 2.288
serious non-bonded atom clash: 1182 1206 1.546
serious non-bonded atom clash: 1193 1206 2.273
serious non-bonded atom clash: 1196 1213 2.142
serious non-bonded atom clash: 1196 1220 1.403
serious non-bonded atom clash: 1197 1220 2.283
serious non-bonded atom clash: 1207 1220 2.102
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: 12 6 8 8 15 29 30 149 133 170 167 191 213 220 245
<< 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: GLY:OXT GLY
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 154
Number of all, selected real atoms : 1224 169
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 756 756
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 44190
Dynamic pairs routine : 5, NATM_SEL 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 : -1074.9771
<< end of ENERGY.
DOPE score : -1074.977051
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
red2.B99990001.pdb 1253.15369
red2.B99990002.pdb 1180.20642
>> Summary of successfully produced loop models:
Filename molpdf DOPE score
-------------------------------------------------------
red2.BL00010001.pdb 2591.11987 -1439.03320
red2.BL00010002.pdb 3435.46924 -1074.97705
In [52]:
Image(filename='result.png')
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