In [ ]:
! cd /tmp/ ; wget https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb
! env KEY_MODELLER="MODELIRANJE" dpkg -i /tmp/modeller_10.1-1_amd64.deb
--2026-05-01 16:05:27-- https://salilab.org/modeller/10.1/modeller_10.1-1_amd64.deb Resolving salilab.org (salilab.org)... 169.230.79.19 Connecting to salilab.org (salilab.org)|169.230.79.19|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 14404568 (14M) [application/vnd.debian.binary-package] Saving to: ‘modeller_10.1-1_amd64.deb.5’ modeller_10.1-1_amd 100%[===================>] 13.74M 9.11MB/s in 1.5s 2026-05-01 16:05:29 (9.11 MB/s) - ‘modeller_10.1-1_amd64.deb.5’ saved [14404568/14404568] (Reading database ... 120308 files and directories currently installed.) Preparing to unpack /tmp/modeller_10.1-1_amd64.deb ... Unpacking modeller (10.1-1) over (10.1-1) ... Setting up modeller (10.1-1) ...
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! echo -e "install_dir = r'/usr/lib/modeller10.1'\nlicense = 'MODELIRANJE'" > /usr/lib/modeller10.1/modlib/modeller/config.py
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! wget https://files.rcsb.org/download/1b8p.pdb
! wget https://files.rcsb.org/download/1bdm.pdb
--2026-05-01 16:05:32-- https://files.rcsb.org/download/1b8p.pdb Resolving files.rcsb.org (files.rcsb.org)... 3.175.207.56, 3.175.207.75, 3.175.207.24, ... Connecting to files.rcsb.org (files.rcsb.org)|3.175.207.56|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1b8p.pdb.4’ 1b8p.pdb.4 [ <=> ] 237.94K 463KB/s in 0.5s 2026-05-01 16:05:33 (463 KB/s) - ‘1b8p.pdb.4’ saved [243648] --2026-05-01 16:05:33-- https://files.rcsb.org/download/1bdm.pdb Resolving files.rcsb.org (files.rcsb.org)... 3.175.207.56, 3.175.207.75, 3.175.207.24, ... Connecting to files.rcsb.org (files.rcsb.org)|3.175.207.56|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1bdm.pdb.4’ 1bdm.pdb.4 [ <=> ] 467.33K 686KB/s in 0.7s 2026-05-01 16:05:34 (686 KB/s) - ‘1bdm.pdb.4’ saved [478548]
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# Гомологичное моделирование комплекса белка с лигандом
# Будем работать с белком LYS_BPPHV, будем строить комплекс этого лизоцима с лигандом с помощью программы Modeller
#Загрузим модуль
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import sys
sys.path.append('/usr/lib/python3.9/dist-packages')
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from modeller import *
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import sys
import modeller
import _modeller
import modeller.automodel
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env=modeller.Environ()
env.io.hetatm = True
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# Скачаем белок заготовку лизоцима форели
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! wget https://files.rcsb.org/download/1lmp.pdb
--2026-05-01 14:01:51-- https://files.rcsb.org/download/1lmp.pdb Resolving files.rcsb.org (files.rcsb.org)... 3.175.207.24, 3.175.207.56, 3.175.207.54, ... Connecting to files.rcsb.org (files.rcsb.org)|3.175.207.24|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/plain] Saving to: ‘1lmp.pdb.1’ 1lmp.pdb.1 [ <=> ] 126.40K 217KB/s in 0.6s 2026-05-01 14:01:52 (217 KB/s) - ‘1lmp.pdb.1’ saved [129438]
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# Скачаем последовательность LYS_BPPHV
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! wget http://www.uniprot.org/uniprot/P62693.fasta
--2026-05-01 14:01:52-- http://www.uniprot.org/uniprot/P62693.fasta Resolving www.uniprot.org (www.uniprot.org)... 193.62.193.81 Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://www.uniprot.org/uniprot/P62693.fasta [following] --2026-05-01 14:01:53-- https://www.uniprot.org/uniprot/P62693.fasta Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://rest.uniprot.org/uniprot/P62693.fasta [following] --2026-05-01 14:01:54-- https://rest.uniprot.org/uniprot/P62693.fasta Resolving rest.uniprot.org (rest.uniprot.org)... 193.62.192.81 Connecting to rest.uniprot.org (rest.uniprot.org)|193.62.192.81|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://rest.uniprot.org/uniprotkb/P62693.fasta [following] --2026-05-01 14:01:55-- https://rest.uniprot.org/uniprotkb/P62693.fasta Reusing existing connection to rest.uniprot.org:443. HTTP request sent, awaiting response... 200 OK Length: 317 [text/plain] Saving to: ‘P62693.fasta.1’ P62693.fasta.1 100%[===================>] 317 --.-KB/s in 0s 2026-05-01 14:01:55 (117 MB/s) - ‘P62693.fasta.1’ saved [317/317]
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# Создадим объект выравнивание
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alignm=modeller.Alignment(env)
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# Добавим последовательность и структуру
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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
alignm[0].code = 'P62693'
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# Делаем выравнивание и сохраняем
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alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
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! cat all_in_one.ali
>P1;P62693 sequence::: :: :::-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGEV K* >P1;1lmp structureX:1lmp.pdb:1:A:+129:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGI-FQINSRY------------ ------------------WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQD ------------------------------------------------------------------LRSYVAGCG V*
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# Построим модель
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## Выбираем объект для моделирования
s = alignm[0]
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()
P62693 1lmp
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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()
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
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.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 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: 14714 13125
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.
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 : 226
Number of all, selected real atoms : 1784 1784
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13125 13125
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3604
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 : 1741.9506
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 0.004 0.004 9.9609 1.000
2 Bond angle potential : 2468 0 9 1.992 1.992 187.11 1.000
3 Stereochemical cosine torsion poten: 1168 0 49 49.274 49.274 449.72 1.000
4 Stereochemical improper torsion pot: 773 0 0 1.196 1.196 25.568 1.000
5 Soft-sphere overlap restraints : 3604 0 0 0.004 0.004 7.9446 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) : 2408 1 13 0.582 0.582 194.19 1.000
10 Distance restraints 2 (N-O) : 2569 3 24 0.727 0.727 320.31 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 8 5.291 5.291 74.294 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 5 84.495 84.495 60.056 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 1 80.787 80.787 68.340 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 98.044 98.044 46.042 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 91.994 91.994 16.820 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) : 915 0 0 0.541 0.541 13.636 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: 224 101 41 37.473 115.773 255.70 1.000
26 Distance restraints 4 (SDCH-SDCH) : 131 0 1 1.198 1.198 12.265 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 : 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: P62693.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: 36955.2812
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 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 8924 94F 129R CA CA 731 1003 10.19 7.73 2.46 4.66 7.73 2.46 4.66
-------------------------------------------------------------------------------------------------
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 10890 94F 138K N O 730 1087 15.76 10.64 5.12 4.92 10.64 5.12 4.92
-------------------------------------------------------------------------------------------------
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 -157.16 -180.00 22.84 4.57 -180.00 22.84 4.57
2 6681 224E 224E CA C 1760 1766 -155.66 -180.00 24.34 4.87 -180.00 24.34 4.87
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6251 18R 19L C N 141 143 65.22 60.20 5.67 0.45 -63.50 145.66 26.86
1 19L 19L N CA 143 144 26.97 29.60 -41.20
2 6253 20T 21A C N 156 158 55.09 55.40 4.55 0.30 -62.50 139.23 28.29
2 21A 21A N CA 158 159 33.66 38.20 -40.90
3 6254 21A 22Y C N 161 163 64.98 55.90 10.92 0.81 -63.50 149.70 28.28
3 22Y 22Y N CA 163 164 33.43 39.50 -43.40
4 6265 32T 33I C N 262 264 -83.84 -120.60 63.29 4.86 -63.40 136.12 23.05
4 33I 33I N CA 264 265 -178.18 130.30 -43.60
5 6266 33I 34G C N 270 272 78.20 78.70 75.49 2.13 -62.40 149.03 24.19
5 34G 34G N CA 272 273 -90.61 -166.10 -41.20
6 6270 37H 38Y C N 302 304 62.53 55.90 13.03 0.63 -63.50 144.99 27.36
6 38Y 38Y N CA 304 305 28.28 39.50 -43.40
7 6279 46W 47T C N 369 371 -76.78 -124.80 54.83 2.12 -63.20 159.71 19.61
7 47T 47T N CA 371 372 117.03 143.50 -42.10
8 6280 47T 48Q C N 376 378 90.02 -121.10 150.88 6.20 -63.80 -141.26 39.35
8 48Q 48Q N CA 378 379 115.21 139.70 -40.30
9 6281 48Q 49A C N 385 387 -49.92 -68.20 50.74 3.47 -62.50 139.43 23.49
9 49A 49A N CA 387 388 97.96 145.30 -40.90
10 6295 62K 63Y C N 493 495 7.14 -98.40 108.53 5.14 -63.50 162.67 29.28
10 63Y 63Y N CA 495 496 103.13 128.40 -43.40
11 6298 65P 66M C N 517 519 -150.04 -125.60 31.60 0.94 -63.40 -178.95 33.77
11 66M 66M N CA 519 520 160.53 140.50 -40.50
12 6300 67V 68D C N 532 534 -104.24 -96.50 8.30 0.34 -63.30 156.68 17.28
12 68D 68D N CA 534 535 111.23 114.20 -40.00
13 6301 68D 69A C N 540 542 -125.76 -134.00 15.34 0.59 -62.50 -173.96 28.16
13 69A 69A N CA 542 543 134.06 147.00 -40.90
14 6302 69A 70Y C N 545 547 -126.32 -124.30 7.96 0.51 -63.50 -177.73 26.07
14 70Y 70Y N CA 547 548 127.70 135.40 -43.40
15 6304 71V 72K C N 564 566 -153.31 -118.00 39.76 1.32 -62.90 -174.64 29.47
15 72K 72K N CA 566 567 157.39 139.10 -40.80
16 6305 72K 73G C N 573 575 -164.13 -167.20 25.94 0.98 82.20 -179.40 13.52
16 73G 73G N CA 575 576 148.84 174.60 8.50
17 6306 73G 74K C N 577 579 -126.84 -118.00 11.23 0.38 -62.90 -175.39 27.79
17 74K 74K N CA 579 580 146.02 139.10 -40.80
18 6307 74K 75A C N 586 588 -124.49 -134.00 9.91 0.24 -62.50 -174.46 33.72
18 75A 75A N CA 588 589 144.22 147.00 -40.90
19 6308 75A 76N C N 591 593 -115.80 -119.90 4.57 0.23 -63.20 -172.58 26.43
19 76N 76N N CA 593 594 139.02 137.00 -41.10
20 6309 76N 77Q C N 599 601 -79.24 -73.00 6.30 0.43 -63.80 178.85 27.12
20 77Q 77Q N CA 601 602 141.52 140.70 -40.30
21 6310 77Q 78N C N 608 610 -134.41 -119.90 31.22 1.05 -63.20 169.91 25.26
21 78N 78N N CA 610 611 164.64 137.00 -41.10
22 6312 79E 80F C N 625 627 -139.87 -124.20 36.58 2.00 -63.20 172.53 19.81
22 80F 80F N CA 627 628 110.25 143.30 -44.30
23 6313 80F 81D C N 636 638 -159.59 -96.50 67.45 2.78 -63.30 -157.58 21.47
23 81D 81D N CA 638 639 138.05 114.20 -40.00
24 6314 81D 82A C N 644 646 -98.42 -68.20 37.94 3.74 -62.50 167.18 25.88
24 82A 82A N CA 646 647 122.38 145.30 -40.90
25 6315 82A 83L C N 649 651 -117.34 -108.50 11.14 0.49 -63.50 -172.58 29.34
25 83L 83L N CA 651 652 139.28 132.50 -41.20
26 6317 84V 85S C N 664 666 -75.37 -72.40 3.31 0.26 -64.10 174.42 13.34
26 85S 85S N CA 666 667 150.95 152.40 -35.00
27 6318 85S 86L C N 670 672 -75.72 -70.70 5.72 0.41 -63.50 174.88 25.00
27 86L 86L N CA 672 673 144.34 141.60 -41.20
28 6319 86L 87A C N 678 680 -128.66 -134.00 10.81 0.67 -62.50 175.64 32.33
28 87A 87A N CA 680 681 156.40 147.00 -40.90
29 6320 87A 88Y C N 683 685 -79.51 -98.40 19.12 0.76 -63.50 175.50 27.04
29 88Y 88Y N CA 685 686 131.37 128.40 -43.40
30 6321 88Y 89N C N 695 697 -100.02 -119.90 20.09 0.76 -63.20 179.07 20.57
30 89N 89N N CA 697 698 134.15 137.00 -41.10
31 6322 89N 90C C N 703 705 58.02 -69.10 133.42 12.34 -117.90 -179.32 6.88
31 90C 90C N CA 705 706 -177.67 141.80 141.10
32 6323 90C 91G C N 709 711 -128.84 -167.20 42.65 0.65 82.20 -150.40 16.09
32 91G 91G N CA 711 712 155.96 174.60 8.50
33 6324 91G 92N C N 713 715 -73.44 -71.20 2.53 0.20 -63.20 177.58 22.77
33 92N 92N N CA 715 716 141.62 142.80 -41.10
34 6326 93V 94F C N 728 730 158.63 -124.20 99.01 2.57 -63.20 176.84 31.88
34 94F 94F N CA 730 731 -154.66 143.30 -44.30
35 6331 98G 99W C N 763 765 -126.83 -124.90 87.98 4.32 -63.00 118.33 13.15
35 99W 99W N CA 765 766 55.44 143.40 -44.20
36 6333 100A 101P C N 782 784 -45.05 -58.70 49.79 3.16 -64.50 135.82 11.19
36 101P 101P N CA 784 785 -78.38 -30.50 147.20
37 6334 101P 102F C N 789 791 -113.30 -124.20 50.85 2.10 58.10 -178.16 20.35
37 102F 102F N CA 791 792 93.64 143.30 32.90
38 6336 103S 104H C N 806 808 -155.98 -125.60 74.39 3.28 -63.20 146.37 15.94
38 104H 104H N CA 808 809 70.90 138.80 -42.30
39 6337 104H 105A C N 816 818 -61.39 -68.20 27.21 2.42 -62.50 147.46 24.11
39 105A 105A N CA 818 819 171.64 145.30 -40.90
40 6339 106Y 107C C N 833 835 -101.99 -117.90 66.36 2.35 -63.00 124.06 13.10
40 107C 107C N CA 835 836 76.67 141.10 -41.10
41 6340 107C 108A C N 839 841 -30.63 -68.20 59.57 3.75 -62.50 143.55 25.20
41 108A 108A N CA 841 842 99.07 145.30 -40.90
42 6366 133L 134N C N 1042 1044 -91.45 -119.90 62.37 2.12 -63.20 125.80 14.35
42 134N 134N N CA 1044 1045 81.49 137.00 -41.10
43 6367 134N 135L C N 1050 1052 -59.25 -63.50 30.94 4.07 -108.50 163.25 9.21
43 135L 135L N CA 1052 1053 -71.85 -41.20 132.50
44 6379 146Q 147N C N 1143 1145 -59.21 -63.20 10.73 1.57 -119.90 178.76 6.60
44 147N 147N N CA 1145 1146 -31.14 -41.10 137.00
45 6380 147N 148N C N 1151 1153 -54.27 -63.20 15.81 1.70 55.90 144.60 17.42
45 148N 148N N CA 1153 1154 -54.15 -41.10 39.50
46 6384 151G 152G C N 1179 1181 -78.80 -80.20 23.26 0.99 82.20 -125.00 17.91
46 152G 152G N CA 1181 1182 -162.68 174.10 8.50
47 6387 154I 155K C N 1199 1201 168.58 -118.00 118.94 4.41 -62.90 154.93 26.97
47 155K 155K N CA 1201 1202 -127.32 139.10 -40.80
48 6388 155K 156M C N 1208 1210 -59.34 -73.00 28.11 2.14 -63.40 151.98 22.38
48 156M 156M N CA 1210 1211 167.57 143.00 -40.50
49 6389 156M 157Y C N 1216 1218 -101.83 -98.40 29.75 3.13 -63.50 147.32 21.55
49 157Y 157Y N CA 1218 1219 98.85 128.40 -43.40
50 6390 157Y 158L C N 1228 1230 -141.30 -108.50 67.74 3.24 -63.50 148.97 25.46
50 158L 158L N CA 1230 1231 -168.23 132.50 -41.20
51 6393 160I 161G C N 1252 1254 175.96 -167.20 17.96 0.26 82.20 -163.79 13.74
51 161G 161G N CA 1254 1255 -179.14 174.60 8.50
52 6394 161G 162L C N 1256 1258 -85.12 -108.50 39.00 1.81 -63.50 144.12 18.88
52 162L 162L N CA 1258 1259 101.28 132.50 -41.20
53 6395 162L 163D C N 1264 1266 -127.63 -96.50 36.63 1.52 -63.30 -174.96 19.91
53 163D 163D N CA 1266 1267 133.50 114.20 -40.00
54 6396 163D 164N C N 1272 1274 -66.18 -71.20 8.55 0.45 -63.20 177.00 21.97
54 164N 164N N CA 1274 1275 135.88 142.80 -41.10
55 6397 164N 165S C N 1280 1282 -72.12 -72.40 7.33 0.42 -64.10 -179.90 13.54
55 165S 165S N CA 1282 1283 145.07 152.40 -35.00
56 6398 165S 166G C N 1286 1288 81.22 78.70 30.50 0.77 82.20 155.00 7.48
56 166G 166G N CA 1288 1289 163.50 -166.10 8.50
57 6399 166G 167K C N 1290 1292 -124.48 -118.00 6.48 0.25 -62.90 -169.95 22.14
57 167K 167K N CA 1292 1293 139.00 139.10 -40.80
58 6400 167K 168A C N 1299 1301 -129.90 -134.00 4.59 0.23 -62.50 -177.08 33.58
58 168A 168A N CA 1301 1302 149.06 147.00 -40.90
59 6401 168A 169K C N 1304 1306 -100.05 -118.00 23.28 0.80 -62.90 169.21 20.24
59 169K 169K N CA 1306 1307 124.28 139.10 -40.80
60 6402 169K 170H C N 1313 1315 -127.73 -125.60 13.95 0.57 -63.20 179.33 19.37
60 170H 170H N CA 1315 1316 125.02 138.80 -42.30
61 6403 170H 171W C N 1323 1325 -120.72 -124.90 29.29 1.32 -63.00 168.78 18.66
61 171W 171W N CA 1325 1326 114.41 143.40 -44.20
62 6404 171W 172Y C N 1337 1339 -130.31 -124.30 11.22 0.85 -63.50 -177.97 25.90
62 172Y 172Y N CA 1339 1340 125.92 135.40 -43.40
63 6406 173V 174S C N 1356 1358 -116.78 -136.60 21.56 0.68 -64.10 -174.64 11.45
63 174S 174S N CA 1358 1359 142.71 151.20 -35.00
64 6407 174S 175D C N 1362 1364 -96.31 -96.50 3.77 0.16 -63.30 154.02 17.27
64 175D 175D N CA 1364 1365 110.44 114.20 -40.00
65 6408 175D 176G C N 1370 1372 67.64 78.70 12.12 0.45 82.20 170.26 8.99
65 176G 176G N CA 1372 1373 -161.14 -166.10 8.50
66 6410 177V 178S C N 1381 1383 -103.03 -72.40 33.61 2.68 -64.10 177.88 11.18
66 178S 178S N CA 1383 1384 138.57 152.40 -35.00
67 6412 179V 180R C N 1394 1396 -109.59 -125.20 24.10 0.76 -63.00 169.85 20.24
67 180R 180R N CA 1396 1397 122.24 140.60 -41.10
68 6413 180R 181H C N 1405 1407 -139.56 -125.60 16.72 0.74 -63.20 -171.91 20.13
68 181H 181H N CA 1407 1408 129.60 138.80 -42.30
69 6415 182V 183R C N 1422 1424 -132.71 -125.20 7.51 0.30 -63.00 -168.46 30.67
69 183R 183R N CA 1424 1425 140.50 140.60 -41.10
70 6416 183R 184T C N 1433 1435 -132.54 -124.80 11.11 0.36 -63.20 -179.70 27.68
70 184T 184T N CA 1435 1436 151.47 143.50 -42.10
71 6418 185I 186R C N 1448 1450 -170.69 -125.20 46.97 1.60 -63.00 -161.61 33.96
71 186R 186R N CA 1450 1451 152.28 140.60 -41.10
72 6419 186R 187M C N 1459 1461 -143.89 -125.60 19.41 0.62 -63.40 -169.65 34.75
72 187M 187M N CA 1461 1462 147.00 140.50 -40.50
73 6420 187M 188L C N 1467 1469 -120.49 -108.50 37.20 1.86 -63.50 161.47 25.95
73 188L 188L N CA 1469 1470 167.72 132.50 -41.20
74 6421 188L 189E C N 1475 1477 -67.23 -69.30 41.65 3.11 -63.60 141.25 18.64
74 189E 189E N CA 1477 1478 100.90 142.50 -40.30
75 6422 189E 190N C N 1484 1486 -144.96 -119.90 37.20 1.10 -63.20 174.71 26.43
75 190N 190N N CA 1486 1487 164.50 137.00 -41.10
76 6424 191Y 192Q C N 1504 1506 -146.05 -121.10 50.04 1.86 -63.80 159.48 27.65
76 192Q 192Q N CA 1506 1507 -176.93 139.70 -40.30
77 6425 192Q 193N C N 1513 1515 -68.18 -71.20 11.79 0.84 -63.20 164.78 20.88
77 193N 193N N CA 1515 1516 154.20 142.80 -41.10
78 6426 193N 194K C N 1521 1523 -60.69 -70.20 14.62 0.88 -62.90 170.11 22.21
78 194K 194K N CA 1523 1524 129.30 140.40 -40.80
79 6427 194K 195W C N 1530 1532 -135.60 -124.90 20.83 0.74 -63.00 170.74 26.23
79 195W 195W N CA 1532 1533 161.27 143.40 -44.20
80 6428 195W 196A C N 1544 1546 -130.85 -134.00 5.40 0.33 -62.50 -178.89 33.34
80 196A 196A N CA 1546 1547 151.39 147.00 -40.90
81 6429 196A 197K C N 1549 1551 -67.44 -70.20 9.93 0.65 -62.90 171.72 22.06
81 197K 197K N CA 1551 1552 130.86 140.40 -40.80
82 6430 197K 198L C N 1558 1560 -114.52 -108.50 12.39 0.71 -63.50 170.68 21.38
82 198L 198L N CA 1560 1561 121.68 132.50 -41.20
83 6431 198L 199N C N 1566 1568 -133.63 -119.90 14.07 0.66 -63.20 -171.35 20.60
83 199N 199N N CA 1568 1569 133.91 137.00 -41.10
84 6432 199N 200L C N 1574 1576 -90.84 -108.50 19.68 1.05 -63.50 179.70 26.60
84 200L 200L N CA 1576 1577 141.19 132.50 -41.20
85 6435 202V 203D C N 1596 1598 -59.33 -70.90 29.41 1.00 -63.30 163.31 20.40
85 203D 203D N CA 1598 1599 123.26 150.30 -40.00
86 6436 203D 204T C N 1604 1606 -79.62 -78.10 28.70 1.28 -63.20 164.07 20.00
86 204T 204T N CA 1606 1607 121.14 149.80 -42.10
87 6437 204T 205M C N 1611 1613 -77.03 -73.00 6.44 0.40 -63.40 172.01 26.76
87 205M 205M N CA 1613 1614 148.02 143.00 -40.50
88 6438 205M 206F C N 1619 1621 -142.98 -124.20 59.24 2.27 -63.20 140.97 24.47
88 206F 206F N CA 1621 1622 -160.52 143.30 -44.30
89 6440 207I 208A C N 1638 1640 -50.65 -68.20 17.80 1.60 -62.50 171.25 27.51
89 208A 208A N CA 1640 1641 148.26 145.30 -40.90
90 6443 210I 211E C N 1660 1662 -73.36 -69.30 6.06 0.34 -63.60 172.98 23.60
90 211E 211E N CA 1662 1663 146.99 142.50 -40.30
91 6444 211E 212A C N 1669 1671 -69.18 -68.20 5.83 0.50 -62.50 179.67 29.78
91 212A 212A N CA 1671 1672 139.55 145.30 -40.90
92 6445 212A 213E C N 1674 1676 -133.11 -117.80 21.15 1.12 -63.60 176.76 20.67
92 213E 213E N CA 1676 1677 122.21 136.80 -40.30
93 6446 213E 214F C N 1683 1685 -8.86 -71.40 102.25 9.08 -63.20 108.67 12.34
93 214F 214F N CA 1685 1686 -138.41 140.70 -44.30
94 6447 214F 215G C N 1694 1696 93.07 78.70 57.72 1.08 82.20 129.94 6.85
94 215G 215G N CA 1696 1697 137.99 -166.10 8.50
95 6448 215G 216R C N 1698 1700 -127.17 -125.20 24.48 1.14 -63.00 166.74 26.93
95 216R 216R N CA 1700 1701 165.00 140.60 -41.10
96 6449 216R 217K C N 1709 1711 -158.24 -118.00 89.91 3.66 -62.90 137.95 23.37
96 217K 217K N CA 1711 1712 -140.49 139.10 -40.80
97 6450 217K 218I C N 1718 1720 -151.43 -120.60 73.47 5.31 -63.40 138.72 21.15
97 218I 218I N CA 1720 1721 63.61 130.30 -43.60
98 6451 218I 219D C N 1726 1728 49.28 -63.30 126.15 21.54 -63.30 126.15 21.54
98 219D 219D N CA 1728 1729 16.92 -40.00 -40.00
99 6454 221A 222S C N 1747 1749 51.14 -72.40 141.13 11.33 -72.40 141.13 11.33
99 222S 222S N CA 1749 1750 -139.36 152.40 152.40
100 6455 222S 223G C N 1753 1755 -70.24 -80.20 91.30 3.10 82.20 169.83 7.87
100 223G 223G N CA 1755 1756 83.35 174.10 8.50
101 6457 224E 225V C N 1766 1768 -30.19 -62.40 33.36 4.82 -125.40 -168.98 10.96
101 225V 225V N CA 1768 1769 -51.10 -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 1 24 37 136 135 207 182 197 253 254 274
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 226
Number of all, selected real atoms : 1784 1784
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13125 13125
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3525
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 : 1723.5474
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 0.004 0.004 9.0218 1.000
2 Bond angle potential : 2468 1 5 1.922 1.922 169.99 1.000
3 Stereochemical cosine torsion poten: 1168 0 58 51.177 51.177 466.84 1.000
4 Stereochemical improper torsion pot: 773 0 1 1.151 1.151 21.874 1.000
5 Soft-sphere overlap restraints : 3525 0 0 0.004 0.004 6.6453 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) : 2408 1 23 0.517 0.517 233.00 1.000
10 Distance restraints 2 (N-O) : 2569 4 25 0.619 0.619 289.09 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 4 4.728 4.728 59.302 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 3 83.294 83.294 64.913 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 80.345 80.345 72.402 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 84.336 84.336 43.752 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 78.560 78.560 13.888 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) : 915 0 0 0.507 0.507 18.632 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 99 39 36.577 113.967 236.81 1.000
26 Distance restraints 4 (SDCH-SDCH) : 131 0 0 1.318 1.318 17.397 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 : 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: P62693.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: 36250.9531
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 2072 24P 24P N CA 184 185 134.10 108.20 25.91 5.89 108.20 25.91 5.89
-------------------------------------------------------------------------------------------------
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 8924 94F 129R CA CA 731 1003 10.33 7.73 2.60 4.93 7.73 2.60 4.93
-------------------------------------------------------------------------------------------------
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 10890 94F 138K N O 730 1087 15.76 10.64 5.11 4.91 10.64 5.11 4.91
-------------------------------------------------------------------------------------------------
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 6480 23K 23K CA C 176 182 -147.88 -180.00 32.11 6.42 -180.00 32.11 6.42
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6251 18R 19L C N 141 143 56.21 60.20 13.16 0.49 -63.50 145.87 26.81
1 19L 19L N CA 143 144 42.14 29.60 -41.20
2 6253 20T 21A C N 156 158 49.62 55.40 9.98 0.41 -62.50 142.06 28.73
2 21A 21A N CA 158 159 46.34 38.20 -40.90
3 6254 21A 22Y C N 161 163 60.12 55.90 5.52 0.67 -63.50 150.86 28.57
3 22Y 22Y N CA 163 164 43.06 39.50 -43.40
4 6256 23K 24P C N 182 184 -35.38 -58.70 59.45 3.51 -64.50 130.90 11.35
4 24P 24P N CA 184 185 -85.18 -30.50 147.20
5 6257 24P 25V C N 189 191 48.12 -62.40 134.25 16.65 -62.40 134.25 16.65
5 25V 25V N CA 191 192 -118.61 -42.40 -42.40
6 6270 37H 38Y C N 302 304 60.59 55.90 7.64 0.40 -63.50 145.97 27.60
6 38Y 38Y N CA 304 305 33.47 39.50 -43.40
7 6273 40V 41T C N 325 327 -101.31 -124.80 94.42 3.39 -63.20 101.57 11.00
7 41T 41T N CA 327 328 52.04 143.50 -42.10
8 6280 47T 48Q C N 376 378 -71.52 -121.10 76.30 3.95 -63.80 122.25 18.38
8 48Q 48Q N CA 378 379 -162.30 139.70 -40.30
9 6289 56E 57I C N 444 446 -160.05 -120.60 48.05 3.84 -63.40 175.49 26.67
9 57I 57I N CA 446 447 102.87 130.30 -43.60
10 6290 57I 58D C N 452 454 -50.49 -96.50 48.54 2.00 54.50 119.87 9.95
10 58D 58D N CA 454 455 98.73 114.20 40.90
11 6294 61N 62K C N 484 486 -106.38 -62.90 93.45 10.73 -62.90 93.45 10.73
11 62K 62K N CA 486 487 41.92 -40.80 -40.80
12 6295 62K 63Y C N 493 495 -112.79 -98.40 15.34 0.74 -63.50 173.63 25.23
12 63Y 63Y N CA 495 496 123.08 128.40 -43.40
13 6296 63Y 64A C N 505 507 148.29 -134.00 77.99 2.84 -62.50 -127.15 45.91
13 64A 64A N CA 507 508 140.33 147.00 -40.90
14 6298 65P 66M C N 517 519 -166.33 -125.60 45.62 1.38 -63.40 -171.06 36.08
14 66M 66M N CA 519 520 161.06 140.50 -40.50
15 6300 67V 68D C N 532 534 -103.46 -96.50 9.28 0.39 -63.30 165.28 18.34
15 68D 68D N CA 534 535 120.33 114.20 -40.00
16 6301 68D 69A C N 540 542 -113.96 -134.00 21.32 0.50 -62.50 -173.37 33.32
16 69A 69A N CA 542 543 139.71 147.00 -40.90
17 6302 69A 70Y C N 545 547 -117.83 -124.30 10.22 0.42 -63.50 179.32 25.93
17 70Y 70Y N CA 547 548 127.49 135.40 -43.40
18 6304 71V 72K C N 564 566 -132.25 -118.00 22.45 0.82 -62.90 176.91 27.12
18 72K 72K N CA 566 567 156.45 139.10 -40.80
19 6305 72K 73G C N 573 575 -161.85 -167.20 16.63 0.56 82.20 -170.13 14.12
19 73G 73G N CA 575 576 158.85 174.60 8.50
20 6306 73G 74K C N 577 579 -109.80 -118.00 9.17 0.42 -62.90 -177.85 26.43
20 74K 74K N CA 579 580 143.19 139.10 -40.80
21 6307 74K 75A C N 586 588 -114.31 -134.00 21.89 0.50 -62.50 -174.30 28.38
21 75A 75A N CA 588 589 137.43 147.00 -40.90
22 6308 75A 76N C N 591 593 -125.45 -119.90 6.92 0.20 -63.20 -171.66 27.09
22 76N 76N N CA 593 594 141.14 137.00 -41.10
23 6309 76N 77Q C N 599 601 -104.22 -121.10 27.82 0.96 -63.80 162.97 22.05
23 77Q 77Q N CA 601 602 117.58 139.70 -40.30
24 6310 77Q 78N C N 608 610 -135.12 -119.90 19.03 0.55 -63.20 -174.97 27.21
24 78N 78N N CA 610 611 148.42 137.00 -41.10
25 6311 78N 79E C N 616 618 -82.49 -69.30 81.05 6.63 -63.60 104.56 12.99
25 79E 79E N CA 618 619 62.53 142.50 -40.30
26 6312 79E 80F C N 625 627 -163.69 -124.20 54.30 1.44 -63.20 168.40 29.46
26 80F 80F N CA 627 628 -179.43 143.30 -44.30
27 6313 80F 81D C N 636 638 -80.35 -96.50 51.27 2.16 -63.30 106.90 12.26
27 81D 81D N CA 638 639 65.54 114.20 -40.00
28 6314 81D 82A C N 644 646 -72.97 -68.20 8.24 0.52 -62.50 167.41 27.96
28 82A 82A N CA 646 647 152.02 145.30 -40.90
29 6315 82A 83L C N 649 651 -70.69 -70.70 4.87 0.37 -63.50 178.08 24.32
29 83L 83L N CA 651 652 136.73 141.60 -41.20
30 6317 84V 85S C N 664 666 -63.06 -72.40 20.23 0.94 -64.10 169.46 12.34
30 85S 85S N CA 666 667 134.46 152.40 -35.00
31 6318 85S 86L C N 670 672 -76.37 -70.70 5.72 0.49 -63.50 176.92 25.32
31 86L 86L N CA 672 673 142.35 141.60 -41.20
32 6319 86L 87A C N 678 680 -69.40 -68.20 1.20 0.10 -62.50 174.02 28.86
32 87A 87A N CA 680 681 145.22 145.30 -40.90
33 6320 87A 88Y C N 683 685 -116.61 -124.30 9.62 0.48 -63.50 -179.01 26.23
33 88Y 88Y N CA 685 686 129.62 135.40 -43.40
34 6321 88Y 89N C N 695 697 -106.81 -119.90 24.57 0.79 -63.20 163.24 18.35
34 89N 89N N CA 697 698 116.21 137.00 -41.10
35 6323 90C 91G C N 709 711 -140.10 -167.20 47.27 1.28 82.20 -172.44 14.48
35 91G 91G N CA 711 712 135.86 174.60 8.50
36 6324 91G 92N C N 713 715 -77.54 -71.20 10.05 0.53 -63.20 168.91 21.92
36 92N 92N N CA 715 716 150.60 142.80 -41.10
37 6326 93V 94F C N 728 730 158.14 -124.20 96.43 2.50 -63.20 -179.70 32.47
37 94F 94F N CA 730 731 -159.54 143.30 -44.30
38 6331 98G 99W C N 763 765 -127.46 -124.90 101.31 4.98 -63.00 107.73 12.18
38 99W 99W N CA 765 766 42.13 143.40 -44.20
39 6336 103S 104H C N 806 808 -159.56 -125.60 90.07 3.94 -63.20 137.21 15.39
39 104H 104H N CA 808 809 55.38 138.80 -42.30
40 6337 104H 105A C N 816 818 -68.95 -68.20 18.76 1.49 -62.50 155.19 25.75
40 105A 105A N CA 818 819 164.04 145.30 -40.90
41 6340 107C 108A C N 839 841 61.77 55.40 12.13 1.23 -62.50 153.10 31.04
41 108A 108A N CA 841 842 48.52 38.20 -40.90
42 6349 116N 117A C N 913 915 -63.76 -68.20 9.60 0.91 -62.50 165.30 27.15
42 117A 117A N CA 915 916 153.81 145.30 -40.90
43 6350 117A 118G C N 918 920 110.71 78.70 43.72 2.36 -80.20 176.21 9.88
43 118G 118G N CA 920 921 -136.32 -166.10 174.10
44 6351 118G 119G C N 922 924 142.64 82.20 61.17 3.72 -62.40 160.10 26.69
44 119G 119G N CA 924 925 -0.94 8.50 -41.20
45 6366 133L 134N C N 1042 1044 -85.70 -71.20 59.92 4.24 -63.20 127.75 14.84
45 134N 134N N CA 1044 1045 84.66 142.80 -41.10
46 6367 134N 135L C N 1050 1052 -55.49 -63.50 70.08 9.30 -108.50 128.16 7.29
46 135L 135L N CA 1052 1053 -110.82 -41.20 132.50
47 6383 150T 151G C N 1175 1177 140.69 -167.20 52.18 0.93 82.20 178.65 11.44
47 151G 151G N CA 1177 1178 177.31 174.60 8.50
48 6384 151G 152G C N 1179 1181 -118.87 -80.20 56.19 3.93 82.20 -157.91 15.74
48 152G 152G N CA 1181 1182 133.33 174.10 8.50
49 6385 152G 153M C N 1183 1185 -153.66 -125.60 40.35 1.24 -63.40 175.06 33.09
49 153M 153M N CA 1185 1186 169.50 140.50 -40.50
50 6387 154I 155K C N 1199 1201 -130.41 -118.00 47.80 2.12 -62.90 149.98 23.52
50 155K 155K N CA 1201 1202 -174.73 139.10 -40.80
51 6388 155K 156M C N 1208 1210 -60.75 -73.00 22.11 1.71 -63.40 158.11 23.40
51 156M 156M N CA 1210 1211 161.41 143.00 -40.50
52 6389 156M 157Y C N 1216 1218 -65.26 -98.40 35.68 2.01 -63.50 158.59 25.07
52 157Y 157Y N CA 1218 1219 115.18 128.40 -43.40
53 6390 157Y 158L C N 1228 1230 -166.31 -108.50 58.18 2.70 -63.50 -152.92 35.08
53 158L 158L N CA 1230 1231 139.05 132.50 -41.20
54 6394 161G 162L C N 1256 1258 -62.53 -70.70 13.58 0.84 -63.50 171.96 23.93
54 162L 162L N CA 1258 1259 130.75 141.60 -41.20
55 6395 162L 163D C N 1264 1266 -113.82 -96.50 17.34 0.71 -63.30 163.14 17.72
55 163D 163D N CA 1266 1267 115.12 114.20 -40.00
56 6396 163D 164N C N 1272 1274 -117.50 -119.90 12.46 0.51 -63.20 174.53 19.36
56 164N 164N N CA 1274 1275 124.77 137.00 -41.10
57 6397 164N 165S C N 1280 1282 -133.97 -136.60 2.66 0.10 -64.10 -172.29 18.55
57 165S 165S N CA 1282 1283 150.78 151.20 -35.00
58 6398 165S 166G C N 1286 1288 177.29 -167.20 30.92 1.25 82.20 168.70 12.31
58 166G 166G N CA 1288 1289 147.85 174.60 8.50
59 6399 166G 167K C N 1290 1292 -117.72 -118.00 23.46 1.14 -62.90 165.77 19.29
59 167K 167K N CA 1292 1293 115.64 139.10 -40.80
60 6400 167K 168A C N 1299 1301 -156.59 -134.00 22.61 0.78 -62.50 -163.05 37.31
60 168A 168A N CA 1301 1302 146.08 147.00 -40.90
61 6401 168A 169K C N 1304 1306 -133.57 -118.00 19.04 0.92 -62.90 -176.86 21.13
61 169K 169K N CA 1306 1307 128.15 139.10 -40.80
62 6402 169K 170H C N 1313 1315 -127.44 -125.60 2.01 0.08 -63.20 -169.16 28.07
62 170H 170H N CA 1315 1316 137.99 138.80 -42.30
63 6403 170H 171W C N 1323 1325 -120.88 -124.90 4.34 0.23 -63.00 -179.70 26.40
63 171W 171W N CA 1325 1326 145.05 143.40 -44.20
64 6404 171W 172Y C N 1337 1339 -113.37 -98.40 15.51 0.68 -63.50 175.01 25.43
64 172Y 172Y N CA 1339 1340 124.35 128.40 -43.40
65 6406 173V 174S C N 1356 1358 -100.52 -72.40 31.48 2.52 -64.10 177.05 11.19
65 174S 174S N CA 1358 1359 138.26 152.40 -35.00
66 6407 174S 175D C N 1362 1364 -100.07 -96.50 18.77 0.78 -63.30 140.67 15.51
66 175D 175D N CA 1364 1365 95.78 114.20 -40.00
67 6408 175D 176G C N 1370 1372 70.87 78.70 9.22 0.51 82.20 179.83 9.30
67 176G 176G N CA 1372 1373 -170.97 -166.10 8.50
68 6410 177V 178S C N 1381 1383 -115.50 -136.60 22.94 0.72 -64.10 -175.49 11.41
68 178S 178S N CA 1383 1384 142.21 151.20 -35.00
69 6412 179V 180R C N 1394 1396 -95.91 -72.10 30.24 2.62 -63.00 167.62 20.62
69 180R 180R N CA 1396 1397 123.26 141.90 -41.10
70 6413 180R 181H C N 1405 1407 -113.98 -125.60 20.98 0.56 -63.20 171.34 18.83
70 181H 181H N CA 1407 1408 121.34 138.80 -42.30
71 6415 182V 183R C N 1422 1424 -132.03 -125.20 11.31 0.63 -63.00 -174.03 21.47
71 183R 183R N CA 1424 1425 131.59 140.60 -41.10
72 6416 183R 184T C N 1433 1435 -131.54 -124.80 6.74 0.36 -63.20 -172.43 28.56
72 184T 184T N CA 1435 1436 143.23 143.50 -42.10
73 6418 185I 186R C N 1448 1450 -164.03 -125.20 48.89 1.44 -63.00 179.68 30.95
73 186R 186R N CA 1450 1451 170.31 140.60 -41.10
74 6419 186R 187M C N 1459 1461 -83.77 -73.00 59.75 4.23 -63.40 126.38 17.38
74 187M 187M N CA 1461 1462 84.23 143.00 -40.50
75 6420 187M 188L C N 1467 1469 -140.18 -108.50 38.58 1.71 -63.50 -178.70 29.92
75 188L 188L N CA 1469 1470 154.51 132.50 -41.20
76 6421 188L 189E C N 1475 1477 -88.80 -69.30 27.09 2.49 -63.60 165.92 20.84
76 189E 189E N CA 1477 1478 123.70 142.50 -40.30
77 6422 189E 190N C N 1484 1486 -127.39 -119.90 34.62 1.39 -63.20 161.42 23.82
77 190N 190N N CA 1486 1487 170.80 137.00 -41.10
78 6423 190N 191Y C N 1492 1494 -123.32 -124.30 22.48 1.23 -63.50 169.63 29.92
78 191Y 191Y N CA 1494 1495 157.86 135.40 -43.40
79 6424 191Y 192Q C N 1504 1506 -59.49 -73.00 13.53 0.95 -63.80 179.78 26.21
79 192Q 192Q N CA 1506 1507 139.97 140.70 -40.30
80 6425 192Q 193N C N 1513 1515 -68.00 -71.20 7.26 0.55 -63.20 169.66 21.48
80 193N 193N N CA 1515 1516 149.31 142.80 -41.10
81 6426 193N 194K C N 1521 1523 103.04 56.60 109.28 11.38 -62.90 -116.41 41.17
81 194K 194K N CA 1523 1524 137.53 38.60 -40.80
82 6427 194K 195W C N 1530 1532 -106.52 -124.90 23.16 0.74 -63.00 178.87 20.24
82 195W 195W N CA 1532 1533 129.30 143.40 -44.20
83 6428 195W 196A C N 1544 1546 -62.80 -68.20 15.57 1.07 -62.50 171.60 28.11
83 196A 196A N CA 1546 1547 130.70 145.30 -40.90
84 6429 196A 197K C N 1549 1551 -160.13 -118.00 47.09 1.56 -62.90 -173.58 29.99
84 197K 197K N CA 1551 1552 160.14 139.10 -40.80
85 6430 197K 198L C N 1558 1560 -88.75 -108.50 34.62 1.62 -63.50 147.44 19.17
85 198L 198L N CA 1560 1561 104.06 132.50 -41.20
86 6431 198L 199N C N 1566 1568 -110.88 -119.90 47.29 1.93 -63.20 140.04 15.41
86 199N 199N N CA 1568 1569 90.58 137.00 -41.10
87 6432 199N 200L C N 1574 1576 -139.84 -108.50 31.69 1.46 -63.50 -165.91 23.90
87 200L 200L N CA 1576 1577 137.25 132.50 -41.20
88 6435 202V 203D C N 1596 1598 -103.54 -96.50 18.78 0.78 -63.30 142.59 15.62
88 203D 203D N CA 1598 1599 96.79 114.20 -40.00
89 6436 203D 204T C N 1604 1606 -88.94 -78.10 40.50 1.42 -63.20 131.62 18.60
89 204T 204T N CA 1606 1607 -171.18 149.80 -42.10
90 6437 204T 205M C N 1611 1613 -62.03 -73.00 18.37 1.15 -63.40 168.77 25.30
90 205M 205M N CA 1613 1614 128.26 143.00 -40.50
91 6438 205M 206F C N 1619 1621 -105.38 -124.20 33.88 1.04 -63.20 164.92 20.27
91 206F 206F N CA 1621 1622 115.13 143.30 -44.30
92 6441 208A 209E C N 1643 1645 -148.53 -117.80 31.31 1.01 -63.60 -163.78 30.91
92 209E 209E N CA 1645 1646 142.82 136.80 -40.30
93 6443 210I 211E C N 1660 1662 -129.27 -117.80 31.17 1.70 -63.60 162.02 18.91
93 211E 211E N CA 1662 1663 107.81 136.80 -40.30
94 6444 211E 212A C N 1669 1671 70.64 -68.20 139.27 12.17 -62.50 -149.67 31.94
94 212A 212A N CA 1671 1672 156.28 145.30 -40.90
95 6445 212A 213E C N 1674 1676 -97.85 -117.80 23.54 1.17 -63.60 173.80 25.11
95 213E 213E N CA 1676 1677 149.30 136.80 -40.30
96 6446 213E 214F C N 1683 1685 65.59 -71.40 139.60 10.31 -63.20 -163.72 22.33
96 214F 214F N CA 1685 1686 167.58 140.70 -44.30
97 6447 214F 215G C N 1694 1696 -127.73 -167.20 52.24 1.89 82.20 -140.86 6.63
97 215G 215G N CA 1696 1697 -151.18 174.60 8.50
98 6448 215G 216R C N 1698 1700 -122.49 -125.20 94.58 4.63 -63.00 102.74 17.79
98 216R 216R N CA 1700 1701 -124.87 140.60 -41.10
99 6449 216R 217K C N 1709 1711 -74.08 -62.90 62.54 7.58 -62.90 62.54 7.58
99 217K 217K N CA 1711 1712 20.73 -40.80 -40.80
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 26 149 123 204 165 197 202 245 259
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P62693.B99990001.pdb 1741.95056
P62693.B99990002.pdb 1723.54736
In [ ]:
# Посмотрим результат
In [ ]:
!pip install py3Dmol
import py3Dmol
with open("P62693.B99990001.pdb", "r") as f:
pdb_data = f.read()
view = py3Dmol.view(width=400, height=300)
view.addModel(pdb_data, 'pdb')
view.setStyle({'cartoon': {'color': 'spectrum'}})
view.zoomTo()
view.show()
Requirement already satisfied: py3Dmol in /usr/local/lib/python3.12/dist-packages (2.5.4)
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
In [ ]:
# Лизоцим без лиганда выглядит растрёпанным
In [ ]:
# Надо добавить лиганд к последовательности
In [ ]:
!cat all_in_one.ali
>P1;P62693 sequence::: :: :::-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVPWEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGKA NQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQT GGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGEV K* >P1;1lmp structureX:1lmp.pdb:1:A:+129:A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGI-FQINSRY------------ ------------------WCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQD ------------------------------------------------------------------LRSYVAGCG V*
In [ ]:
%%writefile all_in_one_2.ali
>P1;P62693
sequence::: :: :::-1.00:-1.00
MKVSQNGLNLIKEFEGCRLTAYKPVP-WEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGK
ANQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQ
TGGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGE
VK/...*
>P1;1lmp
structureX:1lmp:1:A:3:B::::
KVYDRCELARALKASGMDGYAGNSLPNWVCLS--KWESSYNTQATNRNTDGSTDYGIFQIN--------------
-----------SRYWCD-----DGRTPGAKNVCG-----------------IRCSQLLTDDLT------------
---------------------------VAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV--------
--/...*
Overwriting all_in_one_2.ali
In [ ]:
#structureX:1lmp.pdb:1 :A: 132 :A:undefined:undefined:-1.00:-1.00
In [ ]:
!cat all_in_one_2.ali
>P1;P62693 sequence::: :: :::-1.00:-1.00 MKVSQNGLNLIKEFEGCRLTAYKPVP-WEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGK ANQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQ TGGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGE VK/...* >P1;1lmp structureX:1lmp:1:A:3:B:::: KVYDRCELARALKASGMDGYAGNSLPNWVCLS--KWESSYNTQATNRNTDGSTDYGIFQIN-------------- -----------SRYWCD-----DGRTPGAKNVCG-----------------IRCSQLLTDDLT------------ ---------------------------VAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV-------- --/...*
In [ ]:
#Поместим лиганд в другое место
In [ ]:
class mymodel(AutoModel):
def special_constraints(self, aln):
pass
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('CG:83:A','O6:229:B')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one_2.ali', knowns='1lmp', sequence='P62693')
a.name='P62693_ligand'
a.starting_model = 1
a.ending_model = 2
a.make()
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16033 14444
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.
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 : 14444 14444
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4150
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 : 2114.7380
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 35.810 1.000
2 Bond angle potential : 2468 1 8 2.236 2.236 235.64 1.000
3 Stereochemical cosine torsion poten: 1168 0 57 50.441 50.441 471.22 1.000
4 Stereochemical improper torsion pot: 773 1 2 1.998 1.998 58.961 1.000
5 Soft-sphere overlap restraints : 4150 2 2 0.008 0.008 30.779 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) : 2356 0 5 0.598 0.598 145.04 1.000
10 Distance restraints 2 (N-O) : 2508 2 15 0.781 0.781 256.38 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 4 5.610 5.610 83.503 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 3 85.372 85.372 81.505 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 1 77.121 77.121 85.416 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 1 85.748 85.748 49.266 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 80.835 80.835 16.379 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) : 900 0 0 0.532 0.532 15.948 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 97 42 39.528 116.722 317.16 1.000
26 Distance restraints 4 (SDCH-SDCH) : 177 0 0 1.513 1.513 13.959 1.000
27 Distance restraints 5 (X-Y) : 1401 11 24 0.139 0.139 217.77 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: P62693.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: 36919.3203
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 2773 87A 87A N CA 680 681 129.65 107.00 22.65 6.51 107.00 22.65 6.51
-------------------------------------------------------------------------------------------------
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 10700 86L 52D N O 672 413 6.29 2.95 3.33 7.64 2.95 3.33 7.64
2 10702 86L 54Q N O 672 428 12.02 7.81 4.20 4.68 7.81 4.20 4.68
-------------------------------------------------------------------------------------------------
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 6544 87A 87A CA C 681 683 -132.52 -180.00 47.48 9.49 -180.00 47.48 9.49
-------------------------------------------------------------------------------------------------
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 6235 2K 3V C N 16 18 -59.93 -62.40 39.34 4.84 -125.40 150.07 8.56
1 3V 3V N CA 18 19 -81.66 -42.40 143.30
2 6236 3V 4S C N 23 25 143.97 -136.60 79.44 3.19 -72.40 143.65 10.33
2 4S 4S N CA 25 26 149.92 151.20 152.40
3 6251 18R 19L C N 141 143 63.50 60.20 6.12 0.23 -63.50 142.96 26.37
3 19L 19L N CA 143 144 24.44 29.60 -41.20
4 6253 20T 21A C N 156 158 56.98 55.40 8.77 0.41 -62.50 138.71 28.21
4 21A 21A N CA 158 159 29.57 38.20 -40.90
5 6254 21A 22Y C N 161 163 63.99 55.90 14.04 0.71 -124.30 -157.48 16.81
5 22Y 22Y N CA 163 164 28.03 39.50 135.40
6 6263 30M 31Y C N 243 245 -133.07 -63.50 69.63 11.87 -63.50 69.63 11.87
6 31Y 31Y N CA 245 246 -40.46 -43.40 -43.40
7 6265 32T 33I C N 262 264 -62.43 -63.40 8.91 1.49 -120.60 175.00 7.91
7 33I 33I N CA 264 265 -34.75 -43.60 130.30
8 6266 33I 34G C N 270 272 100.74 82.20 28.13 2.13 -62.40 177.87 33.59
8 34G 34G N CA 272 273 29.66 8.50 -41.20
9 6269 36G 37H C N 292 294 -150.93 -63.20 111.21 13.18 -63.20 111.21 13.18
9 37H 37H N CA 294 295 26.04 -42.30 -42.30
10 6270 37H 38Y C N 302 304 54.50 55.90 6.97 0.59 -124.30 -153.79 11.27
10 38Y 38Y N CA 304 305 32.67 39.50 135.40
11 6282 49A 50Q C N 390 392 81.30 55.10 28.88 2.67 -121.10 -166.92 9.53
11 50Q 50Q N CA 392 393 28.15 40.30 139.70
12 6287 54Q 55L C N 427 429 68.18 -70.70 150.76 15.05 -108.50 -170.77 9.88
12 55L 55L N CA 429 430 -159.73 141.60 132.50
13 6293 60N 61N C N 476 478 -153.16 -119.90 33.43 1.47 -63.20 -163.46 21.18
13 61N 61N N CA 478 479 133.65 137.00 -41.10
14 6294 61N 62K C N 484 486 -170.81 -118.00 55.28 1.87 -62.90 -163.87 31.86
14 62K 62K N CA 486 487 155.43 139.10 -40.80
15 6295 62K 63Y C N 493 495 -126.54 -124.30 32.60 1.63 -63.50 161.48 28.75
15 63Y 63Y N CA 495 496 167.93 135.40 -43.40
16 6296 63Y 64A C N 505 507 -81.90 -68.20 18.16 1.16 -62.50 163.03 27.71
16 64A 64A N CA 507 508 157.23 145.30 -40.90
17 6297 64A 65P C N 510 512 -72.18 -58.70 21.80 1.38 -64.50 160.75 12.40
17 65P 65P N CA 512 513 -13.37 -30.50 147.20
18 6298 65P 66M C N 517 519 -108.39 -125.60 19.42 0.58 -63.40 177.80 23.44
18 66M 66M N CA 519 520 131.51 140.50 -40.50
19 6300 67V 68D C N 532 534 -141.06 -96.50 44.56 1.82 -63.30 172.32 18.29
19 68D 68D N CA 534 535 113.78 114.20 -40.00
20 6301 68D 69A C N 540 542 -130.20 -134.00 22.64 1.19 -62.50 178.89 26.95
20 69A 69A N CA 542 543 124.68 147.00 -40.90
21 6302 69A 70Y C N 545 547 -136.77 -124.30 22.67 1.72 -63.50 175.86 24.76
21 70Y 70Y N CA 547 548 116.47 135.40 -43.40
22 6304 71V 72K C N 564 566 -146.23 -118.00 37.60 1.30 -62.90 176.20 27.86
22 72K 72K N CA 566 567 163.94 139.10 -40.80
23 6306 73G 74K C N 577 579 -71.28 -70.20 17.11 1.21 -62.90 161.94 21.50
23 74K 74K N CA 579 580 157.47 140.40 -40.80
24 6309 76N 77Q C N 599 601 69.88 -73.00 143.04 10.09 -63.80 -140.39 38.87
24 77Q 77Q N CA 601 602 133.93 140.70 -40.30
25 6311 78N 79E C N 616 618 139.57 -117.80 102.68 3.69 -63.60 -121.41 40.03
25 79E 79E N CA 618 619 139.89 136.80 -40.30
26 6312 79E 80F C N 625 627 -90.70 -71.40 21.61 1.23 -63.20 167.54 25.12
26 80F 80F N CA 627 628 150.43 140.70 -44.30
27 6313 80F 81D C N 636 638 -137.21 -96.50 40.78 1.66 -63.30 168.94 17.94
27 81D 81D N CA 638 639 111.91 114.20 -40.00
28 6314 81D 82A C N 644 646 -165.05 -134.00 31.95 1.35 -62.50 -153.16 39.37
28 82A 82A N CA 646 647 139.48 147.00 -40.90
29 6315 82A 83L C N 649 651 -132.49 -108.50 51.17 2.91 -63.50 145.85 17.87
29 83L 83L N CA 651 652 87.30 132.50 -41.20
30 6317 84V 85S C N 664 666 156.34 -136.60 83.86 2.58 -64.10 -173.69 23.41
30 85S 85S N CA 666 667 -158.44 151.20 -35.00
31 6320 87A 88Y C N 683 685 19.94 -63.50 85.19 13.83 -63.50 85.19 13.83
31 88Y 88Y N CA 685 686 -60.55 -43.40 -43.40
32 6324 91G 92N C N 713 715 -74.22 -71.20 5.58 0.43 -63.20 179.54 21.86
32 92N 92N N CA 715 716 138.10 142.80 -41.10
33 6325 92N 93V C N 721 723 -68.21 -62.40 11.24 1.77 -125.40 174.33 9.75
33 93V 93V N CA 723 724 -52.01 -42.40 143.30
34 6328 95V 96A C N 746 748 -64.28 -68.20 4.24 0.40 -62.50 172.20 28.31
34 96A 96A N CA 748 749 146.91 145.30 -40.90
35 6329 96A 97D C N 751 753 -73.87 -96.50 39.10 1.64 -63.30 122.77 14.54
35 97D 97D N CA 753 754 82.32 114.20 -40.00
36 6330 97D 98G C N 759 761 55.21 78.70 24.36 1.04 82.20 170.31 9.60
36 98G 98G N CA 761 762 -159.65 -166.10 8.50
37 6331 98G 99W C N 763 765 -135.75 -124.90 11.03 0.53 -63.00 -171.06 28.51
37 99W 99W N CA 765 766 141.43 143.40 -44.20
38 6335 102F 103S C N 800 802 -155.09 -64.10 105.75 13.91 -72.40 144.67 6.61
38 103S 103S N CA 802 803 -88.89 -35.00 152.40
39 6336 103S 104H C N 806 808 78.43 -125.60 156.85 5.82 -63.20 -142.93 35.91
39 104H 104H N CA 808 809 122.20 138.80 -42.30
40 6337 104H 105A C N 816 818 -72.16 -68.20 52.49 4.37 -62.50 134.21 21.54
40 105A 105A N CA 818 819 92.96 145.30 -40.90
41 6340 107C 108A C N 839 841 57.94 -68.20 128.89 11.75 55.40 133.63 8.26
41 108A 108A N CA 841 842 171.80 145.30 38.20
42 6341 108A 109S C N 844 846 171.38 -136.60 52.28 2.21 -64.10 -141.98 24.79
42 109S 109S N CA 846 847 146.04 151.20 -35.00
43 6342 109S 110M C N 850 852 -135.32 -125.60 27.43 1.46 -63.40 171.19 21.36
43 110M 110M N CA 852 853 114.85 140.50 -40.50
44 6345 112P 113K C N 873 875 -146.54 -118.00 44.63 1.64 -62.90 168.08 26.81
44 113K 113K N CA 875 876 173.41 139.10 -40.80
45 6346 113K 114Y C N 882 884 -49.81 -98.40 53.63 2.87 -63.50 166.07 25.66
45 114Y 114Y N CA 884 885 151.10 128.40 -43.40
46 6347 114Y 115R C N 894 896 -55.16 -72.10 21.20 1.38 -63.00 170.43 23.55
46 115R 115R N CA 896 897 129.15 141.90 -41.10
47 6348 115R 116N C N 905 907 -148.27 -119.90 45.61 1.38 -63.20 169.15 25.88
47 116N 116N N CA 907 908 172.71 137.00 -41.10
48 6349 116N 117A C N 913 915 -67.33 -68.20 5.53 0.41 -62.50 179.32 29.63
48 117A 117A N CA 915 916 139.84 145.30 -40.90
49 6350 117A 118G C N 918 920 158.14 -167.20 36.57 1.01 82.20 172.08 11.82
49 118G 118G N CA 920 921 162.92 174.60 8.50
50 6351 118G 119G C N 922 924 -128.10 -167.20 39.75 0.62 82.20 -141.67 16.65
50 119G 119G N CA 924 925 167.43 174.60 8.50
51 6352 119G 120Q C N 926 928 51.48 -73.00 130.91 9.98 -63.80 -179.80 23.21
51 120Q 120Q N CA 928 929 -178.79 140.70 -40.30
52 6354 121V 122L C N 942 944 -90.96 -108.50 18.22 0.82 -63.50 170.99 22.32
52 122L 122L N CA 944 945 127.57 132.50 -41.20
53 6355 122L 123Q C N 950 952 -97.60 -121.10 25.73 1.19 -63.80 172.85 27.22
53 123Q 123Q N CA 952 953 150.18 139.70 -40.30
54 6357 124G 125L C N 963 965 -136.39 -108.50 33.84 1.50 -63.50 -177.66 29.83
54 125L 125L N CA 965 966 151.66 132.50 -41.20
55 6370 137N 138K C N 1077 1079 64.40 56.60 16.48 1.77 -62.90 158.20 27.45
55 138K 138K N CA 1079 1080 53.12 38.60 -40.80
56 6373 140V 141S C N 1100 1102 -150.83 -136.60 18.88 1.04 -64.10 -165.77 12.36
56 141S 141S N CA 1102 1103 138.79 151.20 -35.00
57 6374 141S 142S C N 1106 1108 -148.54 -136.60 26.75 1.51 -64.10 -177.09 11.74
57 142S 142S N CA 1108 1109 127.26 151.20 -35.00
58 6375 142S 143N C N 1112 1114 -119.80 -119.90 5.67 0.26 -63.20 -178.52 20.13
58 143N 143N N CA 1114 1115 131.33 137.00 -41.10
59 6376 143N 144S C N 1120 1122 -118.71 -136.60 20.07 0.62 -64.10 -174.68 11.43
59 144S 144S N CA 1122 1123 142.09 151.20 -35.00
60 6377 144S 145N C N 1126 1128 -63.74 -71.20 11.33 0.90 -63.20 167.58 20.98
60 145N 145N N CA 1128 1129 151.33 142.80 -41.10
61 6378 145N 146Q C N 1134 1136 174.43 -121.10 68.87 2.18 -63.80 -162.29 35.05
61 146Q 146Q N CA 1136 1137 163.93 139.70 -40.30
62 6379 146Q 147N C N 1143 1145 -78.60 -71.20 7.53 0.58 -63.20 178.16 23.13
62 147N 147N N CA 1145 1146 141.41 142.80 -41.10
63 6380 147N 148N C N 1151 1153 -67.44 -71.20 11.05 0.81 -63.20 165.76 20.96
63 148N 148N N CA 1153 1154 153.19 142.80 -41.10
64 6381 148N 149Q C N 1159 1161 -122.11 -121.10 34.30 1.62 -63.80 156.95 26.16
64 149Q 149Q N CA 1161 1162 173.99 139.70 -40.30
65 6382 149Q 150T C N 1168 1170 -63.97 -78.10 21.16 0.75 -63.20 176.15 22.54
65 150T 150T N CA 1170 1171 134.04 149.80 -42.10
66 6383 150T 151G C N 1175 1177 79.56 78.70 9.20 0.30 82.20 165.47 8.17
66 151G 151G N CA 1177 1178 -156.94 -166.10 8.50
67 6384 151G 152G C N 1179 1181 -164.94 -167.20 3.64 0.14 82.20 -156.82 14.77
67 152G 152G N CA 1181 1182 177.46 174.60 8.50
68 6385 152G 153M C N 1183 1185 -73.99 -73.00 24.15 1.62 -63.40 152.74 23.64
68 153M 153M N CA 1185 1186 167.12 143.00 -40.50
69 6387 154I 155K C N 1199 1201 -149.84 -118.00 38.63 1.29 -62.90 -179.46 28.64
69 155K 155K N CA 1201 1202 160.97 139.10 -40.80
70 6389 156M 157Y C N 1216 1218 -122.91 -124.30 13.49 0.66 -63.50 175.73 25.18
70 157Y 157Y N CA 1218 1219 121.98 135.40 -43.40
71 6390 157Y 158L C N 1228 1230 -109.17 -108.50 43.15 2.33 -63.50 150.26 23.68
71 158L 158L N CA 1230 1231 175.65 132.50 -41.20
72 6393 160I 161G C N 1252 1254 95.71 78.70 65.70 1.21 82.20 122.68 6.63
72 161G 161G N CA 1254 1255 130.44 -166.10 8.50
73 6394 161G 162L C N 1256 1258 -125.75 -108.50 35.13 2.00 -63.50 156.05 19.20
73 162L 162L N CA 1258 1259 101.89 132.50 -41.20
74 6396 163D 164N C N 1272 1274 -70.83 -71.20 33.09 2.11 -63.20 151.00 18.47
74 164N 164N N CA 1274 1275 109.71 142.80 -41.10
75 6400 167K 168A C N 1299 1301 -69.07 -68.20 2.03 0.13 -62.50 172.09 28.53
75 168A 168A N CA 1301 1302 147.13 145.30 -40.90
76 6401 168A 169K C N 1304 1306 -116.85 -118.00 19.65 0.94 -62.90 169.12 19.72
76 169K 169K N CA 1306 1307 119.49 139.10 -40.80
77 6402 169K 170H C N 1313 1315 -144.99 -125.60 23.78 0.59 -63.20 -175.72 28.36
77 170H 170H N CA 1315 1316 152.57 138.80 -42.30
78 6403 170H 171W C N 1323 1325 -72.14 -71.30 3.91 0.32 -63.00 179.61 21.92
78 171W 171W N CA 1325 1326 135.18 139.00 -44.20
79 6404 171W 172Y C N 1337 1339 -134.99 -124.30 22.41 0.88 -63.50 176.61 31.56
79 172Y 172Y N CA 1339 1340 155.10 135.40 -43.40
80 6405 172Y 173V C N 1349 1351 -64.93 -62.40 3.12 0.38 -125.40 -173.77 10.41
80 173V 173V N CA 1351 1352 -40.56 -42.40 143.30
81 6406 173V 174S C N 1356 1358 -69.43 -72.40 22.09 1.20 -64.10 165.60 11.69
81 174S 174S N CA 1358 1359 130.51 152.40 -35.00
82 6407 174S 175D C N 1362 1364 -133.94 -63.30 108.10 17.71 -63.30 108.10 17.71
82 175D 175D N CA 1364 1365 -121.83 -40.00 -40.00
83 6408 175D 176G C N 1370 1372 -179.68 -167.20 17.39 0.38 82.20 -156.58 14.28
83 176G 176G N CA 1372 1373 -173.30 174.60 8.50
84 6409 176G 177V C N 1374 1376 -137.26 -125.40 40.78 1.69 -62.40 154.61 24.13
84 177V 177V N CA 1376 1377 -177.68 143.30 -42.40
85 6410 177V 178S C N 1381 1383 64.94 -64.10 145.50 14.94 -64.10 145.50 14.94
85 178S 178S N CA 1383 1384 -102.23 -35.00 -35.00
86 6423 190N 191Y C N 1492 1494 69.31 55.90 161.18 12.28 -124.30 178.54 10.93
86 191Y 191Y N CA 1494 1495 -159.88 39.50 135.40
87 6436 203D 204T C N 1604 1606 56.91 55.90 7.25 0.44 -124.80 -149.89 12.74
87 204T 204T N CA 1606 1607 32.32 39.50 143.50
88 6439 206F 207I C N 1630 1632 -100.85 -120.60 74.88 3.55 -63.40 108.35 16.69
88 207I 207I N CA 1632 1633 58.07 130.30 -43.60
89 6445 212A 213E C N 1674 1676 65.96 54.60 33.71 1.82 -63.60 139.22 23.76
89 213E 213E N CA 1676 1677 10.66 42.40 -40.30
90 6448 215G 216R C N 1698 1700 -68.46 -72.10 25.62 1.89 -63.00 157.73 20.95
90 216R 216R N CA 1700 1701 116.53 141.90 -41.10
91 6449 216R 217K C N 1709 1711 -115.90 -118.00 10.67 0.54 -62.90 177.72 26.23
91 217K 217K N CA 1711 1712 149.56 139.10 -40.80
92 6451 218I 219D C N 1726 1728 -98.07 -96.50 21.75 0.92 -63.30 179.30 20.27
92 219D 219D N CA 1728 1729 135.90 114.20 -40.00
93 6452 219D 220M C N 1734 1736 -114.45 -125.60 11.15 0.43 -63.40 -173.49 31.93
93 220M 220M N CA 1736 1737 140.11 140.50 -40.50
94 6453 220M 221A C N 1742 1744 -132.41 -134.00 4.97 0.31 -62.50 -178.59 33.47
94 221A 221A N CA 1744 1745 151.70 147.00 -40.90
95 6454 221A 222S C N 1747 1749 -125.53 -136.60 11.57 0.55 -64.10 -178.84 17.45
95 222S 222S N CA 1749 1750 154.57 151.20 -35.00
96 6455 222S 223G C N 1753 1755 -84.30 -80.20 4.85 0.36 82.20 -126.99 7.37
96 223G 223G N CA 1755 1756 171.51 174.10 8.50
97 6456 223G 224E C N 1757 1759 -93.51 -117.80 30.91 0.94 -63.60 160.78 19.94
97 224E 224E N CA 1759 1760 117.68 136.80 -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 13273 86L 228. CA C7 673 1806 8.99 8.02 0.97 4.86 8.02 0.97 4.86
2 13274 86L 228. CA C8 673 1807 10.36 9.16 1.21 6.04 9.16 1.21 6.04
3 13279 86L 228. CA O7 673 1813 8.13 6.89 1.24 6.21 6.89 1.24 6.21
4 13291 87A 228. CA C6 681 1805 8.67 7.67 0.99 4.97 7.67 0.99 4.97
5 13297 87A 228. CA O6 681 1812 7.52 6.36 1.16 5.78 6.36 1.16 5.78
6 14444 83L 229. CG O6 654 1826 3.81 3.00 0.81 8.15 3.00 0.81 8.15
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 31 173 157 228 214 257 293 266 303
<< 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.
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 : 14444 14444
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4159
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 : 2159.5608
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 7 0.010 0.010 51.334 1.000
2 Bond angle potential : 2468 3 33 2.526 2.526 296.68 1.000
3 Stereochemical cosine torsion poten: 1168 0 66 51.089 51.089 472.80 1.000
4 Stereochemical improper torsion pot: 773 0 3 1.480 1.480 36.856 1.000
5 Soft-sphere overlap restraints : 4159 1 4 0.010 0.010 44.728 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) : 2356 0 8 0.653 0.653 182.34 1.000
10 Distance restraints 2 (N-O) : 2508 3 14 0.777 0.777 267.41 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 225 2 7 5.650 5.650 84.709 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 2 82.758 82.758 59.937 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 82.257 82.257 76.323 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 81.580 81.580 40.949 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 81.879 81.879 15.122 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) : 900 0 0 0.580 0.580 13.585 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 99 43 38.700 113.733 293.20 1.000
26 Distance restraints 4 (SDCH-SDCH) : 177 0 1 1.649 1.649 17.486 1.000
27 Distance restraints 5 (X-Y) : 1401 9 18 0.133 0.133 206.11 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: P62693.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: 37178.4609
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 2491 60N 61N C N 476 478 140.10 120.00 20.10 4.57 120.00 20.10 4.57
2 2947 102F 103S C N 800 802 145.74 120.00 25.74 5.85 120.00 25.74 5.85
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10700 86L 52D N O 672 413 6.95 2.95 4.00 9.16 2.95 4.00 9.16
2 10701 86L 53S N O 672 419 10.66 6.96 3.71 5.00 6.96 3.71 5.00
3 10702 86L 54Q N O 672 428 12.03 7.81 4.22 4.70 7.81 4.22 4.70
-------------------------------------------------------------------------------------------------
Feature 13 : Mainchain Omega dihedral restraints
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6543 86L 86L CA C 673 678 -146.78 -180.00 33.22 6.64 -180.00 33.22 6.64
2 6544 87A 87A CA C 681 683 -142.47 -180.00 37.53 7.50 -180.00 37.53 7.50
-------------------------------------------------------------------------------------------------
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 65.72 60.20 9.40 0.39 -63.50 143.84 26.52
1 19L 19L N CA 143 144 21.99 29.60 -41.20
2 6253 20T 21A C N 156 158 57.50 55.40 5.31 0.19 -62.50 141.10 28.68
2 21A 21A N CA 158 159 33.32 38.20 -40.90
3 6254 21A 22Y C N 161 163 66.50 55.90 17.62 0.91 -124.30 -158.20 16.74
3 22Y 22Y N CA 163 164 25.43 39.50 135.40
4 6263 30M 31Y C N 243 245 -90.90 -63.50 49.47 9.13 -63.50 49.47 9.13
4 31Y 31Y N CA 245 246 -84.60 -43.40 -43.40
5 6264 31Y 32T C N 255 257 -134.88 -124.80 57.63 2.77 -63.20 147.45 15.61
5 32T 32T N CA 257 258 86.75 143.50 -42.10
6 6266 33I 34G C N 270 272 93.09 82.20 18.11 0.50 -62.40 159.44 29.64
6 34G 34G N CA 272 273 -5.96 8.50 -41.20
7 6269 36G 37H C N 292 294 -157.41 -125.60 107.23 4.59 -63.20 122.75 14.33
7 37H 37H N CA 294 295 36.39 138.80 -42.30
8 6270 37H 38Y C N 302 304 62.33 55.90 22.49 1.16 -124.30 -150.59 17.35
8 38Y 38Y N CA 304 305 17.95 39.50 135.40
9 6282 49A 50Q C N 390 392 82.53 55.10 29.74 2.84 -121.10 -168.30 9.46
9 50Q 50Q N CA 392 393 28.81 40.30 139.70
10 6287 54Q 55L C N 427 429 90.57 60.20 149.39 11.52 -108.50 166.67 7.51
10 55L 55L N CA 429 430 175.87 29.60 132.50
11 6293 60N 61N C N 476 478 -151.86 -119.90 56.09 3.04 -63.20 159.01 17.12
11 61N 61N N CA 478 479 90.90 137.00 -41.10
12 6294 61N 62K C N 484 486 -152.34 -118.00 34.55 1.24 -62.90 -162.29 31.02
12 62K 62K N CA 486 487 142.88 139.10 -40.80
13 6295 62K 63Y C N 493 495 -123.34 -124.30 12.04 0.60 -63.50 177.21 25.39
13 63Y 63Y N CA 495 496 123.40 135.40 -43.40
14 6296 63Y 64A C N 505 507 -137.38 -134.00 7.54 0.46 -62.50 -166.11 35.78
14 64A 64A N CA 507 508 140.26 147.00 -40.90
15 6298 65P 66M C N 517 519 -175.48 -125.60 53.15 1.69 -63.40 -164.11 37.74
15 66M 66M N CA 519 520 158.84 140.50 -40.50
16 6300 67V 68D C N 532 534 -104.70 -96.50 25.41 1.06 -63.30 136.58 14.87
16 68D 68D N CA 534 535 90.16 114.20 -40.00
17 6301 68D 69A C N 540 542 -117.62 -134.00 29.00 1.08 -62.50 172.98 26.26
17 69A 69A N CA 542 543 123.06 147.00 -40.90
18 6302 69A 70Y C N 545 547 -145.48 -124.30 32.62 1.37 -63.50 176.57 32.00
18 70Y 70Y N CA 547 548 160.21 135.40 -43.40
19 6304 71V 72K C N 564 566 -110.82 -118.00 17.30 0.90 -62.90 171.21 25.08
19 72K 72K N CA 566 567 154.83 139.10 -40.80
20 6305 72K 73G C N 573 575 -156.94 -167.20 34.57 1.19 82.20 179.78 13.65
20 73G 73G N CA 575 576 141.59 174.60 8.50
21 6306 73G 74K C N 577 579 -127.19 -118.00 42.11 2.14 -62.90 152.97 17.59
21 74K 74K N CA 579 580 98.00 139.10 -40.80
22 6307 74K 75A C N 586 588 172.97 -134.00 85.07 2.92 -62.50 163.27 32.91
22 75A 75A N CA 588 589 -146.48 147.00 -40.90
23 6308 75A 76N C N 591 593 -57.22 -71.20 39.71 2.92 -63.20 139.07 17.07
23 76N 76N N CA 593 594 179.96 142.80 -41.10
24 6309 76N 77Q C N 599 601 -45.32 -73.00 30.01 1.91 -63.80 170.42 26.04
24 77Q 77Q N CA 601 602 129.11 140.70 -40.30
25 6310 77Q 78N C N 608 610 -159.08 -119.90 45.35 1.36 -63.20 -174.26 28.54
25 78N 78N N CA 610 611 159.82 137.00 -41.10
26 6311 78N 79E C N 616 618 -110.66 -117.80 9.10 0.28 -63.60 177.80 21.48
26 79E 79E N CA 618 619 131.16 136.80 -40.30
27 6312 79E 80F C N 625 627 -84.07 -71.40 14.32 1.18 -63.20 179.55 23.56
27 80F 80F N CA 627 628 134.03 140.70 -44.30
28 6313 80F 81D C N 636 638 -115.69 -96.50 19.57 0.80 -63.30 159.25 17.21
28 81D 81D N CA 638 639 110.39 114.20 -40.00
29 6314 81D 82A C N 644 646 -131.46 -134.00 12.60 0.65 -62.50 -171.39 28.45
29 82A 82A N CA 646 647 134.65 147.00 -40.90
30 6315 82A 83L C N 649 651 -117.01 -108.50 55.09 3.06 -63.50 130.73 16.07
30 83L 83L N CA 651 652 78.07 132.50 -41.20
31 6317 84V 85S C N 664 666 160.35 -136.60 73.45 2.24 -64.10 -167.89 23.62
31 85S 85S N CA 666 667 -171.13 151.20 -35.00
32 6320 87A 88Y C N 683 685 40.53 -98.40 139.98 5.87 -63.50 -173.62 34.43
32 88Y 88Y N CA 685 686 111.24 128.40 -43.40
33 6321 88Y 89N C N 695 697 95.77 55.90 56.16 3.37 -63.20 164.18 26.37
33 89N 89N N CA 697 698 -0.05 39.50 -41.10
34 6324 91G 92N C N 713 715 -169.45 -119.90 81.90 2.51 -63.20 157.81 25.32
34 92N 92N N CA 715 716 -157.78 137.00 -41.10
35 6327 94F 95V C N 739 741 -62.07 -62.40 6.52 0.81 -125.40 179.34 10.08
35 95V 95V N CA 741 742 -48.91 -42.40 143.30
36 6328 95V 96A C N 746 748 -115.91 -134.00 21.71 0.53 -62.50 -176.17 28.04
36 96A 96A N CA 748 749 135.01 147.00 -40.90
37 6329 96A 97D C N 751 753 67.46 -96.50 171.16 6.96 -63.30 -155.95 22.34
37 97D 97D N CA 753 754 163.35 114.20 -40.00
38 6336 103S 104H C N 806 808 -69.51 -125.60 77.05 3.49 -63.20 126.23 16.18
38 104H 104H N CA 808 809 -168.37 138.80 -42.30
39 6337 104H 105A C N 816 818 66.02 55.40 19.35 0.76 -62.50 143.10 29.09
39 105A 105A N CA 818 819 22.02 38.20 -40.90
40 6339 106Y 107C C N 833 835 -104.36 -117.90 72.41 2.63 -63.00 118.52 12.41
40 107C 107C N CA 835 836 69.97 141.10 -41.10
41 6340 107C 108A C N 839 841 -67.04 -68.20 11.32 0.95 55.40 170.30 9.20
41 108A 108A N CA 841 842 156.56 145.30 38.20
42 6341 108A 109S C N 844 846 -160.00 -136.60 32.25 1.03 -64.10 179.39 19.92
42 109S 109S N CA 846 847 173.39 151.20 -35.00
43 6342 109S 110M C N 850 852 -105.23 -125.60 26.97 0.81 -63.40 168.60 22.28
43 110M 110M N CA 852 853 122.82 140.50 -40.50
44 6345 112P 113K C N 873 875 -120.82 -118.00 44.26 2.11 -62.90 147.75 22.65
44 113K 113K N CA 875 876 -176.73 139.10 -40.80
45 6346 113K 114Y C N 882 884 -117.52 -124.30 22.50 1.49 -63.50 168.63 29.49
45 114Y 114Y N CA 884 885 156.85 135.40 -43.40
46 6347 114Y 115R C N 894 896 -56.03 -72.10 24.68 1.60 -63.00 164.42 22.68
46 115R 115R N CA 896 897 123.17 141.90 -41.10
47 6348 115R 116N C N 905 907 -145.06 -119.90 50.96 1.68 -63.20 160.09 24.56
47 116N 116N N CA 907 908 -178.68 137.00 -41.10
48 6349 116N 117A C N 913 915 -62.07 -68.20 6.39 0.48 -62.50 175.64 28.76
48 117A 117A N CA 915 916 143.46 145.30 -40.90
49 6350 117A 118G C N 918 920 71.16 78.70 16.15 0.24 82.20 160.71 8.36
49 118G 118G N CA 920 921 -151.82 -166.10 8.50
50 6351 118G 119G C N 922 924 -163.72 -167.20 15.64 0.56 82.20 -170.87 14.02
50 119G 119G N CA 924 925 159.35 174.60 8.50
51 6352 119G 120Q C N 926 928 -119.90 -121.10 11.84 0.58 -63.80 177.32 29.06
51 120Q 120Q N CA 928 929 151.48 139.70 -40.30
52 6354 121V 122L C N 942 944 -88.13 -108.50 42.27 2.03 -63.50 138.86 18.02
52 122L 122L N CA 944 945 95.46 132.50 -41.20
53 6355 122L 123Q C N 950 952 -161.51 -121.10 54.73 1.75 -63.80 173.27 30.38
53 123Q 123Q N CA 952 953 176.61 139.70 -40.30
54 6356 123Q 124G C N 959 961 93.32 78.70 41.51 0.66 82.20 146.97 7.69
54 124G 124G N CA 961 962 155.05 -166.10 8.50
55 6357 124G 125L C N 963 965 -116.84 -108.50 10.97 0.61 -63.50 174.91 21.88
55 125L 125L N CA 965 966 125.37 132.50 -41.20
56 6358 125L 126V C N 971 973 65.84 -73.50 139.43 9.97 -125.40 168.76 6.57
56 126V 126V N CA 973 974 144.10 139.20 143.30
57 6368 135L 136F C N 1058 1060 -102.71 -124.20 70.68 3.76 -63.20 112.24 18.19
57 136F 136F N CA 1060 1061 -149.36 143.30 -44.30
58 6370 137N 138K C N 1077 1079 -90.19 -70.20 20.13 1.52 -62.90 -179.10 22.14
58 138K 138K N CA 1079 1080 138.03 140.40 -40.80
59 6373 140V 141S C N 1100 1102 -126.64 -136.60 10.32 0.35 -64.10 -172.74 17.96
59 141S 141S N CA 1102 1103 148.49 151.20 -35.00
60 6375 142S 143N C N 1112 1114 -151.75 -119.90 35.22 1.10 -63.20 -171.10 28.58
60 143N 143N N CA 1114 1115 152.04 137.00 -41.10
61 6376 143N 144S C N 1120 1122 -149.06 -136.60 19.83 1.12 -64.10 -169.26 12.14
61 144S 144S N CA 1122 1123 135.78 151.20 -35.00
62 6377 144S 145N C N 1126 1128 -146.31 -119.90 27.92 1.37 -63.20 -171.61 20.34
62 145N 145N N CA 1128 1129 127.96 137.00 -41.10
63 6378 145N 146Q C N 1134 1136 -165.42 -121.10 52.67 1.62 -63.80 -177.55 31.94
63 146Q 146Q N CA 1136 1137 168.16 139.70 -40.30
64 6379 146Q 147N C N 1143 1145 -77.24 -71.20 49.60 3.35 -63.20 135.39 16.19
64 147N 147N N CA 1145 1146 93.57 142.80 -41.10
65 6380 147N 148N C N 1151 1153 -138.91 -119.90 20.73 0.66 -63.20 -170.58 27.97
65 148N 148N N CA 1153 1154 145.27 137.00 -41.10
66 6381 148N 149Q C N 1159 1161 -128.64 -121.10 41.75 2.10 -63.80 153.32 19.89
66 149Q 149Q N CA 1161 1162 98.63 139.70 -40.30
67 6382 149Q 150T C N 1168 1170 -157.49 -124.80 36.16 1.46 -63.20 -175.19 29.73
67 150T 150T N CA 1170 1171 158.96 143.50 -42.10
68 6383 150T 151G C N 1175 1177 64.73 78.70 18.28 0.47 82.20 163.75 8.82
68 151G 151G N CA 1177 1178 -154.32 -166.10 8.50
69 6384 151G 152G C N 1179 1181 158.81 -167.20 34.09 0.71 82.20 -179.45 12.28
69 152G 152G N CA 1181 1182 171.99 174.60 8.50
70 6385 152G 153M C N 1183 1185 -79.14 -73.00 31.77 2.26 -63.40 153.14 21.68
70 153M 153M N CA 1185 1186 111.82 143.00 -40.50
71 6388 155K 156M C N 1208 1210 -112.48 -125.60 34.43 1.33 -63.40 157.04 20.22
71 156M 156M N CA 1210 1211 108.67 140.50 -40.50
72 6389 156M 157Y C N 1216 1218 -75.07 -98.40 23.63 0.94 -63.50 175.97 27.33
72 157Y 157Y N CA 1218 1219 132.18 128.40 -43.40
73 6390 157Y 158L C N 1228 1230 -87.31 -108.50 21.86 0.99 -63.50 170.01 22.35
73 158L 158L N CA 1230 1231 127.13 132.50 -41.20
74 6394 161G 162L C N 1256 1258 -70.51 -70.70 0.20 0.02 -63.50 177.27 25.02
74 162L 162L N CA 1258 1259 141.67 141.60 -41.20
75 6395 162L 163D C N 1264 1266 -93.65 -70.90 37.06 1.33 -63.30 143.69 19.68
75 163D 163D N CA 1266 1267 179.56 150.30 -40.00
76 6396 163D 164N C N 1272 1274 -89.42 -71.20 49.48 3.66 -63.20 140.36 16.24
76 164N 164N N CA 1274 1275 96.79 142.80 -41.10
77 6399 166G 167K C N 1290 1292 -90.85 -70.20 23.53 1.46 -62.90 169.83 23.68
77 167K 167K N CA 1292 1293 151.69 140.40 -40.80
78 6400 167K 168A C N 1299 1301 -95.83 -68.20 33.41 3.28 -62.50 170.71 26.54
78 168A 168A N CA 1301 1302 126.52 145.30 -40.90
79 6401 168A 169K C N 1304 1306 -162.06 -118.00 44.67 1.57 -62.90 -160.79 31.78
79 169K 169K N CA 1306 1307 146.43 139.10 -40.80
80 6402 169K 170H C N 1313 1315 -107.78 -125.60 51.58 1.59 -63.20 139.98 15.28
80 170H 170H N CA 1315 1316 90.39 138.80 -42.30
81 6403 170H 171W C N 1323 1325 -142.09 -124.90 19.37 0.65 -63.00 -178.39 28.03
81 171W 171W N CA 1325 1326 152.32 143.40 -44.20
82 6404 171W 172Y C N 1337 1339 -133.66 -124.30 20.19 0.79 -63.50 177.75 31.69
82 172Y 172Y N CA 1339 1340 153.28 135.40 -43.40
83 6405 172Y 173V C N 1349 1351 -61.10 -62.40 4.99 0.57 -125.40 -178.74 10.20
83 173V 173V N CA 1351 1352 -47.22 -42.40 143.30
84 6406 173V 174S C N 1356 1358 -86.07 -72.40 15.68 0.85 -64.10 166.36 13.48
84 174S 174S N CA 1358 1359 160.09 152.40 -35.00
85 6407 174S 175D C N 1362 1364 -102.27 -96.50 12.21 0.51 -63.30 169.50 18.90
85 175D 175D N CA 1364 1365 124.96 114.20 -40.00
86 6408 175D 176G C N 1370 1372 157.36 -167.20 99.44 4.09 82.20 104.90 8.06
86 176G 176G N CA 1372 1373 81.68 174.60 8.50
87 6409 176G 177V C N 1374 1376 -110.80 -125.40 75.18 3.34 -62.40 121.97 13.43
87 177V 177V N CA 1376 1377 69.56 143.30 -42.40
88 6423 190N 191Y C N 1492 1494 70.79 55.90 162.38 12.48 -124.30 177.55 10.80
88 191Y 191Y N CA 1494 1495 -158.80 39.50 135.40
89 6436 203D 204T C N 1604 1606 49.88 55.90 8.48 0.51 -124.80 -159.70 7.71
89 204T 204T N CA 1606 1607 45.48 39.50 143.50
90 6439 206F 207I C N 1630 1632 -105.27 -63.40 92.07 14.04 -63.40 92.07 14.04
90 207I 207I N CA 1632 1633 38.40 -43.60 -43.60
91 6445 212A 213E C N 1674 1676 62.66 54.60 23.92 1.29 -63.60 139.87 24.00
91 213E 213E N CA 1676 1677 19.88 42.40 -40.30
92 6448 215G 216R C N 1698 1700 46.84 57.30 22.63 1.11 -63.00 147.98 26.67
92 216R 216R N CA 1700 1701 58.07 38.00 -41.10
93 6449 216R 217K C N 1709 1711 -49.68 -70.20 20.54 1.47 -62.90 -179.62 22.73
93 217K 217K N CA 1711 1712 139.30 140.40 -40.80
94 6451 218I 219D C N 1726 1728 -71.40 -70.90 12.11 0.57 -63.30 157.82 19.98
94 219D 219D N CA 1728 1729 162.39 150.30 -40.00
95 6452 219D 220M C N 1734 1736 -69.34 -73.00 18.39 1.19 -63.40 165.58 24.27
95 220M 220M N CA 1736 1737 124.98 143.00 -40.50
96 6453 220M 221A C N 1742 1744 -84.54 -68.20 19.38 1.28 -62.50 164.85 28.15
96 221A 221A N CA 1744 1745 155.73 145.30 -40.90
97 6454 221A 222S C N 1747 1749 -121.03 -136.60 18.97 0.58 -64.10 -175.64 11.36
97 222S 222S N CA 1749 1750 140.35 151.20 -35.00
98 6455 222S 223G C N 1753 1755 -144.00 -167.20 32.09 0.70 82.20 -163.49 14.96
98 223G 223G N CA 1755 1756 152.42 174.60 8.50
99 6456 223G 224E C N 1757 1759 -131.49 -117.80 16.63 0.49 -63.60 -173.72 28.67
99 224E 224E N CA 1759 1760 146.24 136.80 -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 13273 86L 228. CA C7 673 1806 9.10 8.02 1.08 5.42 8.02 1.08 5.42
2 13274 86L 228. CA C8 673 1807 10.46 9.16 1.30 6.51 9.16 1.30 6.51
3 13279 86L 228. CA O7 673 1813 8.20 6.89 1.32 6.59 6.89 1.32 6.59
4 13297 87A 228. CA O6 681 1812 7.30 6.36 0.94 4.68 6.36 0.94 4.68
5 14444 83L 229. CG O6 654 1826 3.93 3.00 0.93 9.33 3.00 0.93 9.33
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 31 31 164 179 227 180 234 277 286 305
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P62693.B99990001.pdb 2114.73804
P62693.B99990002.pdb 2159.56079
In [ ]:
from IPython.display import Image
Image('1.png')
Out[ ]:
In [ ]:
#Постройте структуру лизоцима с лигандом где все аминокислоты аланин
#и сравните скор функцию с "нативной" последовательностью.
In [ ]:
def evaluate_model(pdb_file):
mdl = complete_pdb(env, pdb_file)
atmsel = selection(mdl)
# Используем DOPE score (чем ниже, тем стабильнее модель)
return atmsel.assess_dope()
# 1. Считаем скор для нативной модели
score_native = evaluate_model('P62693_ligand.B99990001.pdb')
# 2. Запускаем моделирование для Poly-ALA (нужно создать новый объект a_ala)
# Предположим, вы создали файл 'poly_ala.ali'
a_ala = mymodel(env, alnfile='poly_ala.ali', knowns='1lmp', sequence='P62693_ALA')
a_ala.make()
score_ala = evaluate_model('P62693_ALA.B99990001.pdb')
print(f"Native DOPE score: {score_native}")
print(f"Poly-ALA DOPE score: {score_ala}")
In [ ]:
from modeller.scripts import complete_pdb
In [ ]:
def evaluate_model(pdb_file):
mdl = complete_pdb(env, pdb_file)
atmsel = selection(mdl)
return atmsel.assess_dope()
In [ ]:
score_native = evaluate_model('P62693.B99990001.pdb')
readlinef__W> File: P62693.B99990001.pdb, Line: 6
Modeller will only read the first 80 characters of this line.
selection__W> The class 'selection' is deprecated; use 'Selection' instead
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: LYS:OXT LYS
preppdf_453W> No fixed restraints selected; there may be some dynamic ones.
preppdf_454W> Restraints file was probably not read; use restraints.append().
>> 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 : 0 0
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 326018
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -15983.8193
<< end of ENERGY.
DOPE score : -15983.819336
In [ ]:
%%writefile all_in_one_3.ali
>P1;P62693
sequence::: :: :::-1.00:-1.00
MKVSQNGLNLIKEFEGCRLTAYKPVP-WEQMYTIGWGHYGVTAGTTWTQAQADSQLEIDINNKYAPMVDAYVKGK
ANQNEFDALVSLAYNCGNVFVADGWAPFSHAYCASMIPKYRNAGGQVLQGLVRRRQAELNLFNKPVSSNSNQNNQ
TGGMIKMYLIIGLDNSGKAKHWYVSDGVSVRHVRTIRMLENYQNKWAKLNLPVDTMFIAEIEAEFGRKIDMASGE
VK/AAA*
>P1;1lmp
structureX:1lmp:1:A:3:B::::
KVYDRCELARALKASGMDGYAGNSLPNWVCLS--KWESSYNTQATNRNTDGSTDYGIFQIN--------------
-----------SRYWCD-----DGRTPGAKNVCG-----------------IRCSQLLTDDLT------------
---------------------------VAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV--------
--/...*
Overwriting all_in_one_3.ali
In [ ]:
class mymodel(AutoModel):
def special_constraints(self, aln):
pass
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('CG:83:A','C:228:B')]:
rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance,
feature=modeller.features.distance(
at[x],at[y]),mean=3.0, stdev=0.1))
from modeller import *
from modeller.automodel import *
a = mymodel(env, alnfile='all_in_one_3.ali', knowns='1lmp', sequence='P62693')
a.name='P62693_ligand'
a.starting_model = 1
a.ending_model = 2
a.make()
AutoModel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the AutoModel defaults. If this is not what you
want, clear them before creating the AutoModel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
transfe_404W> At least one template is aligned with model residue 227:B
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 228:B
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
transfe_404W> At least one template is aligned with model residue 229:B
but no coordinates could be transferred. This usually
occurs when your input files do not use the official
PDBv3 atom names. Please check your templates.
buildc__466W> Some coordinates in MODEL not assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
buildc__466W> Some coordinates in MODEL not assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
invent__526W> Inventing the mainchain model coordinates.
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.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
distance___W> The class 'distance' is deprecated; use 'Distance' instead
gaussian___W> The class 'gaussian' is deprecated; use 'Gaussian' instead
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14695 13098
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90: -90.6178
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 : 1800 1800
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13098 13098
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3616
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 : 1450.6034
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 : 1839 0 0 0.004 0.004 9.8290 1.000
2 Bond angle potential : 2488 0 1 1.962 1.962 179.79 1.000
3 Stereochemical cosine torsion poten: 1178 0 43 48.709 48.709 433.87 1.000
4 Stereochemical improper torsion pot: 779 0 0 1.096 1.096 19.551 1.000
5 Soft-sphere overlap restraints : 3616 0 0 0.004 0.004 5.5238 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) : 2356 0 0 0.500 0.500 92.666 1.000
10 Distance restraints 2 (N-O) : 2508 0 2 0.741 0.741 187.00 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: 227 0 1 4.294 4.294 49.357 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 4 79.983 79.983 73.780 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 0 75.335 75.335 71.093 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 82.192 82.192 44.151 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 107.959 107.959 18.435 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) : 900 0 0 0.418 0.418 11.422 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: 225 96 43 34.515 110.897 245.61 1.000
26 Distance restraints 4 (SDCH-SDCH) : 177 0 0 1.109 1.109 8.2811 1.000
27 Distance restraints 5 (X-Y) : 1 0 0 0.091 0.091 0.24599 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: P62693.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: 33946.4492
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 6302 18R 19L C N 141 143 67.65 60.20 18.71 0.65 -63.50 141.70 26.05
1 19L 19L N CA 143 144 12.43 29.60 -41.20
2 6304 20T 21A C N 156 158 55.78 55.40 4.17 0.22 -62.50 140.03 28.46
2 21A 21A N CA 158 159 34.05 38.20 -40.90
3 6305 21A 22Y C N 161 163 61.43 55.90 9.12 0.48 -124.30 -157.49 16.82
3 22Y 22Y N CA 163 164 32.26 39.50 135.40
4 6314 30M 31Y C N 243 245 -51.85 -98.40 59.52 4.14 -63.50 151.55 23.46
4 31Y 31Y N CA 245 246 165.50 128.40 -43.40
5 6317 33I 34G C N 270 272 89.24 78.70 22.58 1.05 -62.40 -175.59 27.38
5 34G 34G N CA 272 273 -146.14 -166.10 -41.20
6 6318 34G 35W C N 274 276 -67.83 -71.30 33.32 2.61 -63.00 143.75 18.27
6 35W 35W N CA 276 277 172.14 139.00 -44.20
7 6319 35W 36G C N 288 290 95.28 78.70 59.58 2.36 -62.40 171.59 27.23
7 36G 36G N CA 290 291 -108.88 -166.10 -41.20
8 6320 36G 37H C N 292 294 -145.61 -125.60 83.14 3.50 -63.20 129.90 14.15
8 37H 37H N CA 294 295 58.11 138.80 -42.30
9 6321 37H 38Y C N 302 304 41.73 55.90 15.15 1.37 -124.30 -170.90 10.52
9 38Y 38Y N CA 304 305 44.88 39.50 135.40
10 6333 49A 50Q C N 390 392 83.37 55.10 41.33 2.49 -121.10 -157.58 10.19
10 50Q 50Q N CA 392 393 10.15 40.30 139.70
11 6338 54Q 55L C N 427 429 92.48 60.20 152.09 11.85 -108.50 165.47 7.44
11 55L 55L N CA 429 430 178.22 29.60 132.50
12 6344 60N 61N C N 476 478 -137.48 -119.90 47.69 1.72 -63.20 156.34 23.70
12 61N 61N N CA 478 479 -178.67 137.00 -41.10
13 6345 61N 62K C N 484 486 -121.93 -118.00 20.70 0.94 -62.90 170.33 25.65
13 62K 62K N CA 486 487 159.42 139.10 -40.80
14 6346 62K 63Y C N 493 495 -60.94 -98.40 39.46 1.84 -63.50 175.82 27.77
14 63Y 63Y N CA 495 496 140.80 128.40 -43.40
15 6347 63Y 64A C N 505 507 -55.73 -68.20 14.00 0.96 -62.50 179.96 29.83
15 64A 64A N CA 507 508 138.94 145.30 -40.90
16 6349 65P 66M C N 517 519 -84.70 -73.00 13.11 1.05 -63.40 178.84 25.11
16 66M 66M N CA 519 520 137.07 143.00 -40.50
17 6352 68D 69A C N 540 542 -131.38 -134.00 4.63 0.28 -62.50 -178.17 33.49
17 69A 69A N CA 542 543 150.82 147.00 -40.90
18 6353 69A 70Y C N 545 547 -98.97 -98.40 12.91 1.37 -63.50 178.86 30.20
18 70Y 70Y N CA 547 548 141.30 128.40 -43.40
19 6355 71V 72K C N 564 566 -107.09 -118.00 15.09 0.53 -62.90 175.14 20.75
19 72K 72K N CA 566 567 128.68 139.10 -40.80
20 6356 72K 73G C N 573 575 -157.74 -167.20 11.28 0.20 82.20 -160.02 14.81
20 73G 73G N CA 575 576 168.44 174.60 8.50
21 6357 73G 74K C N 577 579 -112.46 -118.00 9.75 0.37 -62.90 178.88 21.06
21 74K 74K N CA 579 580 131.08 139.10 -40.80
22 6358 74K 75A C N 586 588 -119.47 -134.00 15.06 0.37 -62.50 -174.97 33.36
22 75A 75A N CA 588 589 143.06 147.00 -40.90
23 6359 75A 76N C N 591 593 -134.06 -119.90 21.21 0.63 -63.20 -179.40 26.59
23 76N 76N N CA 593 594 152.78 137.00 -41.10
24 6360 76N 77Q C N 599 601 -82.86 -73.00 57.36 3.95 -63.80 125.95 17.57
24 77Q 77Q N CA 601 602 84.19 140.70 -40.30
25 6361 77Q 78N C N 608 610 -141.09 -119.90 46.37 1.57 -63.20 160.78 24.45
25 78N 78N N CA 610 611 178.25 137.00 -41.10
26 6362 78N 79E C N 616 618 -69.71 -69.30 8.34 0.62 -63.60 168.98 22.87
26 79E 79E N CA 618 619 150.83 142.50 -40.30
27 6363 79E 80F C N 625 627 -119.31 -124.20 13.46 0.73 -63.20 169.42 27.24
27 80F 80F N CA 627 628 155.84 143.30 -44.30
28 6364 80F 81D C N 636 638 -71.20 -96.50 25.83 1.06 -63.30 149.18 17.95
28 81D 81D N CA 638 639 108.97 114.20 -40.00
29 6365 81D 82A C N 644 646 -140.76 -134.00 7.20 0.17 -62.50 -173.17 34.81
29 82A 82A N CA 646 647 149.46 147.00 -40.90
30 6366 82A 83L C N 649 651 -87.97 -70.70 36.37 2.26 -63.50 147.24 21.92
30 83L 83L N CA 651 652 173.61 141.60 -41.20
31 6368 84V 85S C N 664 666 -178.65 -136.60 43.90 1.45 -64.10 -162.24 22.60
31 85S 85S N CA 666 667 163.79 151.20 -35.00
32 6371 87A 88Y C N 683 685 -136.83 -124.30 23.05 0.91 -63.50 177.69 31.82
32 88Y 88Y N CA 685 686 154.75 135.40 -43.40
33 6372 88Y 89N C N 695 697 65.83 55.90 24.53 1.18 -63.20 141.54 23.18
33 89N 89N N CA 697 698 17.07 39.50 -41.10
34 6375 91G 92N C N 713 715 -168.82 -119.90 55.73 1.70 -63.20 -172.24 29.27
34 92N 92N N CA 715 716 163.68 137.00 -41.10
35 6376 92N 93V C N 721 723 -67.80 -62.40 10.40 1.14 -125.40 -174.04 7.59
35 93V 93V N CA 723 724 -33.51 -42.40 143.30
36 6377 93V 94F C N 728 730 -81.26 -63.20 88.15 13.46 -63.20 88.15 13.46
36 94F 94F N CA 730 731 -130.58 -44.30 -44.30
37 6378 94F 95V C N 739 741 -58.58 -62.40 7.17 1.14 -125.40 -168.34 7.58
37 95V 95V N CA 741 742 -36.33 -42.40 143.30
38 6379 95V 96A C N 746 748 -63.50 -68.20 23.54 2.06 -62.50 150.74 24.75
38 96A 96A N CA 748 749 168.37 145.30 -40.90
39 6380 96A 97D C N 751 753 -55.07 -96.50 50.05 2.08 -63.30 126.37 16.11
39 97D 97D N CA 753 754 86.11 114.20 -40.00
40 6381 97D 98G C N 759 761 -74.56 -62.40 12.39 2.10 82.20 163.75 12.34
40 98G 98G N CA 761 762 -38.81 -41.20 8.50
41 6387 103S 104H C N 806 808 -101.04 -63.20 78.90 12.31 -63.20 78.90 12.31
41 104H 104H N CA 808 809 -111.53 -42.30 -42.30
42 6388 104H 105A C N 816 818 -151.97 -134.00 18.69 0.46 -62.50 -170.58 35.83
42 105A 105A N CA 818 819 152.14 147.00 -40.90
43 6389 105A 106Y C N 821 823 -55.99 -98.40 53.78 3.70 -63.50 155.31 24.26
43 106Y 106Y N CA 823 824 161.47 128.40 -43.40
44 6390 106Y 107C C N 833 835 -70.00 -117.90 74.70 2.12 -63.00 125.07 14.79
44 107C 107C N CA 835 836 83.78 141.10 -41.10
45 6391 107C 108A C N 839 841 -88.69 -68.20 45.39 4.30 55.40 158.74 12.90
45 108A 108A N CA 841 842 104.80 145.30 38.20
46 6392 108A 109S C N 844 846 -105.31 -72.40 54.19 2.48 -64.10 135.94 12.72
46 109S 109S N CA 846 847 -164.55 152.40 -35.00
47 6393 109S 110M C N 850 852 -62.98 -73.00 10.12 0.74 -63.40 177.88 26.52
47 110M 110M N CA 852 853 141.62 143.00 -40.50
48 6396 112P 113K C N 873 875 -84.61 -70.20 33.92 2.13 -62.90 149.68 20.69
48 113K 113K N CA 875 876 171.10 140.40 -40.80
49 6397 113K 114Y C N 882 884 -138.63 -124.30 57.00 2.47 -63.50 146.73 26.86
49 114Y 114Y N CA 884 885 -169.43 135.40 -43.40
50 6398 114Y 115R C N 894 896 -63.58 -72.10 28.54 2.36 -63.00 149.77 20.27
50 115R 115R N CA 896 897 169.13 141.90 -41.10
51 6399 115R 116N C N 905 907 -51.61 -71.20 20.84 1.31 -63.20 177.16 22.79
51 116N 116N N CA 907 908 135.68 142.80 -41.10
52 6400 116N 117A C N 913 915 -140.46 -134.00 14.59 0.62 -62.50 177.11 33.20
52 117A 117A N CA 915 916 160.08 147.00 -40.90
53 6401 117A 118G C N 918 920 -67.05 -62.40 6.26 0.89 82.20 156.03 11.77
53 118G 118G N CA 920 921 -37.01 -41.20 8.50
54 6406 122L 123Q C N 950 952 -52.70 -73.00 25.68 2.00 -63.80 163.65 23.49
54 123Q 123Q N CA 952 953 156.43 140.70 -40.30
55 6407 123Q 124G C N 959 961 173.81 -167.20 19.02 0.39 82.20 -171.27 13.27
55 124G 124G N CA 961 962 173.51 174.60 8.50
56 6408 124G 125L C N 963 965 -85.45 -70.70 30.35 1.89 -63.50 152.27 22.46
56 125L 125L N CA 965 966 168.12 141.60 -41.20
57 6421 137N 138K C N 1077 1079 -160.37 -118.00 57.71 2.01 -62.90 171.34 28.01
57 138K 138K N CA 1079 1080 178.29 139.10 -40.80
58 6424 140V 141S C N 1100 1102 -134.38 -136.60 22.46 1.09 -64.10 178.28 11.10
58 141S 141S N CA 1102 1103 128.85 151.20 -35.00
59 6425 141S 142S C N 1106 1108 -107.85 -136.60 31.04 0.98 -64.10 179.90 11.22
59 142S 142S N CA 1108 1109 139.50 151.20 -35.00
60 6426 142S 143N C N 1112 1114 -156.88 -119.90 37.10 1.61 -63.20 -161.27 21.39
60 143N 143N N CA 1114 1115 134.16 137.00 -41.10
61 6427 143N 144S C N 1120 1122 -64.79 -72.40 17.49 0.82 -64.10 171.65 12.40
61 144S 144S N CA 1122 1123 136.65 152.40 -35.00
62 6428 144S 145N C N 1126 1128 -129.22 -119.90 9.81 0.33 -63.20 -169.35 27.59
62 145N 145N N CA 1128 1129 140.05 137.00 -41.10
63 6429 145N 146Q C N 1134 1136 -103.40 -121.10 61.07 2.56 -63.80 127.84 17.00
63 146Q 146Q N CA 1136 1137 81.26 139.70 -40.30
64 6430 146Q 147N C N 1143 1145 -127.27 -119.90 7.41 0.33 -63.20 -171.43 20.76
64 147N 147N N CA 1145 1146 136.25 137.00 -41.10
65 6431 147N 148N C N 1151 1153 -94.14 -119.90 57.99 1.98 -63.20 129.88 14.75
65 148N 148N N CA 1153 1154 85.04 137.00 -41.10
66 6432 148N 149Q C N 1159 1161 -147.32 -121.10 26.32 0.94 -63.80 -163.66 33.24
66 149Q 149Q N CA 1161 1162 142.01 139.70 -40.30
67 6433 149Q 150T C N 1168 1170 -106.96 -124.80 67.24 2.38 -63.20 128.45 14.07
67 150T 150T N CA 1170 1171 78.66 143.50 -42.10
68 6434 150T 151G C N 1175 1177 58.97 78.70 21.08 0.83 82.20 168.78 9.35
68 151G 151G N CA 1177 1178 -158.67 -166.10 8.50
69 6435 151G 152G C N 1179 1181 139.91 -167.20 55.77 1.53 82.20 159.23 10.44
69 152G 152G N CA 1181 1182 156.91 174.60 8.50
70 6438 154I 155K C N 1199 1201 -73.52 -70.20 3.44 0.23 -62.90 178.23 23.74
70 155K 155K N CA 1201 1202 141.29 140.40 -40.80
71 6439 155K 156M C N 1208 1210 -97.15 -73.00 46.24 2.88 -63.40 141.17 23.78
71 156M 156M N CA 1210 1211 -177.58 143.00 -40.50
72 6441 157Y 158L C N 1228 1230 -142.09 -108.50 33.83 1.66 -63.50 -173.00 22.96
72 158L 158L N CA 1230 1231 128.48 132.50 -41.20
73 6444 160I 161G C N 1252 1254 103.71 78.70 36.83 0.77 82.20 159.81 8.83
73 161G 161G N CA 1254 1255 166.86 -166.10 8.50
74 6445 161G 162L C N 1256 1258 -76.32 -70.70 44.78 3.61 -63.50 138.97 18.60
74 162L 162L N CA 1258 1259 97.18 141.60 -41.20
75 6446 162L 163D C N 1264 1266 -143.10 -96.50 51.44 2.09 -63.30 154.61 16.44
75 163D 163D N CA 1266 1267 92.43 114.20 -40.00
76 6447 163D 164N C N 1272 1274 -119.03 -119.90 24.63 1.14 -63.20 166.90 24.04
76 164N 164N N CA 1274 1275 161.61 137.00 -41.10
77 6448 164N 165S C N 1280 1282 -131.87 -136.60 33.78 1.80 -64.10 155.86 16.14
77 165S 165S N CA 1282 1283 -175.36 151.20 -35.00
78 6451 167K 168A C N 1299 1301 164.46 -134.00 61.76 2.24 -62.50 -138.41 43.30
78 168A 168A N CA 1301 1302 141.89 147.00 -40.90
79 6452 168A 169K C N 1304 1306 -105.52 -118.00 51.99 2.33 -62.90 136.27 15.91
79 169K 169K N CA 1306 1307 88.64 139.10 -40.80
80 6453 169K 170H C N 1313 1315 -138.01 -125.60 29.41 0.86 -63.20 169.63 26.07
80 170H 170H N CA 1315 1316 165.46 138.80 -42.30
81 6457 173V 174S C N 1356 1358 -129.23 -136.60 24.77 1.08 -64.10 175.12 10.84
81 174S 174S N CA 1358 1359 127.55 151.20 -35.00
82 6458 174S 175D C N 1362 1364 -74.06 -70.90 5.93 0.44 -63.30 175.05 22.27
82 175D 175D N CA 1364 1365 145.28 150.30 -40.00
83 6459 175D 176G C N 1370 1372 148.91 -167.20 75.98 3.01 82.20 123.62 8.92
83 176G 176G N CA 1372 1373 112.58 174.60 8.50
84 6474 190N 191Y C N 1492 1494 72.49 55.90 155.88 12.15 -124.30 173.58 10.80
84 191Y 191Y N CA 1494 1495 -165.50 39.50 135.40
85 6487 203D 204T C N 1604 1606 55.84 55.90 7.67 0.54 -124.80 -148.72 12.81
85 204T 204T N CA 1606 1607 31.83 39.50 143.50
86 6490 206F 207I C N 1630 1632 -105.41 -120.60 91.86 4.67 -63.40 93.30 14.23
86 207I 207I N CA 1632 1633 39.71 130.30 -43.60
87 6495 211E 212A C N 1669 1671 59.63 -68.20 132.53 12.29 -68.20 132.53 12.29
87 212A 212A N CA 1671 1672 -179.71 145.30 145.30
88 6496 212A 213E C N 1674 1676 -79.36 -69.30 55.93 4.60 -63.60 128.76 16.35
88 213E 213E N CA 1676 1677 87.49 142.50 -40.30
89 6499 215G 216R C N 1698 1700 -71.27 -72.10 26.00 1.98 -63.00 157.23 20.70
89 216R 216R N CA 1700 1701 115.91 141.90 -41.10
90 6500 216R 217K C N 1709 1711 -62.28 -70.20 8.10 0.63 -62.90 177.12 22.97
90 217K 217K N CA 1711 1712 142.08 140.40 -40.80
91 6502 218I 219D C N 1726 1728 -110.14 -96.50 23.51 0.99 -63.30 179.56 19.80
91 219D 219D N CA 1728 1729 133.35 114.20 -40.00
92 6503 219D 220M C N 1734 1736 -87.69 -73.00 24.17 1.51 -63.40 159.16 25.70
92 220M 220M N CA 1736 1737 162.20 143.00 -40.50
93 6504 220M 221A C N 1742 1744 -71.59 -68.20 12.76 0.91 -62.50 161.76 26.96
93 221A 221A N CA 1744 1745 157.60 145.30 -40.90
94 6505 221A 222S C N 1747 1749 -66.81 -72.40 20.68 1.04 -64.10 167.51 11.98
94 222S 222S N CA 1749 1750 132.48 152.40 -35.00
95 6506 222S 223G C N 1753 1755 -177.34 -167.20 43.37 1.78 82.20 159.53 11.94
95 223G 223G N CA 1755 1756 132.43 174.60 8.50
96 6507 223G 224E C N 1757 1759 -130.08 -117.80 12.40 0.50 -63.60 -172.46 22.11
96 224E 224E N CA 1759 1760 135.07 136.80 -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 14 22 114 127 202 219 224 227 217 255
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1800 1800
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13098 13098
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3867
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 : 1631.2037
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 : 1839 0 0 0.005 0.005 11.534 1.000
2 Bond angle potential : 2488 0 6 2.039 2.039 192.80 1.000
3 Stereochemical cosine torsion poten: 1178 0 53 47.981 47.981 430.81 1.000
4 Stereochemical improper torsion pot: 779 0 0 1.161 1.161 21.169 1.000
5 Soft-sphere overlap restraints : 3867 0 0 0.004 0.004 7.8121 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) : 2356 0 8 0.720 0.720 183.44 1.000
10 Distance restraints 2 (N-O) : 2508 2 6 0.773 0.773 225.48 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: 227 0 3 4.712 4.712 59.425 1.000
14 Sidechain Chi_1 dihedral restraints: 187 0 2 82.287 82.287 66.325 1.000
15 Sidechain Chi_2 dihedral restraints: 146 0 2 76.831 76.831 64.984 1.000
16 Sidechain Chi_3 dihedral restraints: 63 0 0 77.150 77.150 44.382 1.000
17 Sidechain Chi_4 dihedral restraints: 24 0 0 79.210 79.210 13.081 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) : 900 0 0 0.621 0.621 14.354 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: 225 97 43 39.157 110.887 281.65 1.000
26 Distance restraints 4 (SDCH-SDCH) : 177 0 0 1.625 1.625 13.801 1.000
27 Distance restraints 5 (X-Y) : 1 0 0 0.072 0.072 0.15270 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: P62693.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: 34468.6250
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 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 10754 86L 52D N O 672 413 5.76 2.95 2.80 6.19 2.95 2.80 6.19
2 10777 86L 194K N O 672 1531 14.46 10.49 3.97 5.33 10.49 3.97 5.33
-------------------------------------------------------------------------------------------------
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 6302 18R 19L C N 141 143 61.11 60.20 4.76 0.21 -63.50 141.07 26.02
1 19L 19L N CA 143 144 24.93 29.60 -41.20
2 6304 20T 21A C N 156 158 56.60 55.40 6.06 0.27 -62.50 139.77 28.41
2 21A 21A N CA 158 159 32.26 38.20 -40.90
3 6305 21A 22Y C N 161 163 70.12 55.90 25.62 1.27 -124.30 -157.13 16.78
3 22Y 22Y N CA 163 164 18.19 39.50 135.40
4 6316 32T 33I C N 262 264 -59.31 -63.40 10.07 1.80 -120.60 175.74 7.86
4 33I 33I N CA 264 265 -34.40 -43.60 130.30
5 6317 33I 34G C N 270 272 96.16 82.20 14.81 1.13 -62.40 167.71 31.53
5 34G 34G N CA 272 273 13.45 8.50 -41.20
6 6320 36G 37H C N 292 294 -158.96 -125.60 109.51 4.70 -63.20 122.75 14.46
6 37H 37H N CA 294 295 34.49 138.80 -42.30
7 6321 37H 38Y C N 302 304 58.70 55.90 8.32 0.41 -124.30 -154.85 17.04
7 38Y 38Y N CA 304 305 31.67 39.50 135.40
8 6333 49A 50Q C N 390 392 82.70 55.10 42.24 2.42 -121.10 -155.90 10.28
8 50Q 50Q N CA 392 393 8.33 40.30 139.70
9 6338 54Q 55L C N 427 429 90.31 60.20 150.83 11.59 -108.50 167.32 7.53
9 55L 55L N CA 429 430 177.39 29.60 132.50
10 6344 60N 61N C N 476 478 -141.69 -119.90 22.40 0.80 -63.20 -166.60 28.62
10 61N 61N N CA 478 479 142.14 137.00 -41.10
11 6345 61N 62K C N 484 486 -156.18 -118.00 44.34 1.47 -62.90 -176.91 29.33
11 62K 62K N CA 486 487 161.65 139.10 -40.80
12 6346 62K 63Y C N 493 495 -144.26 -124.30 69.18 2.92 -63.50 140.50 26.03
12 63Y 63Y N CA 495 496 -158.37 135.40 -43.40
13 6347 63Y 64A C N 505 507 -54.44 -68.20 17.76 1.14 -62.50 175.17 29.11
13 64A 64A N CA 507 508 134.09 145.30 -40.90
14 6351 67V 68D C N 532 534 -120.11 -96.50 25.15 1.04 -63.30 172.46 18.64
14 68D 68D N CA 534 535 122.84 114.20 -40.00
15 6352 68D 69A C N 540 542 -61.76 -68.20 12.89 0.83 -62.50 175.03 28.72
15 69A 69A N CA 542 543 134.13 145.30 -40.90
16 6353 69A 70Y C N 545 547 61.90 -98.40 160.40 6.29 -63.50 -151.92 38.73
16 70Y 70Y N CA 547 548 122.65 128.40 -43.40
17 6355 71V 72K C N 564 566 -151.34 -118.00 38.54 1.28 -62.90 -176.51 29.11
17 72K 72K N CA 566 567 158.43 139.10 -40.80
18 6356 72K 73G C N 573 575 62.75 78.70 16.14 0.75 82.20 173.25 9.38
18 73G 73G N CA 575 576 -163.65 -166.10 8.50
19 6357 73G 74K C N 577 579 -116.93 -118.00 51.72 2.52 -62.90 139.30 21.32
19 74K 74K N CA 579 580 -169.19 139.10 -40.80
20 6360 76N 77Q C N 599 601 62.81 -73.00 142.65 10.87 -63.80 -174.67 24.04
20 77Q 77Q N CA 601 602 -175.64 140.70 -40.30
21 6361 77Q 78N C N 608 610 -82.18 -71.20 15.50 0.83 -63.20 166.25 21.85
21 78N 78N N CA 610 611 153.74 142.80 -41.10
22 6362 78N 79E C N 616 618 -68.66 -69.30 25.66 1.94 -63.60 157.23 20.69
22 79E 79E N CA 618 619 116.85 142.50 -40.30
23 6363 79E 80F C N 625 627 -170.48 -124.20 70.01 1.95 -63.20 160.86 28.57
23 80F 80F N CA 627 628 -164.16 143.30 -44.30
24 6364 80F 81D C N 636 638 -61.56 -70.90 18.18 0.61 -63.30 174.71 21.67
24 81D 81D N CA 638 639 134.70 150.30 -40.00
25 6365 81D 82A C N 644 646 -76.31 -68.20 18.96 1.26 -62.50 157.27 26.47
25 82A 82A N CA 646 647 162.44 145.30 -40.90
26 6366 82A 83L C N 649 651 -97.21 -70.70 81.25 5.27 -63.50 105.90 16.79
26 83L 83L N CA 651 652 -141.59 141.60 -41.20
27 6368 84V 85S C N 664 666 -130.62 -136.60 42.49 2.27 -64.10 147.58 15.46
27 85S 85S N CA 666 667 -166.74 151.20 -35.00
28 6371 87A 88Y C N 683 685 62.25 -63.50 136.62 25.52 -63.50 136.62 25.52
28 88Y 88Y N CA 685 686 10.02 -43.40 -43.40
29 6375 91G 92N C N 713 715 -161.36 -119.90 47.03 1.44 -63.20 -172.54 28.88
29 92N 92N N CA 715 716 159.19 137.00 -41.10
30 6379 95V 96A C N 746 748 -62.52 -68.20 23.36 2.08 -62.50 151.14 24.77
30 96A 96A N CA 748 749 167.96 145.30 -40.90
31 6381 97D 98G C N 759 761 130.52 78.70 54.82 2.22 82.20 174.32 10.78
31 98G 98G N CA 761 762 175.99 -166.10 8.50
32 6382 98G 99W C N 763 765 -78.67 -124.90 50.09 1.74 -63.00 169.05 20.25
32 99W 99W N CA 765 766 124.13 143.40 -44.20
33 6384 100A 101P C N 782 784 -50.33 -58.70 41.27 2.79 -64.50 142.60 11.40
33 101P 101P N CA 784 785 -70.91 -30.50 147.20
34 6385 101P 102F C N 789 791 -139.00 -124.20 70.12 3.62 58.10 168.19 25.30
34 102F 102F N CA 791 792 74.77 143.30 32.90
35 6387 103S 104H C N 806 808 -139.06 -125.60 42.06 1.81 -63.20 160.34 17.05
35 104H 104H N CA 808 809 98.95 138.80 -42.30
36 6388 104H 105A C N 816 818 -125.57 -134.00 9.03 0.21 -62.50 -173.65 33.91
36 105A 105A N CA 818 819 143.75 147.00 -40.90
37 6389 105A 106Y C N 821 823 -109.80 -98.40 60.94 6.33 -63.50 121.13 17.18
37 106Y 106Y N CA 823 824 68.53 128.40 -43.40
38 6391 107C 108A C N 839 841 -53.17 -68.20 15.04 1.29 55.40 152.79 8.11
38 108A 108A N CA 841 842 145.71 145.30 38.20
39 6392 108A 109S C N 844 846 -66.99 -72.40 10.83 0.50 -64.10 178.05 12.73
39 109S 109S N CA 846 847 143.03 152.40 -35.00
40 6395 111I 112P C N 866 868 -77.62 -58.70 27.04 1.88 -64.50 158.92 12.56
40 112P 112P N CA 868 869 -11.18 -30.50 147.20
41 6396 112P 113K C N 873 875 -67.24 -70.20 15.99 1.23 -62.90 163.15 21.43
41 113K 113K N CA 875 876 156.11 140.40 -40.80
42 6397 113K 114Y C N 882 884 -128.10 -124.30 20.23 0.92 -63.50 173.78 30.80
42 114Y 114Y N CA 884 885 155.27 135.40 -43.40
43 6398 114Y 115R C N 894 896 -73.69 -72.10 37.15 2.89 -63.00 146.27 19.06
43 115R 115R N CA 896 897 104.78 141.90 -41.10
44 6399 115R 116N C N 905 907 -155.43 -119.90 45.29 1.31 -63.20 179.34 27.54
44 116N 116N N CA 907 908 165.09 137.00 -41.10
45 6400 116N 117A C N 913 915 -70.02 -68.20 10.71 0.80 -62.50 163.42 27.16
45 117A 117A N CA 915 916 155.85 145.30 -40.90
46 6401 117A 118G C N 918 920 63.71 78.70 61.82 1.17 82.20 116.11 6.55
46 118G 118G N CA 920 921 -106.13 -166.10 8.50
47 6403 119G 120Q C N 926 928 -74.01 -73.00 14.41 0.96 -63.80 166.94 24.02
47 120Q 120Q N CA 928 929 126.32 140.70 -40.30
48 6405 121V 122L C N 942 944 -74.61 -70.70 4.08 0.33 -63.50 176.38 25.14
48 122L 122L N CA 944 945 142.77 141.60 -41.20
49 6407 123Q 124G C N 959 961 70.51 78.70 15.37 0.75 82.20 172.79 7.80
49 124G 124G N CA 961 962 -179.10 -166.10 8.50
50 6408 124G 125L C N 963 965 -139.84 -108.50 48.41 2.21 -63.50 167.77 28.01
50 125L 125L N CA 965 966 169.40 132.50 -41.20
51 6420 136F 137N C N 1069 1071 -148.68 -63.20 95.58 12.10 -63.20 95.58 12.10
51 137N 137N N CA 1071 1072 1.67 -41.10 -41.10
52 6421 137N 138K C N 1077 1079 -120.01 -118.00 11.98 0.55 -62.90 177.71 26.48
52 138K 138K N CA 1079 1080 150.91 139.10 -40.80
53 6422 138K 139P C N 1086 1088 -46.79 -58.70 30.78 1.82 -64.50 154.94 12.52
53 139P 139P N CA 1088 1089 -58.88 -30.50 147.20
54 6424 140V 141S C N 1100 1102 -104.43 -136.60 47.25 1.55 -64.10 156.86 9.74
54 141S 141S N CA 1102 1103 116.58 151.20 -35.00
55 6425 141S 142S C N 1106 1108 -154.12 -136.60 23.52 0.74 -64.10 -178.06 19.66
55 142S 142S N CA 1108 1109 166.89 151.20 -35.00
56 6426 142S 143N C N 1112 1114 -78.52 -71.20 22.74 1.66 -63.20 163.09 19.58
56 143N 143N N CA 1114 1115 121.27 142.80 -41.10
57 6427 143N 144S C N 1120 1122 -93.75 -72.40 31.73 1.48 -64.10 152.05 13.01
57 144S 144S N CA 1122 1123 175.87 152.40 -35.00
58 6428 144S 145N C N 1126 1128 -136.45 -119.90 36.39 1.24 -63.20 166.47 24.94
58 145N 145N N CA 1128 1129 169.41 137.00 -41.10
59 6429 145N 146Q C N 1134 1136 -76.49 -73.00 13.92 0.98 -63.80 168.01 24.05
59 146Q 146Q N CA 1136 1137 127.23 140.70 -40.30
60 6430 146Q 147N C N 1143 1145 -158.71 -63.20 116.35 19.11 -63.20 116.35 19.11
60 147N 147N N CA 1145 1146 -107.54 -41.10 -41.10
61 6432 148N 149Q C N 1159 1161 -54.32 -73.00 18.72 1.36 -63.80 178.04 25.69
61 149Q 149Q N CA 1161 1162 141.91 140.70 -40.30
62 6433 149Q 150T C N 1168 1170 -138.37 -124.80 29.46 0.93 -63.20 166.22 26.19
62 150T 150T N CA 1170 1171 169.65 143.50 -42.10
63 6434 150T 151G C N 1175 1177 73.15 78.70 41.72 0.96 82.20 133.56 6.94
63 151G 151G N CA 1177 1178 -124.75 -166.10 8.50
64 6435 151G 152G C N 1179 1181 -66.12 -80.20 26.46 0.64 82.20 -153.84 6.58
64 152G 152G N CA 1181 1182 151.69 174.10 8.50
65 6438 154I 155K C N 1199 1201 -162.47 -118.00 71.62 2.65 -62.90 158.98 26.46
65 155K 155K N CA 1201 1202 -164.75 139.10 -40.80
66 6439 155K 156M C N 1208 1210 -88.41 -63.40 92.02 12.04 -63.40 92.02 12.04
66 156M 156M N CA 1210 1211 48.05 -40.50 -40.50
67 6440 156M 157Y C N 1216 1218 -119.11 -124.30 5.79 0.33 -63.50 -175.19 26.73
67 157Y 157Y N CA 1218 1219 132.84 135.40 -43.40
68 6441 157Y 158L C N 1228 1230 -65.87 -70.70 6.56 0.66 -63.50 172.76 24.12
68 158L 158L N CA 1230 1231 146.05 141.60 -41.20
69 6443 159I 160I C N 1244 1246 -60.84 -63.40 5.87 0.90 -120.60 -171.11 8.63
69 160I 160I N CA 1246 1247 -48.89 -43.60 130.30
70 6444 160I 161G C N 1252 1254 -75.13 -80.20 55.05 1.92 82.20 -167.58 7.41
70 161G 161G N CA 1254 1255 119.29 174.10 8.50
71 6445 161G 162L C N 1256 1258 -69.70 -70.70 21.33 1.65 -63.50 156.01 22.02
71 162L 162L N CA 1258 1259 162.91 141.60 -41.20
72 6446 162L 163D C N 1264 1266 -34.47 -70.90 44.79 2.14 -63.30 166.75 22.41
72 163D 163D N CA 1266 1267 124.24 150.30 -40.00
73 6447 163D 164N C N 1272 1274 -116.66 -119.90 3.29 0.12 -63.20 -174.61 20.70
73 164N 164N N CA 1274 1275 136.42 137.00 -41.10
74 6449 165S 166G C N 1286 1288 62.75 78.70 25.11 0.48 82.20 156.42 8.56
74 166G 166G N CA 1288 1289 -146.71 -166.10 8.50
75 6450 166G 167K C N 1290 1292 -116.53 -118.00 2.17 0.11 -62.90 -173.62 27.39
75 167K 167K N CA 1292 1293 140.70 139.10 -40.80
76 6451 167K 168A C N 1299 1301 -158.84 -134.00 53.12 2.21 -62.50 157.94 30.93
76 168A 168A N CA 1301 1302 -166.05 147.00 -40.90
77 6452 168A 169K C N 1304 1306 -53.29 -70.20 17.46 1.17 -62.90 177.10 23.54
77 169K 169K N CA 1306 1307 136.04 140.40 -40.80
78 6454 170H 171W C N 1323 1325 -70.96 -71.30 0.90 0.08 -63.00 176.15 22.51
78 171W 171W N CA 1325 1326 139.83 139.00 -44.20
79 6455 171W 172Y C N 1337 1339 -105.76 -98.40 15.84 1.55 -63.50 179.23 30.60
79 172Y 172Y N CA 1339 1340 142.43 128.40 -43.40
80 6456 172Y 173V C N 1349 1351 -59.44 -62.40 8.01 0.89 -125.40 179.43 10.12
80 173V 173V N CA 1351 1352 -49.84 -42.40 143.30
81 6457 173V 174S C N 1356 1358 -168.66 -136.60 100.14 4.30 -64.10 131.01 16.83
81 174S 174S N CA 1358 1359 -113.93 151.20 -35.00
82 6458 174S 175D C N 1362 1364 -40.94 -70.90 72.69 5.05 -63.30 105.87 11.89
82 175D 175D N CA 1364 1365 -143.48 150.30 -40.00
83 6474 190N 191Y C N 1492 1494 71.04 55.90 155.99 12.05 -124.30 175.03 10.90
83 191Y 191Y N CA 1494 1495 -165.24 39.50 135.40
84 6487 203D 204T C N 1604 1606 50.24 55.90 8.16 0.48 -124.80 -159.34 7.73
84 204T 204T N CA 1606 1607 45.38 39.50 143.50
85 6495 211E 212A C N 1669 1671 49.41 -68.20 127.65 12.20 -68.20 127.65 12.20
85 212A 212A N CA 1671 1672 -165.09 145.30 145.30
86 6496 212A 213E C N 1674 1676 -71.81 -69.30 49.24 3.85 -63.60 133.88 17.41
86 213E 213E N CA 1676 1677 93.33 142.50 -40.30
87 6497 213E 214F C N 1683 1685 -107.24 -124.20 29.63 0.90 -63.20 169.14 20.75
87 214F 214F N CA 1685 1686 119.00 143.30 -44.30
88 6498 214F 215G C N 1694 1696 -55.41 -62.40 6.99 1.25 82.20 146.26 11.16
88 215G 215G N CA 1696 1697 -41.04 -41.20 8.50
89 6499 215G 216R C N 1698 1700 -70.58 -72.10 15.01 1.12 -63.00 168.23 22.23
89 216R 216R N CA 1700 1701 126.96 141.90 -41.10
90 6500 216R 217K C N 1709 1711 -94.04 -118.00 25.65 0.86 -62.90 173.56 21.03
90 217K 217K N CA 1711 1712 129.94 139.10 -40.80
91 6502 218I 219D C N 1726 1728 -85.56 -70.90 22.68 0.84 -63.30 154.02 20.42
91 219D 219D N CA 1728 1729 167.60 150.30 -40.00
92 6503 219D 220M C N 1734 1736 -106.33 -125.60 19.30 0.79 -63.40 -177.00 30.75
92 220M 220M N CA 1736 1737 141.60 140.50 -40.50
93 6504 220M 221A C N 1742 1744 -74.47 -68.20 6.49 0.60 -62.50 175.87 29.42
93 221A 221A N CA 1744 1745 143.64 145.30 -40.90
94 6505 221A 222S C N 1747 1749 -149.74 -136.60 22.30 0.79 -64.10 177.77 19.04
94 222S 222S N CA 1749 1750 169.21 151.20 -35.00
95 6506 222S 223G C N 1753 1755 87.51 78.70 28.33 0.48 82.20 158.56 7.96
95 223G 223G N CA 1755 1756 166.97 -166.10 8.50
96 6507 223G 224E C N 1757 1759 -117.42 -117.80 8.09 0.40 -63.60 177.38 21.19
96 224E 224E N CA 1759 1760 128.72 136.80 -40.30
97 6509 227A 228A C N 1788 1790 67.47 55.40 31.53 1.15 -134.00 -149.87 11.99
97 228A 228A N CA 1790 1791 9.08 38.20 147.00
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 21 29 143 181 217 199 224 250 269 276
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
P62693.B99990001.pdb 1450.60339
P62693.B99990002.pdb 1631.20374
In [ ]:
score_ala = evaluate_model('P62693.B99990001.pdb')
readlinef__W> File: P62693.B99990001.pdb, Line: 6
Modeller will only read the first 80 characters of this line.
selection__W> The class 'selection' is deprecated; use 'Selection' instead
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: LYS:OXT LYS
iatmcls_286W> MODEL atom not classified: ALA:OXT ALA
preppdf_453W> No fixed restraints selected; there may be some dynamic ones.
preppdf_454W> Restraints file was probably not read; use restraints.append().
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 229
Number of all, selected real atoms : 1800 1800
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 0 0
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 303450
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -16115.1543
<< end of ENERGY.
DOPE score : -16115.154297
In [ ]:
Image('2.png')
Out[ ]:
In [ ]:
print(f"Native DOPE score: {score_native}")
print(f"ALA-ligand DOPE score: {score_ala}")
Native DOPE score: -15983.8193359375 ALA-ligand DOPE score: -16115.154296875
In [ ]:
# Более низкий score - это хорошо, но это не обязательно должно быть биологически правильно