Гомологичное моделирование комплекса белка с лигандом¶
In [16]:
import sys
import modeller
import _modeller
import modeller.automodel
In [17]:
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.24, 2020/04/06, r11614
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2020 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo 3.16.0-6-amd64 x86_64
Date and time of compilation : 2020/04/06 19:06:24
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/05/27 22:34:05
In [18]:
alignm=modeller.alignment(env)
In [19]:
#добавим последовательность для моделирования и структуру известного лизоцима форели
alignm.append(file='Q6QGP7.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')
In [20]:
#поправим идентификаторы
alignm[0].code = 'ENLYS_BPT5' #этот белок был использован
alignm[1].code = '1lmp'
In [21]:
#делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [22]:
#посмотрим на получившееся выравнивание
! cat all_in_one.ali
>P1;ENLYS_BPT5 sequence:: : : : :::-1.00:-1.00 MSFKFGKNSEKQLATVKPELQKVARRALELSPYDFTIVQGIRTVAQSAQNIANGTSFLKDPSKSKHITGDAIDFA PYINGKIDWNDLEAFWAVKKAFEQAGKELGIKLRFGADWNASGDYHDEIKRGTYDGGHVELV* >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 ---KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGA KNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCG-----V*
In [23]:
#построим модель и выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
ENLYS_BPT5 1lmp
In [24]:
#создаем объект automodel и проводим моделирование
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()
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
read_to_681_> topology.submodel read from topology file: 3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
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: 11073 10114
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1081 1081
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10114 10114
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2573
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 : 1103.9882
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 : 1105 0 0 0.006 0.006 11.876 1.000
2 Bond angle potential : 1489 0 6 2.276 2.276 147.44 1.000
3 Stereochemical cosine torsion poten: 698 0 30 49.845 49.845 256.68 1.000
4 Stereochemical improper torsion pot: 459 0 0 1.322 1.322 17.242 1.000
5 Soft-sphere overlap restraints : 2573 0 0 0.005 0.005 8.1988 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 2 0.291 0.291 94.250 1.000
10 Distance restraints 2 (N-O) : 2564 4 27 0.519 0.519 282.78 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 4.909 4.909 38.657 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 1 81.922 81.922 41.913 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 2 64.423 64.423 44.381 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 75.182 75.182 27.798 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 79.401 79.401 11.314 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) : 758 0 0 0.330 0.330 10.544 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 37 21 30.595 87.219 104.18 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 0 0.841 0.841 6.7369 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: ENLYS_BPT5.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: 18087.2031
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 9031 117S 113D N O 916 888 5.47 2.88 2.59 5.08 2.88 2.59 5.08
2 9050 118G 113D N O 922 888 6.92 3.98 2.93 5.94 3.98 2.93 5.94
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3752 1M 2S C N 7 9 -150.02 -136.60 66.66 3.08 -64.10 138.40 16.22
1 2S 2S N CA 9 10 -143.51 151.20 -35.00
2 3753 2S 3F C N 13 15 -64.57 -71.40 8.38 0.47 -63.20 179.86 25.07
2 3F 3F N CA 15 16 135.85 140.70 -44.30
3 3754 3F 4K C N 24 26 -106.28 -118.00 26.00 1.06 -62.90 162.58 19.19
3 4K 4K N CA 26 27 115.89 139.10 -40.80
4 3769 18P 19E C N 141 143 68.70 54.60 15.94 1.34 -63.60 152.21 26.19
4 19E 19E N CA 143 144 34.96 42.40 -40.30
5 3774 23V 24A C N 183 185 54.84 55.40 7.38 0.49 -62.50 137.53 27.96
5 24A 24A N CA 185 186 30.84 38.20 -40.90
6 3789 38V 39Q C N 306 308 -130.16 -63.80 82.30 11.13 -63.80 82.30 11.13
6 39Q 39Q N CA 308 309 8.37 -40.30 -40.30
7 3790 39Q 40G C N 315 317 65.58 78.70 33.45 0.51 82.20 144.79 7.86
7 40G 40G N CA 317 318 -135.33 -166.10 8.50
8 3791 40G 41I C N 319 321 -130.97 -120.60 77.61 4.84 -63.40 118.21 17.97
8 41I 41I N CA 321 322 53.39 130.30 -43.60
9 3801 50N 51I C N 394 396 -91.52 -120.60 89.39 4.06 -63.40 93.70 14.52
9 51I 51I N CA 396 397 45.78 130.30 -43.60
10 3802 51I 52A C N 402 404 56.32 55.40 11.99 0.65 -62.50 136.48 27.76
10 52A 52A N CA 404 405 26.24 38.20 -40.90
11 3812 61P 62S C N 475 477 -84.49 -72.40 15.84 1.27 -64.10 178.35 11.86
11 62S 62S N CA 477 478 142.18 152.40 -35.00
12 3819 68T 69G C N 530 532 -94.95 -80.20 35.05 0.82 82.20 -119.53 18.57
12 69G 69G N CA 532 533 -154.10 174.10 8.50
13 3820 69G 70D C N 534 536 -120.25 -63.30 63.41 8.36 54.50 -177.39 23.38
13 70D 70D N CA 536 537 -12.11 -40.00 40.90
14 3824 73D 74F C N 563 565 57.52 58.10 5.87 0.43 -63.20 146.52 26.44
14 74F 74F N CA 565 566 38.74 32.90 -44.30
15 3826 75A 76P C N 579 581 -81.80 -64.50 23.67 1.54 -58.70 167.76 15.77
15 76P 76P N CA 581 582 163.34 147.20 -30.50
16 3827 76P 77Y C N 586 588 -130.88 -124.30 63.24 3.63 -63.50 134.07 18.61
16 77Y 77Y N CA 588 589 72.51 135.40 -43.40
17 3829 78I 79N C N 606 608 -97.77 -119.90 32.77 0.97 -63.20 157.77 18.03
17 79N 79N N CA 608 609 112.83 137.00 -41.10
18 3830 79N 80G C N 614 616 -54.63 -62.40 34.76 5.60 82.20 137.74 9.77
18 80G 80G N CA 616 617 -7.32 -41.20 8.50
19 3851 100A 101G C N 789 791 -61.88 -62.40 0.54 0.10 82.20 152.37 11.59
19 101G 101G N CA 791 792 -41.05 -41.20 8.50
20 3855 104L 105G C N 819 821 -56.92 -62.40 5.75 0.94 82.20 148.33 11.33
20 105G 105G N CA 821 822 -42.94 -41.20 8.50
21 3856 105G 106I C N 823 825 -97.30 -97.30 43.90 4.57 -63.40 131.35 20.49
21 106I 106I N CA 825 826 83.30 127.20 -43.60
22 3857 106I 107K C N 831 833 -55.00 -62.90 64.28 7.95 -118.00 132.27 6.85
22 107K 107K N CA 833 834 -104.59 -40.80 139.10
23 3861 110F 111G C N 870 872 -71.74 -80.20 51.47 1.62 82.20 -167.95 7.15
23 111G 111G N CA 872 873 123.33 174.10 8.50
24 3863 112A 113D C N 879 881 -72.00 -70.90 11.49 0.51 -63.30 158.50 20.10
24 113D 113D N CA 881 882 161.74 150.30 -40.00
25 3864 113D 114W C N 887 889 84.99 58.80 80.89 2.50 -63.00 147.99 24.70
25 114W 114W N CA 889 890 -43.53 33.00 -44.20
26 3867 116A 117S C N 914 916 -142.79 -136.60 27.68 1.51 -64.10 177.60 11.28
26 117S 117S N CA 916 917 124.21 151.20 -35.00
27 3868 117S 118G C N 920 922 126.26 82.20 56.73 2.01 -62.40 171.91 30.11
27 118G 118G N CA 922 923 -27.23 8.50 -41.20
28 3869 118G 119D C N 924 926 -56.57 -63.30 21.04 2.28 -70.90 150.45 8.13
28 119D 119D N CA 926 927 -59.93 -40.00 150.30
29 3870 119D 120Y C N 932 934 -118.19 -98.40 56.02 5.53 -63.50 131.32 18.49
29 120Y 120Y N CA 934 935 75.99 128.40 -43.40
30 3876 125K 126R C N 988 990 -73.53 -125.20 65.78 1.95 -63.00 141.38 18.41
30 126R 126R N CA 990 991 99.89 140.60 -41.10
31 3877 126R 127G C N 999 1001 117.99 82.20 40.35 1.82 -62.40 -177.73 31.15
31 127G 127G N CA 1001 1002 -10.13 8.50 -41.20
32 3879 128T 129Y C N 1010 1012 53.81 55.90 11.66 0.97 -124.30 -152.03 11.18
32 129Y 129Y N CA 1012 1013 28.03 39.50 135.40
33 3880 129Y 130D C N 1022 1024 -100.19 -96.50 31.45 1.32 -63.30 128.38 14.04
33 130D 130D N CA 1024 1025 82.97 114.20 -40.00
34 3883 132G 133H C N 1038 1040 -126.15 -125.60 42.47 1.60 -63.20 150.26 22.89
34 133H 133H N CA 1040 1041 -178.73 138.80 -42.30
35 3884 133H 134V C N 1048 1050 -59.08 -62.40 3.56 0.61 -125.40 -172.32 10.55
35 134V 134V N CA 1050 1051 -41.13 -42.40 143.30
36 3885 134V 135E C N 1055 1057 -96.35 -117.80 21.45 0.78 -63.60 179.81 22.33
36 135E 135E N CA 1057 1058 136.50 136.80 -40.30
37 3886 135E 136L C N 1064 1066 -128.80 -108.50 26.13 1.16 -63.50 -178.04 29.31
37 136L 136L N CA 1066 1067 148.96 132.50 -41.20
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 10 15 93 80 152 126 173 169 177 205
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1081 1081
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10114 10114
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2436
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 855.8093
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 : 1105 0 0 0.005 0.005 8.2417 1.000
2 Bond angle potential : 1489 0 6 2.199 2.199 143.26 1.000
3 Stereochemical cosine torsion poten: 698 0 29 47.942 47.942 239.34 1.000
4 Stereochemical improper torsion pot: 459 0 0 1.118 1.118 11.956 1.000
5 Soft-sphere overlap restraints : 2436 0 0 0.004 0.004 3.6256 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.269 0.269 68.541 1.000
10 Distance restraints 2 (N-O) : 2564 0 12 0.428 0.428 164.56 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 3 5.263 5.263 44.427 1.000
14 Sidechain Chi_1 dihedral restraints: 111 0 1 82.206 82.206 44.353 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 0 81.243 81.243 37.811 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 60.992 60.992 22.708 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 81.804 81.804 13.680 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) : 758 0 0 0.304 0.304 8.5524 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 135 26 12 26.443 74.082 40.797 1.000
26 Distance restraints 4 (SDCH-SDCH) : 107 0 0 0.656 0.656 3.9508 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: ENLYS_BPT5.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: 15828.9141
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 3752 1M 2S C N 7 9 -118.85 -136.60 18.49 0.87 -64.10 177.29 16.67
1 2S 2S N CA 9 10 156.37 151.20 -35.00
2 3753 2S 3F C N 13 15 -92.31 -71.40 32.24 2.85 -63.20 163.09 20.77
2 3F 3F N CA 15 16 116.17 140.70 -44.30
3 3754 3F 4K C N 24 26 -107.08 -118.00 29.43 1.24 -62.90 158.84 18.69
3 4K 4K N CA 26 27 111.77 139.10 -40.80
4 3769 18P 19E C N 141 143 68.76 54.60 16.29 1.33 -63.60 151.96 26.14
4 19E 19E N CA 143 144 34.35 42.40 -40.30
5 3774 23V 24A C N 183 185 57.28 55.40 9.30 0.42 -62.50 138.73 28.21
5 24A 24A N CA 185 186 29.09 38.20 -40.90
6 3789 38V 39Q C N 306 308 -148.07 -121.10 107.00 5.45 -63.80 113.78 14.99
6 39Q 39Q N CA 308 309 36.15 139.70 -40.30
7 3790 39Q 40G C N 315 317 61.76 78.70 19.57 0.65 82.20 166.06 9.08
7 40G 40G N CA 317 318 -156.30 -166.10 8.50
8 3791 40G 41I C N 319 321 -112.07 -97.30 59.48 5.96 -63.40 123.20 18.88
8 41I 41I N CA 321 322 69.58 127.20 -43.60
9 3801 50N 51I C N 394 396 -100.80 -120.60 75.81 3.60 -63.40 107.45 16.55
9 51I 51I N CA 396 397 57.12 130.30 -43.60
10 3802 51I 52A C N 402 404 63.26 55.40 30.20 1.25 -62.50 135.31 27.42
10 52A 52A N CA 404 405 9.04 38.20 -40.90
11 3812 61P 62S C N 475 477 -81.71 -72.40 12.56 1.00 -64.10 179.84 12.09
11 62S 62S N CA 477 478 143.97 152.40 -35.00
12 3819 68T 69G C N 530 532 -109.57 -80.20 29.72 2.10 82.20 -127.12 17.93
12 69G 69G N CA 532 533 169.54 174.10 8.50
13 3820 69G 70D C N 534 536 -73.93 -63.30 11.27 1.57 54.50 149.83 19.42
13 70D 70D N CA 536 537 -36.27 -40.00 40.90
14 3823 72I 73D C N 555 557 -67.97 -63.30 18.17 2.54 -70.90 152.17 7.64
14 73D 73D N CA 557 558 -57.56 -40.00 150.30
15 3827 76P 77Y C N 586 588 59.48 55.90 11.62 1.08 -63.50 154.76 29.32
15 77Y 77Y N CA 588 589 50.55 39.50 -43.40
16 3851 100A 101G C N 789 791 -62.17 -62.40 1.36 0.21 82.20 152.26 11.56
16 101G 101G N CA 791 792 -39.86 -41.20 8.50
17 3855 104L 105G C N 819 821 48.72 78.70 49.41 0.88 82.20 139.40 8.39
17 105G 105G N CA 821 822 -126.82 -166.10 8.50
18 3856 105G 106I C N 823 825 -94.14 -97.30 18.47 1.92 -63.40 155.67 24.53
18 106I 106I N CA 825 826 109.00 127.20 -43.60
19 3857 106I 107K C N 831 833 -56.18 -62.90 30.82 3.69 -118.00 162.26 8.39
19 107K 107K N CA 833 834 -70.88 -40.80 139.10
20 3861 110F 111G C N 870 872 -81.99 -80.20 50.27 2.07 82.20 -159.34 7.74
20 111G 111G N CA 872 873 123.86 174.10 8.50
21 3869 118G 119D C N 924 926 -51.91 -63.30 22.77 2.42 -70.90 151.18 8.41
21 119D 119D N CA 926 927 -59.71 -40.00 150.30
22 3870 119D 120Y C N 932 934 -116.65 -98.40 50.52 4.98 -63.50 135.55 19.18
22 120Y 120Y N CA 934 935 81.29 128.40 -43.40
23 3878 127G 128T C N 1003 1005 -45.42 -63.20 25.04 2.75 -124.80 175.73 9.73
23 128T 128T N CA 1005 1006 -59.73 -42.10 143.50
24 3881 130D 131G C N 1030 1032 68.28 78.70 19.77 0.31 82.20 158.41 8.39
24 131G 131G N CA 1032 1033 -149.30 -166.10 8.50
25 3882 131G 132G C N 1034 1036 94.61 78.70 16.70 0.69 82.20 -179.90 8.11
25 132G 132G N CA 1036 1037 -171.17 -166.10 8.50
26 3886 135E 136L C N 1064 1066 -60.22 -70.70 23.90 1.50 -63.50 161.36 22.59
26 136L 136L N CA 1066 1067 120.13 141.60 -41.20
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 13 81 109 126 129 134 183 174 178
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5.B99990001.pdb 1103.98816
ENLYS_BPT5.B99990002.pdb 855.80927
In [27]:
print('ENLYS_BPT5.B99990001.pdb is green')
display(Image('png_1.png', width=600))
print('ENLYS_BPT5.B99990002.pdb is cyan')
display(Image('png_2.png', width=600))
ENLYS_BPT5.B99990001.pdb is green
ENLYS_BPT5.B99990002.pdb is cyan
Добавим его лиганд в белок¶
In [28]:
#добавляем лиганд
seq_lig = ''
for res in alignm[0].residues:
seq_lig += res.code
for lig in alignm[1].residues[-3:]:
seq_lig += lig.code
alignm.append_sequence(seq_lig)
alignm[2].code = 'ENLYS_BPT5_lig'
del alignm[0]
In [29]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [30]:
! cat all_in_one2.ali
>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 ---KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGA KNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRS--------YVAGCGV* >P1;ENLYS_BPT5_lig sequence::1 : :+140 : :undefined:undefined:-1.00:-1.00 MSFKFGKNSEKQLATVKPELQKVARRALELSPYDFTIVQGIRTVAQSAQNIANGTSFLKDPSKSKHITGDAIDFA PYINGKIDWNDLEAFWAVKKAFEQAGKELGIKLRFGADWNASGDYHDEIKRGTYDGGHVELVCGV*
In [31]:
# выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
# создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
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()
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: 11183 10207
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1098 1098
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10207 10207
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2500
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 : 863.1703
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 : 1122 0 0 0.005 0.005 7.7540 1.000
2 Bond angle potential : 1512 0 2 2.098 2.098 127.50 1.000
3 Stereochemical cosine torsion poten: 706 0 29 48.933 48.933 257.39 1.000
4 Stereochemical improper torsion pot: 465 0 0 1.150 1.150 12.564 1.000
5 Soft-sphere overlap restraints : 2500 0 0 0.004 0.004 4.3876 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 0 0.246 0.246 64.020 1.000
10 Distance restraints 2 (N-O) : 2564 0 7 0.423 0.423 127.60 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: 139 0 3 4.633 4.633 35.191 1.000
14 Sidechain Chi_1 dihedral restraints: 113 0 2 84.178 84.178 44.233 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 2 67.712 67.712 42.972 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 66.598 66.598 25.424 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 99.008 99.008 12.479 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) : 785 0 0 0.426 0.426 8.9724 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: 138 27 19 32.916 77.319 88.877 1.000
26 Distance restraints 4 (SDCH-SDCH) : 111 0 0 0.742 0.742 3.8083 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: ENLYS_BPT5_lig.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: 16280.4062
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 3806 1M 2S C N 7 9 -69.89 -72.40 7.81 0.38 -64.10 -179.91 13.40
1 2S 2S N CA 9 10 145.00 152.40 -35.00
2 3807 2S 3F C N 13 15 -84.44 -71.40 16.72 1.44 -63.20 175.82 23.02
2 3F 3F N CA 15 16 130.23 140.70 -44.30
3 3808 3F 4K C N 24 26 -125.25 -118.00 25.30 1.30 -62.90 167.69 19.38
3 4K 4K N CA 26 27 114.86 139.10 -40.80
4 3822 17K 18P C N 134 136 -79.55 -64.50 36.07 3.50 -58.70 146.41 10.50
4 18P 18P N CA 136 137 114.42 147.20 -30.50
5 3823 18P 19E C N 141 143 -50.85 -69.30 68.11 4.53 -63.60 117.93 16.43
5 19E 19E N CA 143 144 76.93 142.50 -40.30
6 3828 23V 24A C N 183 185 55.20 55.40 5.40 0.34 -62.50 138.86 28.22
6 24A 24A N CA 185 186 32.80 38.20 -40.90
7 3843 38V 39Q C N 306 308 -154.31 -121.10 98.86 5.10 -63.80 125.47 16.43
7 39Q 39Q N CA 308 309 46.59 139.70 -40.30
8 3844 39Q 40G C N 315 317 61.67 78.70 17.17 0.81 82.20 173.69 9.45
8 40G 40G N CA 317 318 -163.97 -166.10 8.50
9 3845 40G 41I C N 319 321 -106.70 -97.30 53.35 5.43 -63.40 125.96 19.41
9 41I 41I N CA 321 322 74.68 127.20 -43.60
10 3856 51I 52A C N 402 404 85.63 55.40 40.75 2.31 -62.50 156.91 31.71
10 52A 52A N CA 404 405 10.87 38.20 -40.90
11 3866 61P 62S C N 475 477 -87.83 -72.40 16.63 1.32 -64.10 -179.65 14.61
11 62S 62S N CA 477 478 146.21 152.40 -35.00
12 3869 64S 65K C N 496 498 -124.21 -62.90 61.50 10.27 -62.90 61.50 10.27
12 65K 65K N CA 498 499 -45.59 -40.80 -40.80
13 3873 68T 69G C N 530 532 -122.64 -62.40 70.52 10.67 82.20 155.70 9.94
13 69G 69G N CA 532 533 -4.53 -41.20 8.50
14 3878 73D 74F C N 563 565 51.64 58.10 19.22 1.04 -63.20 149.24 26.88
14 74F 74F N CA 565 566 51.00 32.90 -44.30
15 3881 76P 77Y C N 586 588 58.14 55.90 9.95 0.87 -63.50 152.88 28.96
15 77Y 77Y N CA 588 589 49.19 39.50 -43.40
16 3905 100A 101G C N 789 791 -61.77 -62.40 2.38 0.39 82.20 151.58 11.49
16 101G 101G N CA 791 792 -38.91 -41.20 8.50
17 3909 104L 105G C N 819 821 -58.94 -62.40 4.47 0.84 82.20 148.72 11.28
17 105G 105G N CA 821 822 -38.37 -41.20 8.50
18 3915 110F 111G C N 870 872 -78.09 -80.20 48.23 1.79 82.20 -161.31 7.48
18 111G 111G N CA 872 873 125.91 174.10 8.50
19 3924 119D 120Y C N 932 934 53.52 55.90 4.02 0.21 -63.50 145.30 27.53
19 120Y 120Y N CA 934 935 42.74 39.50 -43.40
20 3929 124I 125K C N 979 981 -168.52 -118.00 98.29 3.86 -62.90 142.58 24.45
20 125K 125K N CA 981 982 -136.58 139.10 -40.80
21 3930 125K 126R C N 988 990 -148.07 -125.20 27.87 0.82 -63.00 -176.71 30.52
21 126R 126R N CA 990 991 156.54 140.60 -41.10
22 3931 126R 127G C N 999 1001 81.10 78.70 41.28 1.08 82.20 144.19 6.94
22 127G 127G N CA 1001 1002 152.69 -166.10 8.50
23 3933 128T 129Y C N 1010 1012 -147.20 -124.30 30.60 1.42 -63.50 -178.63 32.85
23 129Y 129Y N CA 1012 1013 155.70 135.40 -43.40
24 3934 129Y 130D C N 1022 1024 58.37 54.50 88.30 6.80 -63.30 -151.66 33.39
24 130D 130D N CA 1024 1025 129.12 40.90 -40.00
25 3936 131G 132G C N 1034 1036 -145.41 -167.20 57.23 1.85 82.20 174.17 13.51
25 132G 132G N CA 1036 1037 121.68 174.60 8.50
26 3937 132G 133H C N 1038 1040 -145.66 -125.60 92.16 3.10 -63.20 121.29 20.21
26 133H 133H N CA 1040 1041 -131.25 138.80 -42.30
27 3941 136L 137V C N 1072 1074 72.65 55.90 46.81 2.30 -125.40 -140.94 12.33
27 137V 137V N CA 1074 1075 -4.21 39.50 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 16 74 94 127 123 139 205 195 173
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1098 1098
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10207 10207
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2552
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 : 887.0933
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 : 1122 0 0 0.006 0.006 9.6930 1.000
2 Bond angle potential : 1512 0 6 2.165 2.165 135.41 1.000
3 Stereochemical cosine torsion poten: 706 0 30 48.652 48.652 247.28 1.000
4 Stereochemical improper torsion pot: 465 0 0 1.209 1.209 14.988 1.000
5 Soft-sphere overlap restraints : 2552 0 0 0.005 0.005 6.2709 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 0 2 0.304 0.304 71.907 1.000
10 Distance restraints 2 (N-O) : 2564 0 6 0.438 0.438 146.79 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: 139 0 4 5.046 5.046 41.742 1.000
14 Sidechain Chi_1 dihedral restraints: 113 0 0 80.424 80.424 35.304 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 1 64.463 64.463 32.758 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 75.418 75.418 32.512 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 86.333 86.333 11.699 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) : 785 0 0 0.423 0.423 8.7772 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: 138 31 22 36.191 79.352 85.570 1.000
26 Distance restraints 4 (SDCH-SDCH) : 111 0 0 0.889 0.889 6.3906 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: ENLYS_BPT5_lig.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: 16351.5791
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 3806 1M 2S C N 7 9 -83.61 -72.40 19.37 0.89 -64.10 158.01 12.71
1 2S 2S N CA 9 10 168.20 152.40 -35.00
2 3807 2S 3F C N 13 15 -74.56 -71.40 3.23 0.20 -63.20 174.65 25.02
2 3F 3F N CA 15 16 141.41 140.70 -44.30
3 3808 3F 4K C N 24 26 -96.55 -118.00 28.65 0.99 -62.90 164.39 19.76
3 4K 4K N CA 26 27 120.11 139.10 -40.80
4 3822 17K 18P C N 134 136 -80.45 -64.50 36.51 3.58 -58.70 146.48 10.44
4 18P 18P N CA 136 137 114.36 147.20 -30.50
5 3823 18P 19E C N 141 143 -42.34 -69.30 74.61 4.73 -63.60 115.21 16.56
5 19E 19E N CA 143 144 72.93 142.50 -40.30
6 3828 23V 24A C N 183 185 54.15 55.40 4.71 0.39 -62.50 138.44 28.13
6 24A 24A N CA 185 186 33.66 38.20 -40.90
7 3843 38V 39Q C N 306 308 -143.23 -63.80 98.23 13.30 -63.80 98.23 13.30
7 39Q 39Q N CA 308 309 17.48 -40.30 -40.30
8 3845 40G 41I C N 319 321 32.22 -97.30 138.41 7.86 -63.40 155.01 28.74
8 41I 41I N CA 321 322 78.40 127.20 -43.60
9 3848 43T 44V C N 345 347 -104.10 -125.40 80.80 3.42 -62.40 115.54 12.81
9 44V 44V N CA 347 348 65.36 143.30 -42.40
10 3855 50N 51I C N 394 396 -98.07 -120.60 81.71 3.84 -63.40 101.47 15.64
10 51I 51I N CA 396 397 51.76 130.30 -43.60
11 3856 51I 52A C N 402 404 60.02 55.40 24.56 1.12 -62.50 134.29 27.27
11 52A 52A N CA 404 405 14.08 38.20 -40.90
12 3866 61P 62S C N 475 477 -83.64 -72.40 14.12 1.14 -64.10 179.92 12.01
12 62S 62S N CA 477 478 143.86 152.40 -35.00
13 3873 68T 69G C N 530 532 -93.88 -80.20 13.70 0.93 82.20 -118.74 7.83
13 69G 69G N CA 532 533 173.43 174.10 8.50
14 3874 69G 70D C N 534 536 -77.63 -63.30 15.67 2.10 54.50 151.71 19.69
14 70D 70D N CA 536 537 -33.65 -40.00 40.90
15 3878 73D 74F C N 563 565 57.93 58.10 4.14 0.33 -63.20 145.90 26.33
15 74F 74F N CA 565 566 37.04 32.90 -44.30
16 3880 75A 76P C N 579 581 -81.14 -64.50 22.44 1.47 -58.70 168.74 15.79
16 76P 76P N CA 581 582 162.26 147.20 -30.50
17 3881 76P 77Y C N 586 588 -128.95 -124.30 56.85 3.21 -63.50 138.57 19.32
17 77Y 77Y N CA 588 589 78.75 135.40 -43.40
18 3905 100A 101G C N 789 791 -61.84 -62.40 0.95 0.17 82.20 152.13 11.56
18 101G 101G N CA 791 792 -40.43 -41.20 8.50
19 3909 104L 105G C N 819 821 26.15 78.70 93.17 1.53 82.20 112.60 7.97
19 105G 105G N CA 821 822 -89.16 -166.10 8.50
20 3915 110F 111G C N 870 872 -77.37 -80.20 50.74 1.86 82.20 -163.34 7.47
20 111G 111G N CA 872 873 123.44 174.10 8.50
21 3924 119D 120Y C N 932 934 51.64 55.90 12.79 0.64 -63.50 149.25 28.27
21 120Y 120Y N CA 934 935 51.56 39.50 -43.40
22 3929 124I 125K C N 979 981 -107.18 -118.00 93.87 4.69 -62.90 97.49 15.31
22 125K 125K N CA 981 982 -127.65 139.10 -40.80
23 3930 125K 126R C N 988 990 52.59 57.30 17.81 0.90 -63.00 150.43 27.23
23 126R 126R N CA 990 991 55.18 38.00 -41.10
24 3931 126R 127G C N 999 1001 -132.30 -167.20 36.09 0.53 82.20 -146.02 16.29
24 127G 127G N CA 1001 1002 165.40 174.60 8.50
25 3932 127G 128T C N 1003 1005 -89.77 -78.10 32.60 1.09 -63.20 140.20 19.75
25 128T 128T N CA 1005 1006 -179.76 149.80 -42.10
26 3934 129Y 130D C N 1022 1024 -115.47 -96.50 26.04 1.07 -63.30 146.01 15.68
26 130D 130D N CA 1024 1025 96.37 114.20 -40.00
27 3936 131G 132G C N 1034 1036 111.49 78.70 57.93 0.96 82.20 140.72 8.26
27 132G 132G N CA 1036 1037 146.14 -166.10 8.50
28 3937 132G 133H C N 1038 1040 -108.42 -125.60 73.35 2.44 -63.20 118.74 12.76
28 133H 133H N CA 1040 1041 67.49 138.80 -42.30
29 3938 133H 134V C N 1048 1050 -154.40 -125.40 55.97 1.89 -62.40 156.35 25.28
29 134V 134V N CA 1050 1051 -168.82 143.30 -42.40
30 3940 135E 136L C N 1064 1066 -57.02 -63.50 11.05 1.37 -70.70 168.80 13.32
30 136L 136L N CA 1066 1067 -50.15 -41.20 141.60
31 3941 136L 137V C N 1072 1074 -62.87 -62.40 4.14 0.55 -125.40 -178.69 10.18
31 137V 137V N CA 1074 1075 -46.51 -42.40 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 9 17 87 95 145 132 135 183 194 177
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5_lig.B99990001.pdb 863.17035
ENLYS_BPT5_lig.B99990002.pdb 887.09326
In [32]:
print('ENLYS_BPT5_lig.B99990001.pdb is yellow \nScore - 926.23694')
display(Image('png_3.png', width=600))
print('ENLYS_BPT5_lig.B99990002.pdb is grey \nScore - 955.03845')
display(Image('png_4.png', width=600))
ENLYS_BPT5_lig.B99990001.pdb is yellow Score - 926.23694
ENLYS_BPT5_lig.B99990002.pdb is grey Score - 955.03845
Переместим лиганд в другое место¶
In [33]:
! rm ENLYS_BPT5_lig.rsr
In [34]:
class mymodel(modeller.automodel.automodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
for x,y in [('O:123','CA:114')]:
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_one2.ali', knowns=pdb.code, sequence=s.code)
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()
In [35]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
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: 11184 10208
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1098 1098
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10208 10208
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2685
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 : 1321.1288
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 : 1122 0 0 0.007 0.007 16.864 1.000
2 Bond angle potential : 1512 1 7 2.371 2.371 159.81 1.000
3 Stereochemical cosine torsion poten: 706 0 29 48.788 48.788 260.45 1.000
4 Stereochemical improper torsion pot: 465 0 0 1.407 1.407 18.878 1.000
5 Soft-sphere overlap restraints : 2685 0 0 0.005 0.005 8.5191 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 3 16 0.596 0.596 198.51 1.000
10 Distance restraints 2 (N-O) : 2564 2 20 0.672 0.672 268.45 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: 139 0 4 5.192 5.192 44.187 1.000
14 Sidechain Chi_1 dihedral restraints: 113 0 4 87.107 87.107 60.216 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 0 79.365 79.365 38.172 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 1 86.595 86.595 35.150 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 1 82.081 82.081 14.738 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) : 785 0 0 0.396 0.396 13.070 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: 138 33 18 32.139 81.806 116.57 1.000
26 Distance restraints 4 (SDCH-SDCH) : 111 0 0 0.865 0.865 8.6359 1.000
27 Distance restraints 5 (X-Y) : 1 1 1 1.413 1.413 58.908 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: ENLYS_BPT5_lig.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: 19592.7051
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 2463 123E 124I C N 971 973 139.81 120.00 19.80 4.50 120.00 19.80 4.50
-------------------------------------------------------------------------------------------------
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 3806 1M 2S C N 7 9 -87.05 -72.40 14.66 1.04 -64.10 173.71 14.08
1 2S 2S N CA 9 10 152.81 152.40 -35.00
2 3807 2S 3F C N 13 15 -139.16 -124.20 23.20 0.66 -63.20 172.32 28.82
2 3F 3F N CA 15 16 161.03 143.30 -44.30
3 3808 3F 4K C N 24 26 -143.95 -118.00 26.04 0.95 -62.90 -164.54 30.23
3 4K 4K N CA 26 27 141.34 139.10 -40.80
4 3822 17K 18P C N 134 136 -77.98 -64.50 41.75 3.85 -58.70 139.52 10.04
4 18P 18P N CA 136 137 107.68 147.20 -30.50
5 3823 18P 19E C N 141 143 -53.02 -69.30 65.86 4.44 -63.60 119.45 16.51
5 19E 19E N CA 143 144 78.68 142.50 -40.30
6 3828 23V 24A C N 183 185 52.44 55.40 4.70 0.21 -62.50 141.63 28.71
6 24A 24A N CA 185 186 41.85 38.20 -40.90
7 3843 38V 39Q C N 306 308 -138.22 -121.10 17.16 0.67 -63.80 -166.27 25.32
7 39Q 39Q N CA 308 309 138.57 139.70 -40.30
8 3844 39Q 40G C N 315 317 -50.19 -62.40 15.42 2.90 82.20 138.38 10.44
8 40G 40G N CA 317 318 -31.78 -41.20 8.50
9 3845 40G 41I C N 319 321 158.53 -120.60 140.94 10.80 -63.40 149.95 24.65
9 41I 41I N CA 321 322 14.88 130.30 -43.60
10 3856 51I 52A C N 402 404 83.64 55.40 43.12 2.04 -62.50 153.36 30.92
10 52A 52A N CA 404 405 5.62 38.20 -40.90
11 3866 61P 62S C N 475 477 -78.86 -72.40 14.88 1.09 -64.10 174.62 11.85
11 62S 62S N CA 477 478 139.00 152.40 -35.00
12 3869 64S 65K C N 496 498 -135.74 -62.90 72.90 12.07 -62.90 72.90 12.07
12 65K 65K N CA 498 499 -43.71 -40.80 -40.80
13 3873 68T 69G C N 530 532 -77.97 -62.40 18.41 2.77 82.20 165.06 12.27
13 69G 69G N CA 532 533 -31.37 -41.20 8.50
14 3878 73D 74F C N 563 565 47.64 58.10 26.00 1.34 -63.20 149.95 26.93
14 74F 74F N CA 565 566 56.70 32.90 -44.30
15 3881 76P 77Y C N 586 588 61.70 55.90 12.99 1.34 -63.50 156.87 29.72
15 77Y 77Y N CA 588 589 51.12 39.50 -43.40
16 3905 100A 101G C N 789 791 -60.33 -62.40 5.29 0.90 82.20 149.42 11.29
16 101G 101G N CA 791 792 -36.34 -41.20 8.50
17 3909 104L 105G C N 819 821 -57.93 -62.40 4.91 0.77 82.20 149.37 11.41
17 105G 105G N CA 821 822 -43.23 -41.20 8.50
18 3910 105G 106I C N 823 825 -92.81 -97.30 36.07 3.76 -63.40 138.18 21.71
18 106I 106I N CA 825 826 91.41 127.20 -43.60
19 3911 106I 107K C N 831 833 -55.57 -62.90 66.23 8.23 -118.00 130.22 6.75
19 107K 107K N CA 833 834 -106.62 -40.80 139.10
20 3915 110F 111G C N 870 872 -70.85 -80.20 54.94 1.71 82.20 -170.67 7.15
20 111G 111G N CA 872 873 119.96 174.10 8.50
21 3921 116A 117S C N 914 916 -89.63 -72.40 79.36 4.10 -64.10 98.49 8.89
21 117S 117S N CA 916 917 -130.13 152.40 -35.00
22 3922 117S 118G C N 920 922 54.74 78.70 72.01 1.18 -62.40 130.27 20.35
22 118G 118G N CA 922 923 -98.19 -166.10 -41.20
23 3924 119D 120Y C N 932 934 65.80 55.90 34.07 1.75 -63.50 138.74 25.82
23 120Y 120Y N CA 934 935 6.90 39.50 -43.40
24 3928 123E 124I C N 971 973 -132.41 -120.60 31.76 1.40 -63.40 171.14 30.58
24 124I 124I N CA 973 974 159.79 130.30 -43.60
25 3929 124I 125K C N 979 981 -125.70 -118.00 31.19 1.39 -62.90 162.50 24.86
25 125K 125K N CA 981 982 169.32 139.10 -40.80
26 3930 125K 126R C N 988 990 -179.37 -125.20 108.39 3.83 -63.00 143.76 26.15
26 126R 126R N CA 990 991 -125.52 140.60 -41.10
27 3931 126R 127G C N 999 1001 -76.45 -80.20 21.87 1.05 82.20 -125.37 17.84
27 127G 127G N CA 1001 1002 -164.35 174.10 8.50
28 3932 127G 128T C N 1003 1005 -90.29 -63.20 81.64 12.26 -63.20 81.64 12.26
28 128T 128T N CA 1005 1006 -119.11 -42.10 -42.10
29 3933 128T 129Y C N 1010 1012 -68.80 -98.40 30.16 1.36 -63.50 166.07 26.08
29 129Y 129Y N CA 1012 1013 122.59 128.40 -43.40
30 3934 129Y 130D C N 1022 1024 56.30 54.50 16.61 1.08 -63.30 135.82 23.19
30 130D 130D N CA 1024 1025 24.38 40.90 -40.00
31 3935 130D 131G C N 1030 1032 -65.60 -62.40 3.53 0.55 82.20 155.46 11.78
31 131G 131G N CA 1032 1033 -39.71 -41.20 8.50
32 3937 132G 133H C N 1038 1040 -155.43 -125.60 53.76 1.43 -63.20 162.82 26.22
32 133H 133H N CA 1040 1041 -176.48 138.80 -42.30
33 3941 136L 137V C N 1072 1074 61.93 55.90 23.52 1.25 -125.40 -145.93 11.76
33 137V 137V N CA 1074 1075 16.76 39.50 143.30
-------------------------------------------------------------------------------------------------
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 10208 123E 114W O CA 972 890 4.41 3.00 1.41 14.13 3.00 1.41 14.13
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 13 14 87 96 155 154 162 171 205 210
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1098 1098
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10208 10208
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2629
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 : 1228.2654
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 : 1122 0 0 0.006 0.006 11.723 1.000
2 Bond angle potential : 1512 1 7 2.179 2.179 137.27 1.000
3 Stereochemical cosine torsion poten: 706 0 38 50.301 50.301 270.61 1.000
4 Stereochemical improper torsion pot: 465 0 0 1.216 1.216 14.220 1.000
5 Soft-sphere overlap restraints : 2629 0 0 0.004 0.004 5.0032 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 2405 4 14 0.617 0.617 185.46 1.000
10 Distance restraints 2 (N-O) : 2564 2 28 0.700 0.700 258.41 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: 139 0 3 4.302 4.302 30.333 1.000
14 Sidechain Chi_1 dihedral restraints: 113 0 2 83.909 83.909 45.072 1.000
15 Sidechain Chi_2 dihedral restraints: 90 0 2 71.271 71.271 41.580 1.000
16 Sidechain Chi_3 dihedral restraints: 38 0 0 70.830 70.830 25.986 1.000
17 Sidechain Chi_4 dihedral restraints: 19 0 0 95.297 95.297 15.637 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) : 785 0 0 0.441 0.441 11.819 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: 138 36 21 35.119 84.960 121.80 1.000
26 Distance restraints 4 (SDCH-SDCH) : 111 0 0 1.056 1.056 10.686 1.000
27 Distance restraints 5 (X-Y) : 1 1 1 1.202 1.202 42.647 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: ENLYS_BPT5_lig.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: 18282.7734
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 2463 123E 124I C N 971 973 140.09 120.00 20.09 4.57 120.00 20.09 4.57
-------------------------------------------------------------------------------------------------
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 3806 1M 2S C N 7 9 -70.21 -72.40 15.63 0.85 -64.10 172.03 12.11
1 2S 2S N CA 9 10 136.92 152.40 -35.00
2 3807 2S 3F C N 13 15 -138.15 -124.20 23.28 1.29 -63.20 -175.16 21.46
2 3F 3F N CA 15 16 124.66 143.30 -44.30
3 3808 3F 4K C N 24 26 -134.80 -118.00 25.73 1.31 -62.90 175.79 20.23
3 4K 4K N CA 26 27 119.61 139.10 -40.80
4 3823 18P 19E C N 141 143 65.14 54.60 11.10 1.08 -63.60 151.17 26.01
4 19E 19E N CA 143 144 38.93 42.40 -40.30
5 3828 23V 24A C N 183 185 56.67 55.40 5.42 0.23 -62.50 140.19 28.50
5 24A 24A N CA 185 186 32.93 38.20 -40.90
6 3843 38V 39Q C N 306 308 -141.53 -63.80 99.05 13.27 -63.80 99.05 13.27
6 39Q 39Q N CA 308 309 21.08 -40.30 -40.30
7 3845 40G 41I C N 319 321 38.24 -97.30 143.55 7.94 -63.40 159.97 29.73
7 41I 41I N CA 321 322 79.93 127.20 -43.60
8 3855 50N 51I C N 394 396 -100.74 -120.60 75.54 3.58 -63.40 107.71 16.59
8 51I 51I N CA 396 397 57.42 130.30 -43.60
9 3856 51I 52A C N 402 404 54.68 55.40 10.74 0.71 -62.50 135.67 27.59
9 52A 52A N CA 404 405 27.48 38.20 -40.90
10 3863 58L 59K C N 451 453 -106.82 -62.90 71.69 8.41 -62.90 71.69 8.41
10 59K 59K N CA 453 454 15.86 -40.80 -40.80
11 3866 61P 62S C N 475 477 -83.51 -72.40 14.67 1.18 -64.10 178.88 11.94
11 62S 62S N CA 477 478 142.83 152.40 -35.00
12 3873 68T 69G C N 530 532 -124.16 -62.40 73.11 11.00 82.20 154.00 9.93
12 69G 69G N CA 532 533 -2.08 -41.20 8.50
13 3878 73D 74F C N 563 565 54.57 58.10 14.70 0.89 -63.20 149.11 26.89
13 74F 74F N CA 565 566 47.17 32.90 -44.30
14 3881 76P 77Y C N 586 588 56.76 55.90 11.14 0.84 -63.50 152.64 28.92
14 77Y 77Y N CA 588 589 50.61 39.50 -43.40
15 3905 100A 101G C N 789 791 -68.68 -80.20 11.83 0.69 82.20 -137.94 6.67
15 101G 101G N CA 791 792 171.43 174.10 8.50
16 3906 101G 102K C N 793 795 65.01 56.60 48.79 2.90 -62.90 131.69 22.64
16 102K 102K N CA 795 796 -9.46 38.60 -40.80
17 3909 104L 105G C N 819 821 -59.08 -62.40 3.72 0.70 82.20 149.23 11.34
17 105G 105G N CA 821 822 -39.53 -41.20 8.50
18 3910 105G 106I C N 823 825 -97.37 -97.30 51.49 5.36 -63.40 124.05 19.30
18 106I 106I N CA 825 826 75.71 127.20 -43.60
19 3911 106I 107K C N 831 833 -47.56 -62.90 68.28 8.16 -118.00 133.64 6.91
19 107K 107K N CA 833 834 -107.33 -40.80 139.10
20 3915 110F 111G C N 870 872 -73.12 -80.20 50.61 1.65 82.20 -166.45 7.22
20 111G 111G N CA 872 873 123.99 174.10 8.50
21 3921 116A 117S C N 914 916 -125.74 -136.60 28.44 1.17 -64.10 171.38 10.59
21 117S 117S N CA 916 917 124.91 151.20 -35.00
22 3922 117S 118G C N 920 922 117.97 82.20 47.26 1.61 -62.40 -179.39 31.44
22 118G 118G N CA 922 923 -22.38 8.50 -41.20
23 3924 119D 120Y C N 932 934 54.51 55.90 9.65 0.78 -63.50 138.95 26.27
23 120Y 120Y N CA 934 935 29.95 39.50 -43.40
24 3928 123E 124I C N 971 973 -150.41 -120.60 39.59 1.75 -63.40 -177.84 33.01
24 124I 124I N CA 973 974 156.36 130.30 -43.60
25 3929 124I 125K C N 979 981 -77.94 -118.00 40.07 1.52 -62.90 -179.98 24.23
25 125K 125K N CA 981 982 139.81 139.10 -40.80
26 3930 125K 126R C N 988 990 -113.76 -125.20 13.78 0.73 -63.00 178.02 27.56
26 126R 126R N CA 990 991 148.27 140.60 -41.10
27 3931 126R 127G C N 999 1001 168.23 -167.20 55.66 2.27 82.20 144.54 10.68
27 127G 127G N CA 1001 1002 124.65 174.60 8.50
28 3933 128T 129Y C N 1010 1012 -111.22 -98.40 12.98 0.52 -63.50 176.36 25.73
28 129Y 129Y N CA 1012 1013 126.38 128.40 -43.40
29 3934 129Y 130D C N 1022 1024 55.34 54.50 6.13 0.39 -63.30 140.27 23.91
29 130D 130D N CA 1024 1025 34.83 40.90 -40.00
30 3935 130D 131G C N 1030 1032 -85.49 -80.20 5.76 0.29 82.20 -122.71 7.42
30 131G 131G N CA 1032 1033 176.39 174.10 8.50
31 3936 131G 132G C N 1034 1036 -87.81 -80.20 16.40 0.38 82.20 -112.49 18.88
31 132G 132G N CA 1036 1037 -171.37 174.10 8.50
32 3937 132G 133H C N 1038 1040 -109.30 -125.60 47.62 1.47 -63.20 143.94 15.71
32 133H 133H N CA 1040 1041 94.06 138.80 -42.30
33 3938 133H 134V C N 1048 1050 -117.39 -125.40 75.84 3.96 -62.40 113.14 17.67
33 134V 134V N CA 1050 1051 -141.28 143.30 -42.40
34 3940 135E 136L C N 1064 1066 41.19 -70.70 127.08 12.79 -70.70 127.08 12.79
34 136L 136L N CA 1066 1067 -158.15 141.60 141.60
35 3942 137V 138C C N 1079 1081 -134.20 -63.00 99.32 11.38 -63.00 99.32 11.38
35 138C 138C N CA 1081 1082 28.15 -41.10 -41.10
36 3943 138C 139G C N 1085 1087 62.21 78.70 41.88 0.64 82.20 137.57 7.67
36 139G 139G N CA 1087 1088 -127.60 -166.10 8.50
-------------------------------------------------------------------------------------------------
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 10208 123E 114W O CA 972 890 4.20 3.00 1.20 12.02 3.00 1.20 12.02
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 11 17 103 92 155 151 117 196 216 200
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ENLYS_BPT5_lig.B99990001.pdb 1321.12878
ENLYS_BPT5_lig.B99990002.pdb 1228.26538
In [36]:
print('ENLYS_BPT5_lig.B99990001.pdb is purple')
display(Image('png_5.png', width=600))
print('ENLYS_BPT5_lig.B99990002.pdb is light-green')
display(Image('png_6.png', width=600))
ENLYS_BPT5_lig.B99990001.pdb is purple
ENLYS_BPT5_lig.B99990002.pdb is light-green
Заменим всех аминокислот на Ala¶
In [37]:
alignm = modeller.alignment(env)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
ala_prot = 'A' * 120 + '...'
alignm.append_sequence(ala_prot)
alignm[0].code = 'pdb'
alignm[1].code = 'ala_changed'
In [38]:
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
In [39]:
## Выбираем объект для моделирования
s = alignm[1]
pdb = alignm[0]
print(s.code, pdb.code)
## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns=pdb.code, sequence=s.code)
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ala_changed pdb
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
----------------------------------------------
110 1 110 117 A A 12.552
END OF TABLE
buildc__467W> All coordinates in MODEL have been assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
buildc__467W> All coordinates in MODEL have been assigned.
buildc__468W> Some coordinates in MODEL are still undefined.
invent__526W> Inventing the mainchain model coordinates.
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF
IUPAC atoms : C N
Atom indices : 599 601
Residues : ALA CYS
addprm__440W> Adding params (mean,force,period): 1.3258 300.0000 0
For atoms: C UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF
IUPAC atoms : CB CA
Atom indices : 605 602
Residues : CYS CYS
addprm__440W> Adding params (mean,force,period): 1.5447 300.0000 0
For atoms: UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CC UNDF
IUPAC atoms : C CA
Atom indices : 613 612
Residues : VAL VAL
addprm__440W> Adding params (mean,force,period): 1.5664 300.0000 0
For atoms: CC UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CT1 C UNDF
IUPAC atoms : CA C N
Atom indices : 597 599 601
Residues : ALA ALA CYS
addprm__440W> Adding params (mean,force,period): 121.2296 60.0000 0
For atoms: CT1 C UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF UNDF
IUPAC atoms : C N CA
Atom indices : 599 601 602
Residues : ALA CYS CYS
addprm__440W> Adding params (mean,force,period): 119.8740 60.0000 0
For atoms: C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C O
IUPAC atoms : N C O
Atom indices : 601 599 600
Residues : CYS ALA ALA
addprm__440W> Adding params (mean,force,period): 126.2406 60.0000 0
For atoms: UNDF C O
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF
IUPAC atoms : N CA CB
Atom indices : 601 602 605
Residues : CYS CYS CYS
addprm__440W> Adding params (mean,force,period): 108.4854 60.0000 0
For atoms: UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF CC
IUPAC atoms : N CA C
Atom indices : 611 612 613
Residues : VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 104.5036 60.0000 0
For atoms: UNDF UNDF CC
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF CC OC
IUPAC atoms : CA C O
Atom indices : 612 613 614
Residues : VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 110.1571 60.0000 0
For atoms: UNDF CC OC
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C CT1 CT3
IUPAC atoms : N C CA CB
Atom indices : 601 599 597 598
Residues : CYS ALA ALA ALA
addprm__440W> Adding params (mean,force,period): 131.0444 10.0000 3
For atoms: UNDF C CT1 CT3
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF C CT1 NH1
IUPAC atoms : N C CA N
Atom indices : 601 599 597 596
Residues : CYS ALA ALA ALA
addprm__440W> Adding params (mean,force,period): 7.8145 10.0000 3
For atoms: UNDF C CT1 NH1
generat_607W> Cannot find params in params file:
CHARMM atoms : O C UNDF UNDF
IUPAC atoms : O C N CA
Atom indices : 600 599 601 602
Residues : ALA ALA CYS CYS
addprm__440W> Adding params (mean,force,period): 4.1120 10.0000 3
For atoms: O C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : CT1 C UNDF UNDF
IUPAC atoms : CA C N CA
Atom indices : 597 599 601 602
Residues : ALA ALA CYS CYS
addprm__440W> Adding params (mean,force,period): -174.0557 10.0000 3
For atoms: CT1 C UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF UNDF
IUPAC atoms : SG CB CA N
Atom indices : 606 605 602 601
Residues : CYS CYS CYS CYS
addprm__440W> Adding params (mean,force,period): -64.4538 10.0000 3
For atoms: UNDF UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : C UNDF UNDF UNDF
IUPAC atoms : C N CA CB
Atom indices : 599 601 602 605
Residues : ALA CYS CYS CYS
addprm__440W> Adding params (mean,force,period): 144.4096 10.0000 3
For atoms: C UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF CC
IUPAC atoms : CG1 CB CA C
Atom indices : 616 615 612 613
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): -175.3415 10.0000 3
For atoms: UNDF UNDF UNDF CC
generat_607W> Cannot find params in params file:
CHARMM atoms : OC CC UNDF UNDF
IUPAC atoms : O C CA CB
Atom indices : 614 613 612 615
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): -99.4752 10.0000 3
For atoms: OC CC UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF UNDF UNDF
IUPAC atoms : C CA N O
Atom indices : 603 602 607 604
Residues : CYS CYS GLY CYS
addprm__440W> Adding params (mean,force,period): 1.0526 60.0000 0
For atoms: UNDF UNDF UNDF UNDF
generat_607W> Cannot find params in params file:
CHARMM atoms : UNDF UNDF CC UNDF
IUPAC atoms : CA N C CB
Atom indices : 612 611 613 615
Residues : VAL VAL VAL VAL
addprm__440W> Adding params (mean,force,period): 29.9746 60.0000 0
For atoms: UNDF UNDF CC UNDF
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: 8209 7602
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 618 618
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 7602 7602
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1064
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 : 776.2300
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 : 617 0 0 0.006 0.006 6.7998 1.000
2 Bond angle potential : 862 0 8 2.542 2.542 110.46 1.000
3 Stereochemical cosine torsion poten: 256 1 35 74.191 74.191 261.84 1.000
4 Stereochemical improper torsion pot: 246 4 5 3.190 3.190 52.034 1.000
5 Soft-sphere overlap restraints : 1064 0 0 0.001 0.001 0.22419 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) : 2233 0 6 0.412 0.412 104.21 1.000
10 Distance restraints 2 (N-O) : 2371 0 8 0.447 0.447 139.56 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: 122 0 5 5.033 5.033 36.447 1.000
14 Sidechain Chi_1 dihedral restraints: 2 0 1 106.268 106.268 4.2729 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 708 0 0 0.380 0.380 6.2780 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: 121 19 14 32.124 66.145 50.387 1.000
26 Distance restraints 4 (SDCH-SDCH) : 64 0 0 0.874 0.874 3.7228 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: ala_changed.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: 11218.4834
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 3 : Stereochemical cosine torsion potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1730 122G 123V C N 609 611 105.95 124.45 -18.50 7.14 124.45 -18.50 7.14
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1976 121C 121C C CA 603 602 24.01 1.05 22.96 5.72 1.05 22.96 5.72
2 1977 121C 121C CA N 602 601 24.20 1.05 23.15 5.76 1.05 23.15 5.76
3 1980 123V 123V CB CG2 615 617 23.09 1.05 22.04 5.49 1.05 22.04 5.49
4 1981 123V 123V O CA 614 612 20.02 0.00 20.02 6.31 0.00 20.02 6.31
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1996 15A 16A C N 74 76 81.55 55.40 29.30 2.30 -62.50 158.39 32.17
1 16A 16A N CA 76 77 24.97 38.20 -40.90
2 1998 17A 18A C N 84 86 -51.26 -62.50 11.51 2.30 -134.00 -166.81 11.92
2 18A 18A N CA 86 87 -38.43 -40.90 147.00
3 1999 18A 19A C N 89 91 -143.52 -134.00 99.24 5.83 -62.50 120.45 18.45
3 19A 19A N CA 91 92 48.22 147.00 -40.90
4 2001 20A 21A C N 99 101 63.26 -68.20 142.10 13.56 -62.50 173.72 27.00
4 21A 21A N CA 101 102 -160.75 145.30 -40.90
5 2017 36A 37A C N 179 181 67.87 55.40 15.77 0.99 -62.50 147.70 30.04
5 37A 37A N CA 181 182 28.54 38.20 -40.90
6 2018 37A 38A C N 184 186 59.73 55.40 8.95 0.33 -62.50 141.49 28.77
6 38A 38A N CA 186 187 30.37 38.20 -40.90
7 2029 48A 49A C N 239 241 85.48 55.40 43.01 2.23 -62.50 155.69 31.41
7 49A 49A N CA 241 242 7.47 38.20 -40.90
8 2034 53A 54A C N 264 266 89.02 -134.00 143.03 3.45 -62.50 -159.72 31.48
8 54A 54A N CA 266 267 -171.87 147.00 -40.90
9 2037 56A 57A C N 279 281 60.57 55.40 12.29 1.16 -62.50 152.61 30.92
9 57A 57A N CA 281 282 49.34 38.20 -40.90
10 2047 66A 67A C N 329 331 80.06 55.40 56.00 2.02 -62.50 145.44 28.96
10 67A 67A N CA 331 332 -12.08 38.20 -40.90
11 2051 70A 71A C N 349 351 56.32 55.40 2.21 0.21 -62.50 143.86 29.20
11 71A 71A N CA 351 352 40.21 38.20 -40.90
12 2054 73A 74A C N 364 366 52.71 55.40 15.37 0.72 -62.50 148.84 30.04
12 74A 74A N CA 366 367 53.33 38.20 -40.90
13 2057 76A 77A C N 379 381 61.60 55.40 11.49 1.18 -62.50 152.58 30.93
13 77A 77A N CA 381 382 47.87 38.20 -40.90
14 2084 103A 104A C N 514 516 75.86 -68.20 156.00 14.90 -62.50 179.24 28.35
14 104A 104A N CA 516 517 -154.85 145.30 -40.90
15 2089 108A 109A C N 539 541 -115.68 -134.00 51.09 2.35 -62.50 149.95 22.65
15 109A 109A N CA 541 542 99.31 147.00 -40.90
16 2090 109A 110A C N 544 546 -134.25 -134.00 2.44 0.14 -62.50 -171.30 34.77
16 110A 110A N CA 546 547 144.57 147.00 -40.90
17 2091 110A 111A C N 549 551 -65.14 -68.20 31.26 2.63 -62.50 142.71 23.52
17 111A 111A N CA 551 552 176.42 145.30 -40.90
18 2094 113A 114A C N 564 566 -172.69 -134.00 86.38 3.66 -62.50 145.40 29.29
18 114A 114A N CA 566 567 -135.77 147.00 -40.90
19 2100 119A 120A C N 594 596 67.77 55.40 33.18 1.22 -62.50 138.94 28.12
19 120A 120A N CA 596 597 7.42 38.20 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 1 2 28 36 58 52 78 96 86 65
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 123
Number of all, selected real atoms : 618 618
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 7602 7602
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1065
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 : 746.1177
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 : 617 0 0 0.006 0.006 7.1667 1.000
2 Bond angle potential : 862 0 10 2.507 2.507 108.33 1.000
3 Stereochemical cosine torsion poten: 256 2 36 75.662 75.662 268.35 1.000
4 Stereochemical improper torsion pot: 246 2 4 2.411 2.411 31.979 1.000
5 Soft-sphere overlap restraints : 1065 0 0 0.003 0.003 1.0730 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) : 2233 1 5 0.396 0.396 87.639 1.000
10 Distance restraints 2 (N-O) : 2371 0 9 0.413 0.413 124.43 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: 122 0 4 4.894 4.894 34.463 1.000
14 Sidechain Chi_1 dihedral restraints: 2 0 2 130.827 130.827 10.630 1.000
15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 708 0 0 0.305 0.305 5.4567 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: 121 22 13 34.582 68.740 64.702 1.000
26 Distance restraints 4 (SDCH-SDCH) : 64 0 0 0.564 0.564 1.8971 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: ala_changed.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: 11256.6455
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 3 : Stereochemical cosine torsion potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1723 121C 121C O C 604 603 -137.64 -115.55 -22.09 5.40 -115.55 -22.09 5.40
2 1729 123V 123V CG2 CB 617 615 -24.95 -4.66 -20.30 6.61 -4.66 -20.30 6.61
-------------------------------------------------------------------------------------------------
Feature 4 : Stereochemical improper torsion potentia
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1977 121C 121C CA N 602 601 19.31 1.05 18.26 4.55 1.05 18.26 4.55
2 1981 123V 123V O CA 614 612 19.41 0.00 19.41 6.12 0.00 19.41 6.12
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1996 15A 16A C N 74 76 78.93 55.40 26.94 2.03 -62.50 156.06 31.71
1 16A 16A N CA 76 77 25.09 38.20 -40.90
2 1998 17A 18A C N 84 86 -51.66 -62.50 10.85 2.06 -134.00 -169.70 11.74
2 18A 18A N CA 86 87 -41.44 -40.90 147.00
3 1999 18A 19A C N 89 91 -135.08 -134.00 76.22 4.35 -62.50 133.19 20.00
3 19A 19A N CA 91 92 70.78 147.00 -40.90
4 2001 20A 21A C N 99 101 54.82 55.40 1.11 0.11 -62.50 140.97 28.62
4 21A 21A N CA 101 102 37.25 38.20 -40.90
5 2002 21A 22A C N 104 106 61.81 55.40 8.24 0.51 -62.50 144.63 29.41
5 22A 22A N CA 106 107 33.03 38.20 -40.90
6 2013 32A 33A C N 159 161 -71.74 -68.20 30.37 2.32 -62.50 143.94 24.05
6 33A 33A N CA 161 162 175.46 145.30 -40.90
7 2014 33A 34A C N 164 166 75.74 -62.50 146.81 25.73 -62.50 146.81 25.73
7 34A 34A N CA 166 167 -90.33 -40.90 -40.90
8 2017 36A 37A C N 179 181 65.95 55.40 13.99 0.81 -62.50 146.24 29.74
8 37A 37A N CA 181 182 29.01 38.20 -40.90
9 2018 37A 38A C N 184 186 61.62 55.40 10.55 0.44 -62.50 142.78 29.04
9 38A 38A N CA 186 187 29.68 38.20 -40.90
10 2029 48A 49A C N 239 241 84.18 55.40 42.03 2.12 -62.50 154.48 31.17
10 49A 49A N CA 241 242 7.57 38.20 -40.90
11 2034 53A 54A C N 264 266 90.50 -134.00 141.02 3.43 -62.50 -157.24 31.85
11 54A 54A N CA 266 267 -173.94 147.00 -40.90
12 2037 56A 57A C N 279 281 60.22 55.40 10.79 1.04 -62.50 151.45 30.70
12 57A 57A N CA 281 282 47.85 38.20 -40.90
13 2047 66A 67A C N 329 331 81.67 55.40 58.04 2.11 -62.50 146.74 29.17
13 67A 67A N CA 331 332 -13.55 38.20 -40.90
14 2051 70A 71A C N 349 351 55.00 55.40 9.30 0.53 -62.50 147.04 29.77
14 71A 71A N CA 351 352 47.49 38.20 -40.90
15 2054 73A 74A C N 364 366 53.62 55.40 15.09 0.77 -62.50 149.45 30.18
15 74A 74A N CA 366 367 53.19 38.20 -40.90
16 2057 76A 77A C N 379 381 63.52 55.40 9.82 1.15 -62.50 151.79 30.82
16 77A 77A N CA 381 382 43.73 38.20 -40.90
17 2084 103A 104A C N 514 516 79.11 -134.00 159.46 3.63 -62.50 179.34 28.58
17 104A 104A N CA 516 517 -150.95 147.00 -40.90
18 2090 109A 110A C N 544 546 -60.03 -68.20 8.79 0.63 -62.50 177.06 28.90
18 110A 110A N CA 546 547 142.06 145.30 -40.90
19 2091 110A 111A C N 549 551 -138.97 -134.00 12.91 0.58 -62.50 177.51 33.19
19 111A 111A N CA 551 552 158.91 147.00 -40.90
20 2092 111A 112A C N 554 556 170.27 -134.00 69.19 1.76 -68.20 128.82 9.39
20 112A 112A N CA 556 557 -172.00 147.00 145.30
21 2100 119A 120A C N 594 596 94.34 55.40 156.72 6.57 -62.50 172.87 29.47
21 120A 120A N CA 596 597 -113.60 38.20 -40.90
22 2101 120A 121C C N 599 601 41.68 -63.00 110.08 16.19 -63.00 110.08 16.19
22 121C 121C N CA 601 602 -75.15 -41.10 -41.10
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 1 7 27 38 70 41 75 81 95 70
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ala_changed.B99990001.pdb 776.23004
ala_changed.B99990002.pdb 746.11774
In [40]:
print('ala_changed.B99990001.pdb is pink')
display(Image('png_7.png', width=600))
print('ala_changed.B99990002.pdb is blue')
display(Image('png_8.png', width=600))
ala_changed.B99990001.pdb is pink
ala_changed.B99990002.pdb is blue
In [ ]: