In [7]:
Image('1LMP_1.png', width=1000)
Out[7]:
import sys
import modeller
import _modeller
import modeller.automodel
from IPython.display import Image
В этом практикуме мы будем предсказывать структуру лизоцима, для которого она не известна, используя за образец лизоцим с известной структурой (PDB ID: 1LMP). Поможет нам в этом программа modeller.
env=modeller.environ()
env.io.hetatm=True
MODELLER 10.2, 2021/11/15, r12267
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2021 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux ilya-Aspire-A514-54 5.15.0-71-generic x86_64
Date and time of compilation : 2021/11/15 19:12:27
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/05/13 14:36:18
environ____W> The class 'environ' is deprecated; use 'Environ' instead
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2023-05-12 17:22:17-- http://www.pdb.org/pdb/files/1lmp.pdb Распознаётся www.pdb.org (www.pdb.org)… ^C
Посмотрим на известную структуру.
Image('1LMP_1.png', width=1000)
! wget http://www.uniprot.org/uniprot/LYS_CRAGI.fasta
--2023-04-28 15:30:35-- http://www.uniprot.org/uniprot/LYS_CRAGI.fasta Распознаётся www.uniprot.org (www.uniprot.org)… 193.62.193.81 Подключение к www.uniprot.org (www.uniprot.org)|193.62.193.81|:80... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 301 Moved Permanently Адрес: https://www.uniprot.org/uniprot/LYS_CRAGI.fasta [переход] --2023-04-28 15:30:36-- https://www.uniprot.org/uniprot/LYS_CRAGI.fasta Подключение к www.uniprot.org (www.uniprot.org)|193.62.193.81|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 301 Moved Permanently Адрес: https://rest.uniprot.org/uniprot/LYS_CRAGI.fasta [переход] --2023-04-28 15:30:36-- https://rest.uniprot.org/uniprot/LYS_CRAGI.fasta Распознаётся rest.uniprot.org (rest.uniprot.org)… 193.62.193.81 Подключение к rest.uniprot.org (rest.uniprot.org)|193.62.193.81|:443... соединение установлено. HTTP-запрос отправлен. Ожидание ответа… 301 Moved Permanently Адрес: https://rest.uniprot.org/uniprotkb/LYS_CRAGI.fasta [переход] --2023-04-28 15:30:36-- https://rest.uniprot.org/uniprotkb/LYS_CRAGI.fasta Повторное использование соединения с rest.uniprot.org:443. HTTP-запрос отправлен. Ожидание ответа… 303 See Other Адрес: /uniprotkb/Q6L6Q6.fasta?from=LYS_CRAGI [переход] --2023-04-28 15:30:36-- https://rest.uniprot.org/uniprotkb/Q6L6Q6.fasta?from=LYS_CRAGI Повторное использование соединения с rest.uniprot.org:443. HTTP-запрос отправлен. Ожидание ответа… 200 OK Длина: нет данных [text/plain] Сохранение в: «LYS_CRAGI.fasta» LYS_CRAGI.fasta [ <=> ] 219 --.-KB/s за 0s 2023-04-28 15:30:36 (17,2 MB/s) - «LYS_CRAGI.fasta» сохранён [219]
alignm=modeller.alignment(env)
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead
alignm.append(file='LYS_CRAGI.fasta', align_codes='all',alignment_format='FASTA')
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
model______W> The class 'model' is deprecated; use 'Model' instead
alignm[0].code='CRAGI'
alignm[1].code='1LMP'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
s = alignm[0]
pdb = alignm[1]
print(s.code, pdb.code)
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()
CRAGI 1LMP
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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
patch_s_522_> Number of disulfides patched in MODEL: 1
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: 11121 10178
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1062 1062
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10178 10178
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2321
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 : 979.9681
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 : 1088 0 0 0.006 0.006 9.2946 1.000
2 Bond angle potential : 1471 0 6 2.310 2.310 149.25 1.000
3 Stereochemical cosine torsion poten: 721 0 39 50.845 50.845 275.79 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.267 1.267 15.360 1.000
5 Soft-sphere overlap restraints : 2321 0 0 0.003 0.003 2.5816 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 0.304 0.304 72.916 1.000
10 Distance restraints 2 (N-O) : 2564 1 6 0.496 0.496 193.04 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 4.889 4.889 38.343 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 2 83.894 83.894 41.173 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 3 81.837 81.837 44.835 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 78.263 78.263 17.303 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 85.164 85.164 10.069 1.000
18 Disulfide distance restraints : 1 0 0 0.011 0.011 0.19125E-01 1.000
19 Disulfide angle restraints : 2 0 0 3.378 3.378 0.50398 1.000
20 Disulfide dihedral angle restraints: 1 0 0 8.202 8.202 0.81715E-01 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) : 828 0 0 0.398 0.398 11.626 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 33 26 33.882 87.367 91.291 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.753 0.753 6.4903 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: CRAGI.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: 18025.8809
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 6810 9V 5L N O 63 44 5.51 2.96 2.55 4.62 2.96 2.55 4.62
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3760 4L 5L C N 35 37 -68.52 -70.70 12.72 0.88 -63.50 170.34 23.37
1 5L 5L N CA 37 38 129.07 141.60 -41.20
2 3771 15F 16T C N 114 116 78.41 55.90 22.58 2.45 -63.20 162.58 28.00
2 16T 16T N CA 116 117 37.77 39.50 -42.10
3 3774 18C 19E C N 138 140 67.39 54.60 26.72 1.36 -63.60 143.76 24.63
3 19E 19E N CA 140 141 18.94 42.40 -40.30
4 3776 20A 21T C N 152 154 50.35 55.90 6.44 0.50 -63.20 141.76 24.39
4 21T 21T N CA 154 155 42.77 39.50 -42.10
5 3777 21T 22I C N 159 161 33.70 -97.30 135.72 6.96 -63.40 166.55 30.72
5 22I 22I N CA 161 162 91.72 127.20 -43.60
6 3779 23S 24S C N 173 175 -70.93 -72.40 8.79 0.57 -64.10 164.07 12.31
6 24S 24S N CA 175 176 161.07 152.40 -35.00
7 3784 28R 29C C N 209 211 -63.95 -63.00 6.25 0.83 -117.90 179.90 7.75
7 29C 29C N CA 211 212 -47.27 -41.10 141.10
8 3786 30I 31C C N 223 225 -62.35 -63.00 0.95 0.11 -117.90 -174.39 7.99
8 31C 31C N CA 225 226 -41.79 -41.10 141.10
9 3790 34E 35S C N 253 255 -101.06 -72.40 72.71 5.24 -64.10 126.12 7.78
9 35S 35S N CA 255 256 85.58 152.40 -35.00
10 3791 35S 36G C N 259 261 124.57 82.20 55.77 1.91 -62.40 173.55 30.43
10 36G 36G N CA 261 262 -27.76 8.50 -41.20
11 3792 36G 37C C N 263 265 63.22 57.40 17.89 0.59 -117.90 -143.46 9.29
11 37C 37C N CA 265 266 19.08 36.00 141.10
12 3800 44Y 45D C N 327 329 -83.30 -70.90 13.86 0.77 -63.30 164.73 21.59
12 45D 45D N CA 329 330 156.49 150.30 -40.00
13 3804 48S 49Y C N 360 362 79.84 55.90 36.25 2.02 -63.50 153.78 28.62
13 49Y 49Y N CA 362 363 12.28 39.50 -43.40
14 3818 62E 63D C N 489 491 -130.40 -63.30 82.56 10.03 -63.30 82.56 10.03
14 63D 63D N CA 491 492 8.09 -40.00 -40.00
15 3821 65G 66K C N 507 509 -120.84 -118.00 30.26 1.43 -62.90 160.78 24.34
15 66K 66K N CA 509 510 169.23 139.10 -40.80
16 3823 67P 68G C N 523 525 118.49 82.20 46.46 1.66 -62.40 -179.70 31.30
16 68G 68G N CA 525 526 -20.50 8.50 -41.20
17 3825 69T 70S C N 534 536 -52.61 -64.10 55.28 3.49 -72.40 120.16 7.76
17 70S 70S N CA 536 537 -89.08 -35.00 152.40
18 3837 81A 82S C N 622 624 155.52 -136.60 70.65 2.34 -64.10 -151.49 25.19
18 82S 82S N CA 624 625 170.82 151.20 -35.00
19 3838 82S 83N C N 628 630 -130.56 -119.90 18.35 0.57 -63.20 -179.95 26.33
19 83N 83N N CA 630 631 151.93 137.00 -41.10
20 3842 86R 87A C N 660 662 -79.80 -68.20 21.96 2.11 -62.50 168.44 26.81
20 87A 87A N CA 662 663 126.65 145.30 -40.90
21 3843 87A 88Y C N 665 667 -104.64 -98.40 52.05 5.47 -63.50 126.97 18.26
21 88Y 88Y N CA 667 668 76.72 128.40 -43.40
22 3844 88Y 89M C N 677 679 -86.60 -73.00 43.28 3.17 -63.40 144.29 19.85
22 89M 89M N CA 679 680 101.91 143.00 -40.50
23 3845 89M 90K C N 685 687 -144.59 -118.00 26.89 1.09 -62.90 -166.08 22.30
23 90K 90K N CA 687 688 135.07 139.10 -40.80
24 3848 92Y 93I C N 717 719 -61.90 -63.40 7.56 1.19 -120.60 -171.92 12.94
24 93I 93I N CA 719 720 -51.01 -43.60 130.30
25 3863 107R 108I C N 820 822 -91.86 -120.60 63.64 2.69 -63.40 120.53 18.87
25 108I 108I N CA 822 823 73.52 130.30 -43.60
26 3865 109H 110N C N 838 840 -72.58 -119.90 50.09 1.67 -63.20 161.94 19.75
26 110N 110N N CA 840 841 120.57 137.00 -41.10
27 3866 110N 111G C N 846 848 117.38 82.20 51.43 1.56 -62.40 -179.81 32.66
27 111G 111G N CA 848 849 -29.01 8.50 -41.20
28 3870 114R 115G C N 872 874 -56.76 -62.40 7.46 1.39 82.20 146.01 11.06
28 115G 115G N CA 874 875 -36.31 -41.20 8.50
29 3882 126E 127K C N 977 979 -66.19 -62.90 3.51 0.61 -118.00 -173.78 9.55
29 127K 127K N CA 979 980 -42.03 -40.80 139.10
30 3883 127K 128V C N 986 988 23.15 -62.40 126.32 20.95 -62.40 126.32 20.95
30 128V 128V N CA 988 989 50.55 -42.40 -42.40
31 3887 131Q 132G C N 1021 1023 -72.58 -62.40 13.55 1.94 82.20 160.06 11.95
31 132G 132G N CA 1023 1024 -32.25 -41.20 8.50
32 3890 134N 135V C N 1039 1041 -133.60 -125.40 38.48 2.09 -62.40 164.33 18.02
32 135V 135V N CA 1041 1042 105.70 143.30 -42.40
33 3891 135V 136N C N 1046 1048 -82.78 -71.20 55.09 3.85 55.90 147.22 13.55
33 136N 136N N CA 1048 1049 88.94 142.80 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 11 46 99 117 120 162 169 175 170
<< 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.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 137
Number of all, selected real atoms : 1062 1062
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 10178 10178
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2339
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 : 869.4388
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 : 1088 0 0 0.005 0.005 6.7925 1.000
2 Bond angle potential : 1471 0 4 2.099 2.099 125.11 1.000
3 Stereochemical cosine torsion poten: 721 0 39 49.671 49.671 261.00 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.083 1.083 11.381 1.000
5 Soft-sphere overlap restraints : 2339 0 0 0.004 0.004 4.2117 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 0.277 0.277 65.717 1.000
10 Distance restraints 2 (N-O) : 2564 0 5 0.424 0.424 142.81 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 0 2 4.876 4.876 38.135 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 1 80.761 80.761 35.655 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 0 85.495 85.495 37.726 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 1 73.780 73.780 20.650 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 103.741 103.741 11.414 1.000
18 Disulfide distance restraints : 1 0 0 0.011 0.011 0.19141E-01 1.000
19 Disulfide angle restraints : 2 0 0 4.309 4.309 0.82007 1.000
20 Disulfide dihedral angle restraints: 1 0 0 16.140 16.140 0.30269 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) : 828 0 0 0.382 0.382 9.9724 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: 135 34 18 34.167 84.838 93.740 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.568 0.568 3.9837 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: CRAGI.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: 17196.8750
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 3761 5L 6G C N 43 45 -66.69 -62.40 4.66 0.74 82.20 156.39 11.84
1 6G 6G N CA 45 46 -39.36 -41.20 8.50
2 3769 13T 14V C N 96 98 -71.44 -73.50 19.84 1.72 -62.40 158.92 20.65
2 14V 14V N CA 98 99 158.94 139.20 -42.40
3 3770 14V 15F C N 103 105 73.23 58.10 27.08 1.45 -63.20 147.00 26.10
3 15F 15F N CA 105 106 10.44 32.90 -44.30
4 3771 15F 16T C N 114 116 47.23 55.90 13.89 0.74 -63.20 144.02 24.68
4 16T 16T N CA 116 117 50.35 39.50 -42.10
5 3774 18C 19E C N 138 140 68.62 54.60 25.91 1.33 -63.60 145.57 24.96
5 19E 19E N CA 140 141 20.61 42.40 -40.30
6 3776 20A 21T C N 152 154 45.34 55.90 13.52 0.91 -63.20 141.02 24.18
6 21T 21T N CA 154 155 47.94 39.50 -42.10
7 3777 21T 22I C N 159 161 37.58 -97.30 139.38 7.07 -63.40 169.12 31.26
7 22I 22I N CA 161 162 92.07 127.20 -43.60
8 3779 23S 24S C N 173 175 -71.05 -72.40 9.66 0.62 -64.10 163.18 12.25
8 24S 24S N CA 175 176 161.97 152.40 -35.00
9 3784 28R 29C C N 209 211 -64.82 -63.00 4.35 0.67 -117.90 -178.23 7.81
9 29C 29C N CA 211 212 -45.05 -41.10 141.10
10 3791 35S 36G C N 259 261 177.00 82.20 96.26 5.77 -62.40 125.02 20.76
10 36G 36G N CA 261 262 -8.25 8.50 -41.20
11 3792 36G 37C C N 263 265 64.62 57.40 13.68 0.51 -117.90 -147.58 9.08
11 37C 37C N CA 265 266 24.39 36.00 141.10
12 3800 44Y 45D C N 327 329 -100.17 -96.50 25.22 1.06 -63.30 -177.09 20.61
12 45D 45D N CA 329 330 139.16 114.20 -40.00
13 3804 48S 49Y C N 360 362 78.04 55.90 33.93 1.87 -63.50 152.66 28.46
13 49Y 49Y N CA 362 363 13.79 39.50 -43.40
14 3818 62E 63D C N 489 491 -136.11 -63.30 87.61 10.81 -63.30 87.61 10.81
14 63D 63D N CA 491 492 8.73 -40.00 -40.00
15 3821 65G 66K C N 507 509 -121.56 -118.00 20.21 0.93 -62.90 170.61 25.66
15 66K 66K N CA 509 510 159.00 139.10 -40.80
16 3822 66K 67P C N 516 518 -76.14 -58.70 23.87 1.74 -64.50 161.83 12.70
16 67P 67P N CA 518 519 -14.21 -30.50 147.20
17 3826 70S 71F C N 540 542 -7.03 -71.40 79.30 4.47 -63.20 149.63 24.46
17 71F 71F N CA 542 543 94.38 140.70 -44.30
18 3828 72K 73A C N 560 562 -121.79 -134.00 46.49 2.30 -62.50 154.84 23.32
18 73A 73A N CA 562 563 102.15 147.00 -40.90
19 3831 75A 76N C N 576 578 -98.29 -119.90 58.58 2.12 -63.20 128.53 14.42
19 76N 76N N CA 578 579 82.55 137.00 -41.10
20 3832 76N 77D C N 584 586 -49.09 -96.50 51.66 2.13 54.50 116.26 9.95
20 77D 77D N CA 586 587 93.68 114.20 40.90
21 3837 81A 82S C N 622 624 127.67 -136.60 99.61 3.31 -64.10 -137.08 28.09
21 82S 82S N CA 624 625 178.73 151.20 -35.00
22 3838 82S 83N C N 628 630 -101.70 -119.90 43.59 1.52 -63.20 143.74 16.16
22 83N 83N N CA 630 631 97.39 137.00 -41.10
23 3839 83N 84C C N 636 638 -62.80 -63.00 2.13 0.27 -117.90 -171.83 8.09
23 84C 84C N CA 638 639 -38.97 -41.10 141.10
24 3840 84C 85V C N 642 644 -61.08 -62.40 1.88 0.22 -125.40 -175.47 10.37
24 85V 85V N CA 644 645 -43.74 -42.40 143.30
25 3841 85V 86R C N 649 651 -103.28 -125.20 43.25 2.39 -63.00 146.66 22.60
25 86R 86R N CA 651 652 177.88 140.60 -41.10
26 3843 87A 88Y C N 665 667 -51.10 -98.40 47.60 1.85 -63.50 177.61 28.82
26 88Y 88Y N CA 667 668 133.77 128.40 -43.40
27 3844 88Y 89M C N 677 679 -146.02 -125.60 24.73 0.73 -63.40 -175.44 34.03
27 89M 89M N CA 679 680 154.46 140.50 -40.50
28 3845 89M 90K C N 685 687 -132.97 -118.00 97.22 4.50 -62.90 109.41 18.29
28 90K 90K N CA 687 688 -124.84 139.10 -40.80
29 3849 93I 94G C N 725 727 -59.58 -62.40 2.99 0.56 82.20 149.92 11.40
29 94G 94G N CA 727 728 -40.22 -41.20 8.50
30 3869 113P 114R C N 861 863 -66.89 -72.10 50.96 4.03 -63.00 126.37 17.33
30 114R 114R N CA 863 864 -167.41 141.90 -41.10
31 3883 127K 128V C N 986 988 -116.70 -125.40 90.23 4.26 -62.40 110.20 12.06
31 128V 128V N CA 988 989 53.49 143.30 -42.40
32 3887 131Q 132G C N 1021 1023 -69.28 -62.40 10.98 1.51 82.20 156.97 11.74
32 132G 132G N CA 1023 1024 -32.64 -41.20 8.50
33 3890 134N 135V C N 1039 1041 -131.97 -125.40 29.90 1.62 -62.40 171.30 18.84
33 135V 135V N CA 1041 1042 114.14 143.30 -42.40
34 3891 135V 136N C N 1046 1048 -66.02 -71.20 31.93 1.91 55.90 141.48 11.04
34 136N 136N N CA 1048 1049 111.29 142.80 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 14 16 78 84 110 97 136 164 184 184
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
CRAGI.B99990001.pdb 979.96808
CRAGI.B99990002.pdb 869.43884
Посмотрим на результат моделирования.
Image('CRAGI.png', width=1000)
Чтобы сравнить структуры выровняем их последовательности с помощью команды align в PyMOL.
Image('modeller_alignment.png', width=1000)
Хотя элементы вторичной структуры похожи, их взаимное расположение заметно изменилось.
Теперь добавим в выравнивание три остатка лиганда, чтобы и в предсказанной структуре он появился.
alignm=modeller.alignment(env)
alignm.append(file='LYS_CRAGI.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'B'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code='CRAGI'
alignm[1].code='1LMP'
alignm.salign()
alignm.write(file='all_in_one_lig.ali', alignment_format='PIR')
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
alignment__W> The class 'alignment' is deprecated; use 'Alignment' instead
model______W> The class 'model' is deprecated; use 'Model' instead
read_pd_459W> Residue type NDG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type NAG not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
SALIGN_____> adding the next group to the alignment; iteration 1
print(s.code, pdb.code)
a = modeller.automodel.automodel(env, alnfile='all_in_one_lig.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
CRAGI 1LMP
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
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
read_to_681_> topology.submodel read from topology file: 3
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 1
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 12522 11579
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_484W> Dihedral still outside +-90: -90.5012
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 : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11579 11579
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2616
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 : 1084.4626
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 : 1088 0 0 0.006 0.006 10.167 1.000
2 Bond angle potential : 1471 0 6 2.264 2.264 146.94 1.000
3 Stereochemical cosine torsion poten: 721 0 33 49.050 49.050 256.51 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.224 1.224 14.986 1.000
5 Soft-sphere overlap restraints : 2616 2 2 0.008 0.008 21.198 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 0.275 0.275 61.938 1.000
10 Distance restraints 2 (N-O) : 2564 1 11 0.495 0.495 203.53 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 6 5.653 5.653 51.255 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 1 85.553 85.553 39.953 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 0 87.254 87.254 40.676 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 74.243 74.243 19.894 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 98.408 98.408 9.7455 1.000
18 Disulfide distance restraints : 1 0 0 0.008 0.008 0.10482E-01 1.000
19 Disulfide angle restraints : 2 0 0 4.231 4.231 0.79056 1.000
20 Disulfide dihedral angle restraints: 1 0 0 15.619 15.619 0.28455 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) : 828 0 0 0.479 0.479 24.823 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 33 27 37.277 85.661 155.49 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.872 0.872 11.117 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.034 0.034 15.150 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: CRAGI.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: 18570.0000
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 6810 9V 5L N O 63 44 5.39 2.96 2.43 4.59 2.96 2.43 4.59
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3760 4L 5L C N 35 37 -62.98 -70.70 8.01 0.65 -63.50 179.36 24.87
1 5L 5L N CA 37 38 139.44 141.60 -41.20
2 3770 14V 15F C N 103 105 -95.74 -71.40 54.64 4.84 -63.20 139.92 17.38
2 15F 15F N CA 105 106 91.78 140.70 -44.30
3 3771 15F 16T C N 114 116 -31.55 -78.10 88.69 2.91 -63.20 120.63 17.58
3 16T 16T N CA 116 117 74.31 149.80 -42.10
4 3774 18C 19E C N 138 140 67.94 54.60 27.09 1.38 -63.60 144.22 24.71
4 19E 19E N CA 140 141 18.83 42.40 -40.30
5 3776 20A 21T C N 152 154 69.41 55.90 61.47 3.39 -63.20 134.36 22.02
5 21T 21T N CA 154 155 -20.46 39.50 -42.10
6 3777 21T 22I C N 159 161 154.85 -63.40 141.91 25.13 -63.40 141.91 25.13
6 22I 22I N CA 161 162 -36.90 -43.60 -43.60
7 3779 23S 24S C N 173 175 -79.43 -72.40 18.11 0.86 -64.10 156.66 12.33
7 24S 24S N CA 175 176 169.09 152.40 -35.00
8 3784 28R 29C C N 209 211 -62.84 -63.00 6.74 0.81 -117.90 179.70 7.75
8 29C 29C N CA 211 212 -47.83 -41.10 141.10
9 3786 30I 31C C N 223 225 -61.78 -63.00 1.71 0.30 -117.90 -172.41 8.08
9 31C 31C N CA 225 226 -39.89 -41.10 141.10
10 3792 36G 37C C N 263 265 67.52 57.40 15.30 0.78 -117.90 -150.08 8.98
10 37C 37C N CA 265 266 24.53 36.00 141.10
11 3800 44Y 45D C N 327 329 -85.95 -70.90 16.35 0.96 -63.30 164.88 21.78
11 45D 45D N CA 329 330 156.69 150.30 -40.00
12 3804 48S 49Y C N 360 362 79.55 55.90 34.92 1.99 -63.50 154.07 28.71
12 49Y 49Y N CA 362 363 13.81 39.50 -43.40
13 3821 65G 66K C N 507 509 -117.56 -118.00 22.08 1.08 -62.90 167.21 24.97
13 66K 66K N CA 509 510 161.18 139.10 -40.80
14 3823 67P 68G C N 523 525 117.67 82.20 40.33 1.79 -62.40 -177.50 31.22
14 68G 68G N CA 525 526 -10.70 8.50 -41.20
15 3825 69T 70S C N 534 536 -53.75 -64.10 50.30 3.18 -72.40 124.77 7.99
15 70S 70S N CA 536 537 -84.23 -35.00 152.40
16 3837 81A 82S C N 622 624 -178.74 -136.60 52.21 1.60 -64.10 -176.73 21.54
16 82S 82S N CA 624 625 -177.99 151.20 -35.00
17 3838 82S 83N C N 628 630 -120.38 -119.90 41.00 1.85 -63.20 152.06 22.26
17 83N 83N N CA 630 631 178.00 137.00 -41.10
18 3842 86R 87A C N 660 662 -59.91 -68.20 10.96 1.08 -62.50 166.65 27.19
18 87A 87A N CA 662 663 152.47 145.30 -40.90
19 3843 87A 88Y C N 665 667 -55.91 -98.40 45.57 2.25 -63.50 171.90 26.89
19 88Y 88Y N CA 667 668 144.87 128.40 -43.40
20 3844 88Y 89M C N 677 679 -112.89 -125.60 85.99 4.35 -63.40 106.19 19.71
20 89M 89M N CA 679 680 -134.45 140.50 -40.50
21 3845 89M 90K C N 685 687 -93.27 -62.90 72.46 11.23 -62.90 72.46 11.23
21 90K 90K N CA 687 688 -106.59 -40.80 -40.80
22 3848 92Y 93I C N 717 719 -55.15 -63.40 12.26 1.88 -120.60 -171.26 13.21
22 93I 93I N CA 719 720 -52.67 -43.60 130.30
23 3850 94G 95S C N 729 731 -60.68 -64.10 41.56 2.83 -72.40 131.70 8.15
23 95S 95S N CA 731 732 -76.42 -35.00 152.40
24 3851 95S 96S C N 735 737 160.76 -64.10 140.50 18.78 -64.10 140.50 18.78
24 96S 96S N CA 737 738 -73.43 -35.00 -35.00
25 3852 96S 97G C N 741 743 24.73 78.70 87.85 1.59 -62.40 103.35 15.53
25 97G 97G N CA 743 744 -96.79 -166.10 -41.20
26 3863 107R 108I C N 820 822 -89.98 -120.60 74.02 3.19 -63.40 109.78 17.17
26 108I 108I N CA 822 823 62.91 130.30 -43.60
27 3865 109H 110N C N 838 840 -64.26 -119.90 55.95 2.17 -63.20 172.21 21.47
27 110N 110N N CA 840 841 131.11 137.00 -41.10
28 3866 110N 111G C N 846 848 126.98 82.20 63.55 1.98 -62.40 170.68 30.30
28 111G 111G N CA 848 849 -36.60 8.50 -41.20
29 3882 126E 127K C N 977 979 -65.12 -62.90 2.91 0.50 -118.00 -174.10 9.54
29 127K 127K N CA 979 980 -42.67 -40.80 139.10
30 3883 127K 128V C N 986 988 31.23 -62.40 126.52 21.29 -62.40 126.52 21.29
30 128V 128V N CA 988 989 42.70 -42.40 -42.40
31 3887 131Q 132G C N 1021 1023 -72.77 -62.40 13.28 1.93 82.20 160.41 11.98
31 132G 132G N CA 1023 1024 -32.90 -41.20 8.50
32 3890 134N 135V C N 1039 1041 -124.60 -125.40 40.55 2.00 -62.40 157.93 17.40
32 135V 135V N CA 1041 1042 102.76 143.30 -42.40
33 3891 135V 136N C N 1046 1048 -65.17 -71.20 31.00 1.83 55.90 141.32 10.93
33 136N 136N N CA 1048 1049 112.39 142.80 39.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 12 21 93 122 131 142 142 175 179 210
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 140
Number of all, selected real atoms : 1105 1105
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11579 11579
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2554
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 : 988.6167
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 : 1088 0 0 0.006 0.006 12.493 1.000
2 Bond angle potential : 1471 0 9 2.372 2.372 159.61 1.000
3 Stereochemical cosine torsion poten: 721 0 30 48.598 48.598 251.17 1.000
4 Stereochemical improper torsion pot: 472 0 0 1.234 1.234 15.327 1.000
5 Soft-sphere overlap restraints : 2554 1 2 0.008 0.008 19.387 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 0.249 0.249 57.618 1.000
10 Distance restraints 2 (N-O) : 2564 0 15 0.471 0.471 201.97 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 136 1 5 5.483 5.483 48.219 1.000
14 Sidechain Chi_1 dihedral restraints: 116 0 1 84.969 84.969 48.482 1.000
15 Sidechain Chi_2 dihedral restraints: 75 0 1 70.392 70.392 33.004 1.000
16 Sidechain Chi_3 dihedral restraints: 31 0 0 67.371 67.371 17.495 1.000
17 Sidechain Chi_4 dihedral restraints: 14 0 0 63.662 63.662 10.556 1.000
18 Disulfide distance restraints : 1 0 0 0.006 0.006 0.66270E-02 1.000
19 Disulfide angle restraints : 2 0 0 1.574 1.574 0.10939 1.000
20 Disulfide dihedral angle restraints: 1 0 0 34.475 34.475 1.1090 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) : 828 0 0 0.403 0.403 15.609 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 25 19 31.378 77.054 71.989 1.000
26 Distance restraints 4 (SDCH-SDCH) : 118 0 0 0.735 0.735 6.5285 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.038 0.038 17.935 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: CRAGI.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: 17013.8594
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 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 3927 36G 36G CA C 262 263 -156.59 -180.00 23.41 4.68 -180.00 23.41 4.68
-------------------------------------------------------------------------------------------------
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 3761 5L 6G C N 43 45 -68.68 -62.40 7.93 1.16 82.20 157.40 11.85
1 6G 6G N CA 45 46 -36.35 -41.20 8.50
2 3769 13T 14V C N 96 98 -74.72 -73.50 24.51 2.08 -62.40 154.41 20.27
2 14V 14V N CA 98 99 163.68 139.20 -42.40
3 3770 14V 15F C N 103 105 73.23 58.10 25.83 1.43 -63.20 147.58 26.24
3 15F 15F N CA 105 106 11.97 32.90 -44.30
4 3771 15F 16T C N 114 116 50.99 55.90 6.78 0.42 -63.20 143.11 24.61
4 16T 16T N CA 116 117 44.18 39.50 -42.10
5 3774 18C 19E C N 138 140 60.52 54.60 13.99 0.72 -63.60 142.51 24.52
5 19E 19E N CA 140 141 29.73 42.40 -40.30
6 3775 19E 20A C N 147 149 -60.63 -62.50 17.86 2.84 -68.20 156.22 12.87
6 20A 20A N CA 149 150 -58.66 -40.90 145.30
7 3776 20A 21T C N 152 154 -88.16 -63.20 77.75 11.63 -63.20 77.75 11.63
7 21T 21T N CA 154 155 -115.73 -42.10 -42.10
8 3779 23S 24S C N 173 175 -78.44 -72.40 13.81 0.64 -64.10 160.82 12.56
8 24S 24S N CA 175 176 164.82 152.40 -35.00
9 3784 28R 29C C N 209 211 -65.15 -63.00 3.68 0.61 -117.90 -177.40 7.84
9 29C 29C N CA 211 212 -44.09 -41.10 141.10
10 3793 37C 38R C N 269 271 -97.39 -63.00 88.15 10.13 57.30 154.70 17.90
10 38R 38R N CA 271 272 40.07 -41.10 38.00
11 3800 44Y 45D C N 327 329 -77.85 -70.90 6.99 0.55 -63.30 171.05 22.02
11 45D 45D N CA 329 330 149.57 150.30 -40.00
12 3804 48S 49Y C N 360 362 79.44 55.90 36.27 1.99 -63.50 153.27 28.52
12 49Y 49Y N CA 362 363 11.91 39.50 -43.40
13 3821 65G 66K C N 507 509 -110.08 -118.00 9.43 0.45 -62.90 -178.77 26.33
13 66K 66K N CA 509 510 144.22 139.10 -40.80
14 3823 67P 68G C N 523 525 124.82 82.20 50.10 2.08 -62.40 174.35 30.11
14 68G 68G N CA 525 526 -17.84 8.50 -41.20
15 3826 70S 71F C N 540 542 53.98 58.10 7.68 0.40 -63.20 143.99 25.98
15 71F 71F N CA 542 543 39.38 32.90 -44.30
16 3828 72K 73A C N 560 562 -129.91 -134.00 65.03 3.60 -62.50 140.25 21.01
16 73A 73A N CA 562 563 82.09 147.00 -40.90
17 3837 81A 82S C N 622 624 -151.87 -136.60 17.32 0.53 -64.10 -172.55 19.89
17 82S 82S N CA 624 625 159.37 151.20 -35.00
18 3838 82S 83N C N 628 630 -115.28 -119.90 13.17 0.69 -63.20 177.39 25.14
18 83N 83N N CA 630 631 149.33 137.00 -41.10
19 3839 83N 84C C N 636 638 -68.42 -63.00 5.41 0.91 -117.90 -175.52 7.89
19 84C 84C N CA 638 639 -41.17 -41.10 141.10
20 3841 85V 86R C N 649 651 62.37 57.30 17.33 1.53 -63.00 157.70 28.65
20 86R 86R N CA 651 652 54.57 38.00 -41.10
21 3844 88Y 89M C N 677 679 -151.32 -125.60 32.33 0.96 -63.40 -177.94 34.01
21 89M 89M N CA 679 680 160.08 140.50 -40.50
22 3845 89M 90K C N 685 687 -143.18 -118.00 51.81 2.07 -62.90 156.90 25.16
22 90K 90K N CA 687 688 -175.61 139.10 -40.80
23 3849 93I 94G C N 725 727 -60.31 -62.40 3.07 0.56 82.20 150.21 11.40
23 94G 94G N CA 727 728 -38.96 -41.20 8.50
24 3883 127K 128V C N 986 988 -112.06 -125.40 94.35 4.34 -62.40 104.81 11.47
24 128V 128V N CA 988 989 49.90 143.30 -42.40
25 3887 131Q 132G C N 1021 1023 -72.50 -62.40 14.16 2.00 82.20 159.73 11.90
25 132G 132G N CA 1023 1024 -31.27 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 8 16 79 117 114 126 174 209 170 173
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
CRAGI.B99990001.pdb 1084.46265
CRAGI.B99990002.pdb 988.61670
Посмотрим на то, что получилось.
Image('modeller.png', width=1000)
А что с лигандом, я не знаю(((