Гомологичное моделирование комплекса белка с лигандом

In [2]:
from IPython.display import Image

def pdb2img(file_name1, file_name2):
    command = ''
    command += f'load {file_name1}, xxx; load {file_name2}, yyy; align xxx, yyy;'
    command += 'as cartoon; as sticks, hetatm; orient; move z, 20;'
    command += 'set ray_trace_mode, 3; set antialias, 3;'
    command += f'ray {1920//2}, {1080//2}; png tmp.png'
    ! pymol -Q -c -d "$command"
    display(Image('tmp.png'))

1. Загрузим модуль

In [3]:
import sys 
import modeller 
import _modeller
import modeller.automodel

2. Зададим некоторые параметры

In [4]:
env=modeller.environ()
env.io.hetatm = True
                         MODELLER 9.18, 2017/02/17, r11002

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2017 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 srv 4.15.0-46-generic x86_64
Date and time of compilation         : 2017/02/17 14:47:45
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2019/04/15 00:33:50

3. Скачаем белок заготовку и последовательность

In [4]:
! wget -q http://www.pdb.org/pdb/files/1lmp.pdb
! wget -q http://www.uniprot.org/uniprot/Q7SID7.fasta

LYS_ANTMY.

4. Создадим объект выравнивание

In [5]:
alignm = modeller.alignment(env)
In [6]:
alignm.append(file='Q7SID7.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')
alignm[0].code = 'seq'
alignm[1].code = 'pdb'
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.
rdpdb___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.

5. Делаем выравнивание и сохраняем

In [7]:
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1

6. Смотрим на содержимое all_in_one.ali

In [8]:
! cat all_in_one.ali
>P1;seq
sequence::     : :     : :::-1.00:-1.00
KRFTRCGLVNELRKQGFD---ENLMRDWVCLVENESARYTDKIANVNKNGSRDYGLFQINDKYWCSKGSTPGKD-
-CNVTCSQLLTDDITVASTCAKKI-YKRTKFDAWSGWDNHCNHSNPDISSC-------*

>P1;pdb
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESS-YNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKN
VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*

7. Построим модель

In [ ]:

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()
seq pdb
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
----------------------------------------------
     18     1   18    22      D     E    8.206
     74     1   73    76      D     C    8.895
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:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
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:    10915    10078


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      120
Number of all, selected real atoms                :      961     961
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    10078   10078
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2077
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                                    :        1050.9645





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              :     980       0      4   0.010   0.010      28.161       1.000
 2 Bond angle potential               :    1322       1      8   2.306   2.306      142.37       1.000
 3 Stereochemical cosine torsion poten:     631       0     24  46.949  46.949      218.93       1.000
 4 Stereochemical improper torsion pot:     405       0      0   1.305   1.305      15.989       1.000
 5 Soft-sphere overlap restraints     :    2077       0      0   0.003   0.003      2.7686       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)      :    2136       0      6   0.415   0.415      138.01       1.000
10 Distance restraints 2 (N-O)        :    2283       1     16   0.472   0.472      230.70       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:     119       0      3   4.818   4.818      32.575       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      1  66.719  66.719      27.497       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      0  62.952  62.952      29.343       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  66.422  66.422      17.049       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  99.861  99.861      13.954       1.000
18 Disulfide distance restraints      :       3       0      0   0.027   0.027     0.38465       1.000
19 Disulfide angle restraints         :       6       0      0   2.505   2.505     0.83154       1.000
20 Disulfide dihedral angle restraints:       3       0      0  26.676  26.676      2.0265       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)  :    1319       0      0   0.427   0.427      29.638       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:     118      11     21  29.517  49.402      88.651       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     523       0      0   0.801   0.801      32.096       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: seq.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:   12907.9912



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   1769  71D  71D N   CA    573  574  127.43  107.00   20.43    5.87  107.00   20.43    5.87

-------------------------------------------------------------------------------------------------

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   8058 108N 104S N   O     864  837    5.48    2.99    2.49    5.89    2.99    2.49    5.89

-------------------------------------------------------------------------------------------------

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   3383  33S  34A C   N     276  278   74.25   55.40   83.65    3.62  -62.50  136.77   26.19
    1         34A  34A N   CA    278  279  -43.30   38.20                  -40.90
    2   3420  70K  71D C   N     571  573 -142.29  -63.30   87.13   14.86  -63.30   87.13   14.86
    2         71D  71D N   CA    573  574  -76.78  -40.00                  -40.00
    3   3444  94I  95Y C   N     744  746  -41.79  -98.40   57.68    2.61  -63.50  162.17   26.85
    3         95Y  95Y N   CA    746  747  117.31  128.40                  -43.40
    4   3447  97R  98T C   N     776  778  -93.95 -124.80   69.18    2.20  -63.20  127.45   14.52
    4         98T  98T N   CA    778  779   81.58  143.50                  -42.10
    5   3448  98T  99K C   N     783  785  -53.25  -62.90   65.72    8.05 -118.00  132.05    6.84
    5         99K  99K N   CA    785  786 -105.81  -40.80                  139.10
    6   3453 103W 104S C   N     830  832  -72.61 -136.60   65.97    3.04  -64.10  157.97   11.97
    6        104S 104S N   CA    832  833  167.26  151.20                  -35.00
    7   3454 104S 105G C   N     836  838   95.49   82.20   73.13    2.88  -62.40  159.44   27.49
    7        105G 105G N   CA    838  839  -63.41    8.50                  -41.20
    8   3458 108N 109H C   N     870  872 -121.55  -63.20   75.69    8.86  -63.20   75.69    8.86
    8        109H 109H N   CA    872  873    5.91  -42.30                  -42.30
    9   3459 109H 110C C   N     880  882 -121.13  -63.00   59.34    9.18  -63.00   59.34    9.18
    9        110C 110C N   CA    882  883  -29.17  -41.10                  -41.10
   10   3467 117I 118S C   N     941  943  -67.60  -72.40   55.07    3.08  -64.10  132.59    9.40
   10        118S 118S N   CA    943  944   97.54  152.40                  -35.00
   11   3468 118S 119S C   N     947  949   64.16   56.90   15.71    1.61  -64.10  154.06   20.07
   11        119S 119S N   CA    949  950   50.34   36.40                  -35.00


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    6   15   42   65   92  108  108  154  138  150


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      120
Number of all, selected real atoms                :      961     961
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    10078   10078
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2017
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                                    :         931.0333





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              :     980       0      5   0.010   0.010      27.403       1.000
 2 Bond angle potential               :    1322       1      9   2.271   2.271      138.44       1.000
 3 Stereochemical cosine torsion poten:     631       0     19  47.052  47.052      218.65       1.000
 4 Stereochemical improper torsion pot:     405       0      0   1.210   1.210      13.882       1.000
 5 Soft-sphere overlap restraints     :    2017       0      0   0.003   0.003      1.5792       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)      :    2136       0      4   0.390   0.390      127.06       1.000
10 Distance restraints 2 (N-O)        :    2283       0      6   0.428   0.428      152.54       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:     119       0      3   4.910   4.910      33.835       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      0  70.435  70.435      29.894       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      1  76.585  76.585      37.824       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  67.827  67.827      19.576       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  85.354  85.354      15.438       1.000
18 Disulfide distance restraints      :       3       0      0   0.022   0.022     0.26230       1.000
19 Disulfide angle restraints         :       6       0      0   2.967   2.967      1.1663       1.000
20 Disulfide dihedral angle restraints:       3       0      0  29.802  29.802      2.4029       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)  :    1319       0      0   0.394   0.394      24.019       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:     118       6     19  31.150  45.794      57.648       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     523       0      0   0.660   0.660      29.406       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: seq.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:   12605.9336



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   1769  71D  71D N   CA    573  574  126.57  107.00   19.57    5.63  107.00   19.57    5.63

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3355   5R   6C C   N      48   50  -67.43  -63.00    4.61    0.69 -117.90 -173.95    7.96
    1          6C   6C N   CA     50   51  -39.82  -41.10                  141.10
    2   3383  33S  34A C   N     276  278  141.70 -134.00  113.63    3.23  -62.50 -177.05   37.19
    2         34A  34A N   CA    278  279 -136.81  147.00                  -40.90
    3   3384  34A  35R C   N     281  283  -80.24  -72.10   75.25    5.96  -63.00  109.55   13.72
    3         35R  35R N   CA    283  284   67.09  141.90                  -41.10
    4   3420  70K  71D C   N     571  573  162.47  -96.50  102.13    4.16  -63.30 -166.59   21.69
    4         71D  71D N   CA    573  574   99.25  114.20                  -40.00
    5   3444  94I  95Y C   N     744  746  -40.86  -98.40   58.66    2.66  -63.50  161.98   26.87
    5         95Y  95Y N   CA    746  747  116.99  128.40                  -43.40
    6   3459 109H 110C C   N     880  882 -108.31  -63.00   45.31    7.55  -63.00   45.31    7.55
    6        110C 110C N   CA    882  883  -41.09  -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    5   10   52   62   96  110  104  131  143  167


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
seq.B99990001.pdb             1050.96448
seq.B99990002.pdb              931.03333

8. Посмотрим результат

In [ ]:
pdb2img('seq.B99990001.pdb', '1lmp.pdb')
pdb2img('seq.B99990002.pdb', '1lmp.pdb')

LIGAND??

9. Добавим три остатка лиганда к концу последовательности

In [ ]:
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 = 'seq_lig'
del alignm[0]
In [ ]:
alignm.salign()
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1
In [ ]:
! cat all_in_one2.ali
>P1;pdb
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESS-YNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKN
VCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*

>P1;seq_lig
sequence::1    : :+123 : :undefined:undefined:-1.00:-1.00
KRFTRCGLVNELRKQGFD---ENLMRDWVCLVENESARYTDKIANVNKNGSRDYGLFQINDKYWCSKGSTPGKD-
-CNVTCSQLLTDDITVASTCAKKI-YKRTKFDAWSGWDNHCNH----SNPDISSC...*
In [ ]:

s = alignm[1]
pdb = alignm[0]

print(s.code, pdb.code)


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()
seq_lig 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()
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
----------------------------------------------
     18     1   18    22      D     E    8.206
     74     1   73    76      D     C    8.895
    118     1  117   122      H     S   13.814
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   120
              atom names           : C     +N
              atom indices         :   959     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   120
              atom names           : C     CA    +N    O
              atom indices         :   959   956     0   960
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    12245    11408
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                   :      123
Number of all, selected real atoms                :     1004    1004
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    11408   11408
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2330
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                                    :        1345.8303





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              :     980       0      5   0.011   0.011      35.380       1.000
 2 Bond angle potential               :    1322       1     13   2.480   2.480      164.02       1.000
 3 Stereochemical cosine torsion poten:     631       0     24  48.272  48.272      226.43       1.000
 4 Stereochemical improper torsion pot:     405       0      1   1.507   1.507      20.735       1.000
 5 Soft-sphere overlap restraints     :    2330       1      2   0.008   0.008      19.116       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)      :    2120       1     13   0.536   0.536      202.23       1.000
10 Distance restraints 2 (N-O)        :    2267       1     26   0.586   0.586      305.45       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:     119       0      4   5.478   5.478      42.119       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      2  75.675  75.675      38.058       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      1  72.896  72.896      45.460       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  77.551  77.551      19.151       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  84.032  84.032      12.880       1.000
18 Disulfide distance restraints      :       3       0      0   0.027   0.027     0.36750       1.000
19 Disulfide angle restraints         :       6       0      0   3.843   3.843      1.9571       1.000
20 Disulfide dihedral angle restraints:       3       0      0  20.495  20.495      1.2303       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)  :    1289       0      0   0.453   0.453      33.177       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:     118      14     24  35.782  61.009      105.30       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     526       0      1   0.775   0.775      50.236       1.000
27 Distance restraints 5 (X-Y)        :    1389       0      2   0.044   0.044      22.545       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: seq_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:   15663.0859



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   1769  71D  71D N   CA    573  574  128.23  107.00   21.23    6.10  107.00   21.23    6.10

-------------------------------------------------------------------------------------------------

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   8050 108N 104S N   O     864  837    5.73    2.99    2.74    6.15    2.99    2.74    6.15

-------------------------------------------------------------------------------------------------

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   3383  33S  34A C   N     276  278  126.95 -134.00  127.07    3.38  -62.50 -165.97   39.46
    1         34A  34A N   CA    278  279 -133.41  147.00                  -40.90
    2   3384  34A  35R C   N     281  283  -78.82  -72.10   74.08    5.84  -63.00  110.36   13.91
    2         35R  35R N   CA    283  284   68.12  141.90                  -41.10
    3   3420  70K  71D C   N     571  573 -142.33  -63.30   84.99   14.45  -63.30   84.99   14.45
    3         71D  71D N   CA    573  574  -71.26  -40.00                  -40.00
    4   3444  94I  95Y C   N     744  746  -47.41  -98.40   56.53    3.44  -63.50  148.26   24.35
    4         95Y  95Y N   CA    746  747  103.99  128.40                  -43.40
    5   3453 103W 104S C   N     830  832  -70.53 -136.60   66.23    2.75  -64.10  169.32   12.66
    5        104S 104S N   CA    832  833  155.80  151.20                  -35.00
    6   3454 104S 105G C   N     836  838  104.91   82.20   72.20    2.40  -62.40  168.37   29.25
    6        105G 105G N   CA    838  839  -60.03    8.50                  -41.20
    7   3458 108N 109H C   N     870  872 -124.12  -63.20   78.79    9.23  -63.20   78.79    9.23
    7        109H 109H N   CA    872  873    7.66  -42.30                  -42.30
    8   3459 109H 110C C   N     880  882 -103.39  -63.00   93.13   14.39  -63.00   93.13   14.39
    8        110C 110C N   CA    882  883 -125.01  -41.10                  -41.10
    9   3461 111N 112H C   N     894  896 -155.84 -125.60   62.63    1.75   56.30 -147.34   32.28
    9        112H 112H N   CA    896  897 -166.36  138.80                   40.80
   10   3462 112H 113S C   N     904  906  -81.73  -72.40    9.45    0.63  -64.10  172.03   13.59
   10        113S 113S N   CA    906  907  153.88  152.40                  -35.00
   11   3463 113S 114N C   N     910  912 -147.70 -119.90   28.15    1.27  -63.20 -166.83   20.86
   11        114N 114N N   CA    912  913  132.61  137.00                  -41.10
   12   3464 114N 115P C   N     918  920   -4.93  -64.50   76.62    5.22  -58.70  140.22   15.97
   12        115P 115P N   CA    920  921   99.00  147.20                  -30.50
   13   3466 116D 117I C   N     933  935  -89.41  -97.30   82.05    8.55  -63.40   92.85   14.43
   13        117I 117I N   CA    935  936   45.53  127.20                  -43.60
   14   3468 118S 119S C   N     947  949   60.83   56.90    3.94    0.48  -64.10  144.05   18.99
   14        119S 119S N   CA    949  950   36.70   36.40                  -35.00


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   17   12   79   76  123  115  133  149  173  190


<< 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                   :      123
Number of all, selected real atoms                :     1004    1004
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    11408   11408
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2384
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                                    :        1408.6130





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              :     980       0      6   0.012   0.012      39.170       1.000
 2 Bond angle potential               :    1322       1     15   2.606   2.606      178.70       1.000
 3 Stereochemical cosine torsion poten:     631       0     29  48.400  48.400      232.08       1.000
 4 Stereochemical improper torsion pot:     405       0      2   1.686   1.686      26.013       1.000
 5 Soft-sphere overlap restraints     :    2384       1      2   0.008   0.008      19.108       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)      :    2120       0     11   0.533   0.533      212.65       1.000
10 Distance restraints 2 (N-O)        :    2267       3     29   0.628   0.628      323.64       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:     119       0      5   5.649   5.649      44.787       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      0  69.263  69.263      25.827       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      1  78.032  78.032      46.031       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  79.766  79.766      15.227       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  98.928  98.928      12.044       1.000
18 Disulfide distance restraints      :       3       0      0   0.023   0.023     0.27174       1.000
19 Disulfide angle restraints         :       6       0      0   3.157   3.157      1.3205       1.000
20 Disulfide dihedral angle restraints:       3       0      0  50.664  50.664      4.6834       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)  :    1289       0      0   0.526   0.526      26.719       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:     118      17     24  35.039  64.552      125.40       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     526       0      0   0.844   0.844      47.185       1.000
27 Distance restraints 5 (X-Y)        :    1389       0      3   0.049   0.049      27.766       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: seq_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:   15766.8105



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   1769  71D  71D N   CA    573  574  130.47  107.00   23.47    6.75  107.00   23.47    6.75

-------------------------------------------------------------------------------------------------

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   7341  69G  46N N   O     560  382   10.78    7.27    3.51    4.77    7.27    3.51    4.77
    2   7351  70K  46N N   O     564  382   12.22    8.66    3.56    5.72    8.66    3.56    5.72

-------------------------------------------------------------------------------------------------

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   3368  18D  19E C   N     150  152 -178.08 -117.80   60.64    2.39  -63.60 -154.68   23.74
    1         19E  19E N   CA    152  153  130.14  136.80                  -40.30
    2   3382  32E  33S C   N     270  272  -93.42  -72.40   57.61    2.76  -64.10  122.52   10.88
    2         33S  33S N   CA    272  273 -153.96  152.40                  -35.00
    3   3384  34A  35R C   N     281  283 -159.61  -63.00   97.97   17.11  -63.00   97.97   17.11
    3         35R  35R N   CA    283  284  -57.41  -41.10                  -41.10
    4   3385  35R  36Y C   N     292  294 -145.68 -124.30   66.95    4.47   55.90  161.71   19.38
    4         36Y  36Y N   CA    294  295   71.96  135.40                   39.50
    5   3395  45K  46N C   N     373  375  -72.16 -119.90   75.90    4.12  -63.20  123.22   15.90
    5         46N  46N N   CA    375  376 -164.00  137.00                  -41.10
    6   3396  46N  47G C   N     381  383  -71.73  -62.40   22.61    3.07   82.20  156.66   11.43
    6         47G  47G N   CA    383  384  -20.61  -41.20                    8.50
    7   3420  70K  71D C   N     571  573  167.16  -96.50   98.70    4.02  -63.30 -174.51   20.85
    7         71D  71D N   CA    573  574   92.77  114.20                  -40.00
    8   3444  94I  95Y C   N     744  746  -48.10  -98.40   55.58    3.36  -63.50  148.96   24.43
    8         95Y  95Y N   CA    746  747  104.76  128.40                  -43.40
    9   3446  96K  97R C   N     765  767  -85.35 -125.20   88.32    3.24  -63.00  105.28   12.86
    9         97R  97R N   CA    767  768   61.78  140.60                  -41.10
   10   3447  97R  98T C   N     776  778 -154.64  -63.20   95.00   13.25  -63.20   95.00   13.25
   10         98T  98T N   CA    778  779  -16.34  -42.10                  -42.10
   11   3448  98T  99K C   N     783  785   52.91  -70.20  146.72   12.16 -118.00 -170.82    8.66
   11         99K  99K N   CA    785  786 -139.79  140.40                  139.10
   12   3458 108N 109H C   N     870  872 -127.87  -63.20   74.63    9.47  -63.20   74.63    9.47
   12        109H 109H N   CA    872  873   -5.06  -42.30                  -42.30
   13   3461 111N 112H C   N     894  896 -178.46 -125.60   83.75    2.14   56.30 -154.47   29.75
   13        112H 112H N   CA    896  897 -156.24  138.80                   40.80
   14   3462 112H 113S C   N     904  906 -113.49 -136.60   23.17    0.88  -64.10 -177.75   16.61
   14        113S 113S N   CA    906  907  149.56  151.20                  -35.00
   15   3463 113S 114N C   N     910  912 -139.70 -119.90   21.97    1.12  -63.20 -174.88   20.06
   15        114N 114N N   CA    912  913  127.47  137.00                  -41.10
   16   3464 114N 115P C   N     918  920   -7.29  -64.50   75.72    5.04  -58.70  138.03   15.61
   16        115P 115P N   CA    920  921   97.60  147.20                  -30.50
   17   3468 118S 119S C   N     947  949   52.31   56.90   15.86    0.69  -64.10  145.09   18.67
   17        119S 119S N   CA    949  950   51.58   36.40                  -35.00


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   16   22   79   88  128  107  133  157  164  177


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
seq_lig.B99990001.pdb         1345.83032
seq_lig.B99990002.pdb         1408.61304

In [ ]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')

10. Поместим лиганд в другое место

In [ ]:
! rm seq_lig.rsr
In [ ]:
class mymodel(modeller.automodel.automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        at = self.atoms
        for x,y in [('N:50','O6:121'), ('N:70', 'O6:123')]:
            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 [ ]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
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
----------------------------------------------
     18     1   18    22      D     E    8.206
     74     1   73    76      D     C    8.895
    118     1  117   122      H     S   13.814
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   120
              atom names           : C     +N
              atom indices         :   959     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   120
              atom names           : C     CA    +N    O
              atom indices         :   959   956     0   960
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    12247    11410
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                   :      123
Number of all, selected real atoms                :     1004    1004
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    11410   11410
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2486
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                                    :        5791.4170





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              :     980       8     16   0.028   0.028      229.13       1.000
 2 Bond angle potential               :    1322      14     29   3.981   3.981      419.47       1.000
 3 Stereochemical cosine torsion poten:     631       0     31  49.164  49.164      234.33       1.000
 4 Stereochemical improper torsion pot:     405       0      5   2.144   2.144      43.653       1.000
 5 Soft-sphere overlap restraints     :    2486       4      7   0.015   0.015      65.633       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)      :    2120      20     59   0.664   0.664      582.03       1.000
10 Distance restraints 2 (N-O)        :    2267      15     66   0.655   0.655      624.69       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:     119       3     10   9.629   9.629      130.12       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      3  73.392  73.392      53.139       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      0  72.590  72.590      39.816       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  79.607  79.607      18.866       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  66.812  66.812      8.8681       1.000
18 Disulfide distance restraints      :       3       0      0   0.010   0.010     0.51714E-01   1.000
19 Disulfide angle restraints         :       6       0      0   1.955   1.955     0.50626       1.000
20 Disulfide dihedral angle restraints:       3       0      0  37.672  37.672      2.5574       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)  :    1289       0      0   0.543   0.543      53.035       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:     118      18     33  45.686  69.470      196.47       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     526       0      0   0.782   0.782      46.657       1.000
27 Distance restraints 5 (X-Y)        :    1391      21     84   0.341   0.341      3042.4       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: seq_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:   20071.8223



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    407  49R  49R C   CA    402  394    1.71    1.49    0.22    6.33    1.49    0.22    6.33
    2    408  49R  50D C   N     402  404    1.54    1.35    0.20    6.96    1.35    0.20    6.96
    3    413  50D  50D N   CA    404  405    1.72    1.43    0.29    9.41    1.43    0.29    9.41
    4    574  69G  70K C   N     562  564    1.51    1.35    0.16    5.81    1.35    0.16    5.81
    5    580  70K  70K N   CA    564  565    1.77    1.43    0.34   11.20    1.43    0.34   11.20
    6    582  70K  70K C   CA    571  565    1.87    1.49    0.38   11.02    1.49    0.38   11.02
    7    583  70K  71D C   N     571  573    1.57    1.35    0.22    7.83    1.35    0.22    7.83
    8    588  71D  71D N   CA    573  574    1.69    1.43    0.26    8.46    1.43    0.26    8.46

-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1521  49R  49R CA  C     394  402  143.54  116.50   27.04    7.78  116.50   27.04    7.78
    2   1532  50D  50D N   CA    404  405  140.40  107.00   33.40    9.60  107.00   33.40    9.60
    3   1649  60Y  60Y N   CA    489  490  125.43  107.00   18.43    5.30  107.00   18.43    5.30
    4   1650  60Y  60Y CA  CB    490  491  129.20  107.50   21.70    5.02  107.50   21.70    5.02
    5   1754  69G  69G CA  C     561  562  136.64  116.50   20.14    5.79  116.50   20.14    5.79
    6   1758  70K  70K N   CA    564  565  151.96  107.00   44.96   12.93  107.00   44.96   12.93
    7   1766  70K  71D C   N     571  573  157.61  120.00   37.61    8.55  120.00   37.61    8.55
    8   1769  71D  71D N   CA    573  574  128.72  107.00   21.72    6.24  107.00   21.72    6.24
    9   1777  71D  72C C   N     579  581  142.56  120.00   22.56    5.13  120.00   22.56    5.13
   10   1780  72C  72C N   CA    581  582  124.21  107.00   17.21    4.95  107.00   17.21    4.95

-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   5510  63S  70K CA  CA    522  565    9.97    7.04    2.93    5.76    7.04    2.93    5.76
    2   5528  64K  70K CA  CA    528  565   11.51    8.85    2.66    5.09    8.85    2.66    5.09
    3   5542  65G  70K CA  CA    537  565   12.29    8.63    3.65    5.13    8.63    3.65    5.13

-------------------------------------------------------------------------------------------------

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   6878  50D  41A N   O     404  342    8.61    6.43    2.18    5.11    6.43    2.18    5.11
    2   6879  50D  42N N   O     404  350    4.80    2.79    2.01    5.39    2.79    2.01    5.39
    3   7273  64K  70K N   O     527  572   11.79    8.56    3.23    5.58    8.56    3.23    5.58
    4   7351  70K  46N N   O     564  382   11.80    8.66    3.14    5.05    8.66    3.14    5.05
    5   7361  70K  64K N   O     564  535   13.86   10.46    3.41    5.39   10.46    3.41    5.39
    6   7364  70K  67T N   O     564  552    7.98    3.64    4.33    5.35    3.64    4.33    5.35

-------------------------------------------------------------------------------------------------

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   3528  60Y  60Y CA  C     490  499 -150.84 -180.00   29.16    5.83 -180.00   29.16    5.83

-------------------------------------------------------------------------------------------------

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   3368  18D  19E C   N     150  152 -146.28  -63.60   94.50   16.25  -63.60   94.50   16.25
    1         19E  19E N   CA    152  153  -86.06  -40.30                  -40.30
    2   3382  32E  33S C   N     270  272 -139.75 -136.60   79.21    4.08  -64.10  131.08    9.21
    2         33S  33S N   CA    272  273   72.06  151.20                  -35.00
    3   3383  33S  34A C   N     276  278  -42.40  -68.20   25.91    2.28  -62.50  172.49   27.35
    3         34A  34A N   CA    278  279  147.79  145.30                  -40.90
    4   3384  34A  35R C   N     281  283   70.15   57.30   32.61    1.57  -63.00  141.93   25.59
    4         35R  35R N   CA    283  284    8.03   38.00                  -41.10
    5   3395  45K  46N C   N     373  375  -76.25 -119.90   74.46    4.03  -63.20  122.27   16.02
    5         46N  46N N   CA    375  376 -162.67  137.00                  -41.10
    6   3396  46N  47G C   N     381  383  -69.59  -62.40   22.07    3.03   82.20  154.50   11.28
    6         47G  47G N   CA    383  384  -20.33  -41.20                    8.50
    7   3409  59K  60Y C   N     487  489  -77.21  -63.50   49.17    8.50  -63.50   49.17    8.50
    7         60Y  60Y N   CA    489  490  -90.62  -43.40                  -43.40
    8   3415  65G  66S C   N     538  540 -140.85 -136.60   60.42    3.15  -64.10  147.48    9.86
    8         66S  66S N   CA    540  541   90.93  151.20                  -35.00
    9   3419  69G  70K C   N     562  564  117.60 -118.00  125.05    4.95  -70.20  172.77   12.93
    9         70K  70K N   CA    564  565  126.39  139.10                  140.40
   10   3420  70K  71D C   N     571  573   90.84  -96.50  174.34    7.10  -63.30 -158.30   33.98
   10         71D  71D N   CA    573  574   90.09  114.20                  -40.00
   11   3459 109H 110C C   N     880  882  -78.78  -63.00   90.25   12.16  -63.00   90.25   12.16
   11        110C 110C N   CA    882  883 -129.95  -41.10                  -41.10
   12   3461 111N 112H C   N     894  896 -160.08 -125.60   65.20    1.77   56.30 -149.91   31.70
   12        112H 112H N   CA    896  897 -165.86  138.80                   40.80
   13   3462 112H 113S C   N     904  906 -122.48 -136.60   20.68    0.68  -64.10 -179.22   11.13
   13        113S 113S N   CA    906  907  136.09  151.20                  -35.00
   14   3463 113S 114N C   N     910  912 -139.42  -63.20   91.38   10.98  -63.20   91.38   10.98
   14        114N 114N N   CA    912  913    9.30  -41.10                  -41.10
   15   3465 115P 116D C   N     925  927  -54.16  -96.50   43.99    1.81  -63.30  142.54   18.16
   15        116D 116D N   CA    927  928  102.25  114.20                  -40.00
   16   3466 116D 117I C   N     933  935  151.01 -120.60  153.01    6.29  -63.40  157.93   29.66
   16        117I 117I N   CA    935  936 -104.80  130.30                  -43.60
   17   3467 117I 118S C   N     941  943  -52.25  -72.40   57.37    2.77  -64.10  134.22   10.47
   17        118S 118S N   CA    943  944   98.69  152.40                  -35.00
   18   3468 118S 119S C   N     947  949  -66.16  -72.40   37.85    2.02  -64.10  150.08   10.75
   18        119S 119S N   CA    949  950  115.07  152.40                  -35.00

-------------------------------------------------------------------------------------------------

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  10370  96K 121. CA  O6    759  974    6.17    5.07    1.10    5.48    5.07    1.10    5.48
    2  10386  97R 121. CA  O6    768  974    8.07    6.81    1.25    6.26    6.81    1.25    6.26
    3  10573 121. 122. C1  O4    962  986    1.62    1.39    0.23    4.61    1.39    0.23    4.61
    4  10963 121. 121. O3  O6    971  974    5.12    4.85    0.27    5.43    4.85    0.27    5.43
    5  10976 121. 121. O4  O6    972  974    3.71    3.43    0.28    5.54    3.43    0.28    5.54
    6  11000 121. 121. O6  O3    974  971    5.12    4.85    0.27    5.43    4.85    0.27    5.43
    7  11001 121. 121. O6  O4    974  972    3.71    3.43    0.28    5.54    3.43    0.28    5.54
    8  11409  50D 121. N   O6    404  974   10.17    3.00    7.17   71.71    3.00    7.17   71.71
    9  11410  70K 123. N   O6    564 1001    8.10    3.00    5.10   51.00    3.00    5.10   51.00


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    2   15   26   90   99  128  125  136  153  168  199


<< 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                   :      123
Number of all, selected real atoms                :     1004    1004
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    11410   11410
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2504
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                                    :        5687.6299





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              :     980       8     16   0.028   0.028      231.17       1.000
 2 Bond angle potential               :    1322      15     24   3.954   3.954      411.29       1.000
 3 Stereochemical cosine torsion poten:     631       0     32  49.667  49.667      239.97       1.000
 4 Stereochemical improper torsion pot:     405       0      4   2.012   2.012      39.177       1.000
 5 Soft-sphere overlap restraints     :    2504       3      7   0.015   0.015      65.874       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)      :    2120      18     57   0.671   0.671      578.23       1.000
10 Distance restraints 2 (N-O)        :    2267      14     57   0.648   0.648      568.02       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:     119       3      5   9.191   9.191      118.55       1.000
14 Sidechain Chi_1 dihedral restraints:     108       0      4  74.340  74.340      43.369       1.000
15 Sidechain Chi_2 dihedral restraints:      76       0      1  77.527  77.527      36.353       1.000
16 Sidechain Chi_3 dihedral restraints:      28       0      0  81.095  81.095      18.277       1.000
17 Sidechain Chi_4 dihedral restraints:      18       0      0  85.723  85.723      11.732       1.000
18 Disulfide distance restraints      :       3       0      0   0.009   0.009     0.42862E-01   1.000
19 Disulfide angle restraints         :       6       0      0   2.213   2.213     0.64894       1.000
20 Disulfide dihedral angle restraints:       3       0      0  23.594  23.594      1.7186       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)  :    1289       0      0   0.581   0.581      59.321       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:     118      17     30  42.202  67.288      159.38       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     526       0      0   0.814   0.814      51.442       1.000
27 Distance restraints 5 (X-Y)        :    1391      21     86   0.342   0.342      3053.1       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: seq_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:   20154.2812



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  1                           : Bond length potential                   
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1    407  49R  49R C   CA    402  394    1.70    1.49    0.21    6.08    1.49    0.21    6.08
    2    408  49R  50D C   N     402  404    1.53    1.35    0.19    6.73    1.35    0.19    6.73
    3    413  50D  50D N   CA    404  405    1.72    1.43    0.29    9.41    1.43    0.29    9.41
    4    574  69G  70K C   N     562  564    1.51    1.35    0.16    5.82    1.35    0.16    5.82
    5    580  70K  70K N   CA    564  565    1.77    1.43    0.34   11.15    1.43    0.34   11.15
    6    582  70K  70K C   CA    571  565    1.87    1.49    0.38   10.93    1.49    0.38   10.93
    7    583  70K  71D C   N     571  573    1.57    1.35    0.23    8.00    1.35    0.23    8.00
    8    588  71D  71D N   CA    573  574    1.69    1.43    0.26    8.62    1.43    0.26    8.62

-------------------------------------------------------------------------------------------------

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   1521  49R  49R CA  C     394  402  143.36  116.50   26.86    7.72  116.50   26.86    7.72
    2   1532  50D  50D N   CA    404  405  141.03  107.00   34.03    9.78  107.00   34.03    9.78
    3   1649  60Y  60Y N   CA    489  490  124.85  107.00   17.85    5.13  107.00   17.85    5.13
    4   1650  60Y  60Y CA  CB    490  491  135.84  107.50   28.34    6.55  107.50   28.34    6.55
    5   1754  69G  69G CA  C     561  562  136.82  116.50   20.32    5.84  116.50   20.32    5.84
    6   1758  70K  70K N   CA    564  565  151.81  107.00   44.81   12.88  107.00   44.81   12.88
    7   1766  70K  71D C   N     571  573  158.24  120.00   38.24    8.69  120.00   38.24    8.69
    8   1769  71D  71D N   CA    573  574  129.22  107.00   22.22    6.39  107.00   22.22    6.39
    9   1777  71D  72C C   N     579  581  141.75  120.00   21.75    4.94  120.00   21.75    4.94
   10   1780  72C  72C N   CA    581  582  123.56  107.00   16.56    4.76  107.00   16.56    4.76

-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   5510  63S  70K CA  CA    522  565   10.06    7.04    3.02    5.94    7.04    3.02    5.94
    2   5528  64K  70K CA  CA    528  565   11.49    8.85    2.64    5.05    8.85    2.64    5.05
    3   5542  65G  70K CA  CA    537  565   12.38    8.63    3.75    5.26    8.63    3.75    5.26

-------------------------------------------------------------------------------------------------

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   6878  50D  41A N   O     404  342    8.59    6.43    2.16    5.06    6.43    2.16    5.06
    2   6879  50D  42N N   O     404  350    4.81    2.79    2.02    5.41    2.79    2.02    5.41
    3   7273  64K  70K N   O     527  572   11.83    8.56    3.27    5.65    8.56    3.27    5.65
    4   7292  65G  70K N   O     536  572   12.74    9.02    3.72    4.54    9.02    3.72    4.54
    5   7361  70K  64K N   O     564  535   13.88   10.46    3.42    5.41   10.46    3.42    5.41
    6   7364  70K  67T N   O     564  552    8.01    3.64    4.37    5.39    3.64    4.37    5.39

-------------------------------------------------------------------------------------------------

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   3528  60Y  60Y CA  C     490  499 -153.27 -180.00   26.73    5.34 -180.00   26.73    5.34

-------------------------------------------------------------------------------------------------

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   3383  33S  34A C   N     276  278   63.72   55.40   88.98    6.05  -62.50 -150.12   41.02
    1         34A  34A N   CA    278  279  126.79   38.20                  -40.90
    2   3384  34A  35R C   N     281  283   61.29   57.30   26.72    1.50  -63.00  134.99   24.46
    2         35R  35R N   CA    283  284   11.58   38.00                  -41.10
    3   3409  59K  60Y C   N     487  489  -77.86  -63.50   47.13    8.21  -63.50   47.13    8.21
    3         60Y  60Y N   CA    489  490  -88.29  -43.40                  -43.40
    4   3415  65G  66S C   N     538  540 -140.27 -136.60   59.54    3.09  -64.10  147.90    9.84
    4         66S  66S N   CA    540  541   91.78  151.20                  -35.00
    5   3419  69G  70K C   N     562  564  116.32 -118.00  126.55    5.04  -70.20  174.23   13.09
    5         70K  70K N   CA    564  565  124.28  139.10                  140.40
    6   3420  70K  71D C   N     571  573   96.05  -96.50  168.58    6.87  -63.30 -151.36   35.15
    6         71D  71D N   CA    573  574   94.67  114.20                  -40.00
    7   3444  94I  95Y C   N     744  746  -54.15  -98.40   49.42    3.06  -63.50  150.07   24.29
    7         95Y  95Y N   CA    746  747  106.38  128.40                  -43.40
    8   3447  97R  98T C   N     776  778  -89.52 -124.80   56.42    1.76  -63.20  143.99   16.85
    8         98T  98T N   CA    778  779   99.47  143.50                  -42.10
    9   3448  98T  99K C   N     783  785  -61.17  -62.90   64.57    8.29 -118.00  128.77    6.67
    9         99K  99K N   CA    785  786 -105.35  -40.80                  139.10
   10   3458 108N 109H C   N     870  872 -124.08  -63.20   76.57    9.12  -63.20   76.57    9.12
   10        109H 109H N   CA    872  873    4.14  -42.30                  -42.30
   11   3459 109H 110C C   N     880  882 -103.52 -117.90   91.44    3.80  -63.00   96.42   14.80
   11        110C 110C N   CA    882  883 -128.59  141.10                  -41.10
   12   3461 111N 112H C   N     894  896 -152.49 -125.60   63.48    1.85   56.30 -143.10   32.96
   12        112H 112H N   CA    896  897 -163.70  138.80                   40.80
   13   3462 112H 113S C   N     904  906 -125.24 -136.60   23.66    0.91  -64.10  176.38   10.88
   13        113S 113S N   CA    906  907  130.45  151.20                  -35.00
   14   3463 113S 114N C   N     910  912 -135.13  -63.20   99.38   11.18  -63.20   99.38   11.18
   14        114N 114N N   CA    912  913   27.48  -41.10                  -41.10
   15   3465 115P 116D C   N     925  927  -22.45  -70.90   60.86    2.83  -63.30  158.80   22.23
   15        116D 116D N   CA    927  928  113.46  150.30                  -40.00
   16   3466 116D 117I C   N     933  935   16.23  -97.30  124.32    7.51  -63.40  144.15   26.46
   16        117I 117I N   CA    935  936   76.55  127.20                  -43.60
   17   3468 118S 119S C   N     947  949   63.97   56.90    8.13    0.67  -64.10  144.72   19.17
   17        119S 119S N   CA    949  950   32.38   36.40                  -35.00

-------------------------------------------------------------------------------------------------

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  10370  96K 121. CA  O6    759  974    6.29    5.07    1.21    6.06    5.07    1.21    6.06
    2  10386  97R 121. CA  O6    768  974    8.17    6.81    1.36    6.78    6.81    1.36    6.78
    3  10573 121. 122. C1  O4    962  986    1.62    1.39    0.23    4.65    1.39    0.23    4.65
    4  10963 121. 121. O3  O6    971  974    5.12    4.85    0.27    5.46    4.85    0.27    5.46
    5  10976 121. 121. O4  O6    972  974    3.71    3.43    0.28    5.51    3.43    0.28    5.51
    6  11000 121. 121. O6  O3    974  971    5.12    4.85    0.27    5.46    4.85    0.27    5.46
    7  11001 121. 121. O6  O4    974  972    3.71    3.43    0.28    5.51    3.43    0.28    5.51
    8  11409  50D 121. N   O6    404  974   10.18    3.00    7.18   71.79    3.00    7.18   71.79
    9  11410  70K 123. N   O6    564 1001    8.10    3.00    5.10   50.98    3.00    5.10   50.98


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    2   24   24   80   91  134  129  131  169  183  183


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
seq_lig.B99990001.pdb         5791.41699
seq_lig.B99990002.pdb         5687.62988

In [5]:
pdb2img('seq_lig.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_lig.B99990002.pdb', '1lmp.pdb')
Before          After
1345.83032    5791.41699
1408.61304    5687.62988

11. Аланиновый лизоцим

In [7]:
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')

seq_ala = 'A' * 120 + '...'
alignm.append_sequence(seq_ala)

alignm[0].code = 'pdb'
alignm[1].code = 'seq_ala'
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.
rdpdb___459W> Residue type  NDG not recognized. 'automodel' model building
              will treat this residue as a rigid body.
              To use real parameters, add the residue type to ${LIB}/restyp.lib,
              its topology to ${LIB}/top_*.lib, and suitable forcefield
              parameters to ${LIB}/par.lib.
In [8]:
alignm.salign()
alignm.write(file='all_in_one3.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1
In [9]:
! cat all_in_one3.ali
>P1;pdb
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV
CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*

>P1;seq_ala
sequence::1    : :+123 : :undefined:undefined:-1.00:-1.00
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [10]:

s = alignm[1]
pdb = alignm[0]

print(s.code, pdb.code)

a = modeller.automodel.automodel(env, alnfile='all_in_one3.ali', knowns=pdb.code, sequence=s.code)

a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
seq_ala pdb
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
----------------------------------------------
     55     1   55    65      A     A   16.730
END OF TABLE
read_to_681_> topology.submodel read from topology file:        3

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     1   120
              atom names           : C     +N
              atom indices         :   599     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     1   120
              atom names           : C     CA    +N    O
              atom indices         :   599   597     0   600
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     8748     8155


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      123
Number of all, selected real atoms                :      644     644
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     8155    8155
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     1121
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         997.4510





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              :     600       0      1   0.008   0.008      12.639       1.000
 2 Bond angle potential               :     839       0      2   2.046   2.046      73.649       1.000
 3 Stereochemical cosine torsion poten:     244       0     32  74.759  74.759      225.05       1.000
 4 Stereochemical improper torsion pot:     240       0      0   0.799   0.799      4.1371       1.000
 5 Soft-sphere overlap restraints     :    1121       1      2   0.011   0.011      15.732       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)      :    1968       8     25   0.756   0.756      256.68       1.000
10 Distance restraints 2 (N-O)        :    2093       7     31   0.745   0.745      337.73       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:     119       0      2   4.466   4.466      27.989       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000      0.0000       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)  :     668       0      0   0.293   0.293      6.0921       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:     118      21     15  29.787  69.049      16.727       1.000
26 Distance restraints 4 (SDCH-SDCH)  :      50       0      1   1.014   1.014      3.8909       1.000
27 Distance restraints 5 (X-Y)        :    1216       0      0   0.040   0.040      17.139       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: seq_ala.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:   11533.6406



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3583  56A  63A CA  CA    277  312   13.35    7.04    6.31    5.95    7.04    6.31    5.95
    2   3584  56A  64A CA  CA    277  317   13.90    7.69    6.22    4.84    7.69    6.22    4.84
    3   3585  56A  65A CA  CA    277  322   11.15    5.45    5.70    6.56    5.45    5.70    6.56
    4   3588  56A  68A CA  CA    277  337   12.30    7.46    4.84    4.70    7.46    4.84    4.70
    5   3589  56A  69A CA  CA    277  342   10.11    6.07    4.03    5.67    6.07    4.03    5.67
    6   3590  56A  70A CA  CA    277  347    9.69    4.69    5.00    7.13    4.69    5.00    7.13

-------------------------------------------------------------------------------------------------

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   4905  38A  55A N   O     186  275    8.30    5.51    2.79    4.76    5.51    2.79    4.76
    2   5216  56A  63A N   O     276  315   14.37    7.89    6.48    5.26    7.89    6.48    5.26
    3   5217  56A  64A N   O     276  320   13.31    7.21    6.09    4.63    7.21    6.09    4.63
    4   5218  56A  65A N   O     276  325   13.65    6.37    7.29    6.89    6.37    7.29    6.89
    5   5221  56A  68A N   O     276  340   12.54    7.02    5.52    5.15    7.02    5.52    5.15
    6   5222  56A  69A N   O     276  345    9.02    2.70    6.33   12.36    2.70    6.33   12.36
    7   5389  71A  56A N   O     351  280    5.73    2.97    2.76    5.84    2.97    2.76    5.84

-------------------------------------------------------------------------------------------------

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   1938  15A  16A C   N      74   76   78.88   55.40   27.01    2.01  -62.50  155.91   31.67
    1         16A  16A N   CA     76   77   24.84   38.20                  -40.90
    2   1941  18A  19A C   N      89   91   58.32   55.40    3.79    0.23  -62.50  143.10   29.08
    2         19A  19A N   CA     91   92   35.79   38.20                  -40.90
    3   1942  19A  20A C   N      94   96  -60.66  -62.50   18.52    2.95  -68.20  155.55   12.81
    3         20A  20A N   CA     96   97  -59.33  -40.90                  145.30
    4   1943  20A  21A C   N      99  101 -124.94 -134.00   75.94    4.09  -62.50  128.66   19.27
    4         21A  21A N   CA    101  102   71.60  147.00                  -40.90
    5   1944  21A  22A C   N     104  106   60.09   55.40   15.41    0.60  -62.50  138.49   28.16
    5         22A  22A N   CA    106  107   23.52   38.20                  -40.90
    6   1959  36A  37A C   N     179  181   66.41   55.40   14.37    0.86  -62.50  146.62   29.82
    6         37A  37A N   CA    181  182   28.96   38.20                  -40.90
    7   1960  37A  38A C   N     184  186   60.98   55.40    9.05    0.40  -62.50  142.92   29.06
    7         38A  38A N   CA    186  187   31.07   38.20                  -40.90
    8   1971  48A  49A C   N     239  241  163.56 -134.00   64.03    1.64  -62.50 -152.92   40.88
    8         49A  49A N   CA    241  242  161.17  147.00                  -40.90
    9   1972  49A  50A C   N     244  246   91.06 -134.00  135.62    4.00  -68.20  159.99   14.06
    9         50A  50A N   CA    246  247  160.51  147.00                  145.30
   10   1976  53A  54A C   N     264  266   58.49  -68.20  142.70   13.83  -62.50  162.27   25.41
   10         54A  54A N   CA    266  267 -149.03  145.30                  -40.90
   11   1979  56A  57A C   N     279  281 -151.24 -134.00   29.94    1.10  -62.50  172.25   32.96
   11         57A  57A N   CA    281  282  171.47  147.00                  -40.90
   12   1980  57A  58A C   N     284  286  -67.21  -68.20    5.56    0.48  -62.50  168.39   27.83
   12         58A  58A N   CA    286  287  150.77  145.30                  -40.90
   13   1984  61A  62A C   N     304  306   60.85   55.40   19.38    0.78  -62.50  137.38   27.93
   13         62A  62A N   CA    306  307   19.60   38.20                  -40.90
   14   1986  63A  64A C   N     314  316  -79.05  -68.20   11.68    1.11  -62.50  178.90   30.16
   14         64A  64A N   CA    316  317  140.97  145.30                  -40.90
   15   1987  64A  65A C   N     319  321  -91.69  -68.20   43.21    4.17  -62.50  152.74   23.77
   15         65A  65A N   CA    321  322  109.03  145.30                  -40.90
   16   1989  66A  67A C   N     329  331  -92.69  -68.20   46.10    4.44  -62.50  150.21   23.32
   16         67A  67A N   CA    331  332  106.24  145.30                  -40.90
   17   1990  67A  68A C   N     334  336  -61.51  -68.20   39.26    2.93  -62.50  147.52   24.22
   17         68A  68A N   CA    336  337  106.62  145.30                  -40.90
   18   2017  94A  95A C   N     469  471   80.11 -134.00  160.28    3.64  -62.50  177.53   28.47
   18         95A  95A N   CA    471  472 -146.62  147.00                  -40.90
   19   2030 107A 108A C   N     534  536   49.18   55.40   10.38    0.44  -62.50  141.82   28.68
   19        108A 108A N   CA    536  537   46.51   38.20                  -40.90
   20   2039 116A 117A C   N     579  581   72.60   55.40   40.93    1.48  -62.50  141.46   28.50
   20        117A 117A N   CA    581  582    1.05   38.20                  -40.90
   21   2041 118A 119A C   N     589  591   66.24   55.40   16.56    0.78  -62.50  144.94   29.47
   21        119A 119A N   CA    591  592   25.69   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    2    3   34   57   66   53   81   97   90   67


<< 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                :      644     644
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     8155    8155
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     1134
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                                    :        1177.2844





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              :     600       0      1   0.008   0.008      11.259       1.000
 2 Bond angle potential               :     839       0      3   2.232   2.232      86.037       1.000
 3 Stereochemical cosine torsion poten:     244       0     34  77.402  77.402      237.34       1.000
 4 Stereochemical improper torsion pot:     240       0      0   1.137   1.137      7.6996       1.000
 5 Soft-sphere overlap restraints     :    1134       1      2   0.011   0.011      15.836       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)      :    1968       7     28   0.785   0.785      281.47       1.000
10 Distance restraints 2 (N-O)        :    2093       9     36   0.799   0.799      391.53       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:     119       0      5   5.185   5.185      37.733       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000      0.0000       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)  :     668       0      0   0.331   0.331      7.7654       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:     118      25     18  35.239  78.101      74.580       1.000
26 Distance restraints 4 (SDCH-SDCH)  :      50       0      1   1.087   1.087      4.5952       1.000
27 Distance restraints 5 (X-Y)        :    1216       0      0   0.045   0.045      21.447       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: seq_ala.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:   12626.5547



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3583  56A  63A CA  CA    277  312   12.97    7.04    5.93    5.60    7.04    5.93    5.60
    2   3584  56A  64A CA  CA    277  317   14.14    7.69    6.45    5.02    7.69    6.45    5.02
    3   3585  56A  65A CA  CA    277  322   10.79    5.45    5.34    6.14    5.45    5.34    6.14
    4   3588  56A  68A CA  CA    277  337   12.25    7.46    4.78    4.64    7.46    4.78    4.64
    5   3589  56A  69A CA  CA    277  342    9.87    6.07    3.79    5.33    6.07    3.79    5.33
    6   3590  56A  70A CA  CA    277  347    9.04    4.69    4.35    6.21    4.69    4.35    6.21

-------------------------------------------------------------------------------------------------

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   4905  38A  55A N   O     186  275    8.19    5.51    2.68    4.57    5.51    2.68    4.57
    2   5033  44A  52A N   O     216  260    5.84    3.15    2.69    4.70    3.15    2.69    4.70
    3   5216  56A  63A N   O     276  315   14.44    7.89    6.56    5.32    7.89    6.56    5.32
    4   5217  56A  64A N   O     276  320   14.37    7.21    7.15    5.43    7.21    7.15    5.43
    5   5218  56A  65A N   O     276  325   12.56    6.37    6.19    5.85    6.37    6.19    5.85
    6   5221  56A  68A N   O     276  340   12.58    7.02    5.56    5.19    7.02    5.56    5.19
    7   5222  56A  69A N   O     276  345    8.45    2.70    5.75   11.24    2.70    5.75   11.24
    8   5389  71A  56A N   O     351  280    5.75    2.97    2.78    5.86    2.97    2.78    5.86
    9   5427  73A  70A N   O     361  350    6.06    3.17    2.89    4.70    3.17    2.89    4.70

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1924   1A   2A C   N       4    6  -66.25  -62.50    7.80    1.17 -134.00 -168.67   11.78
    1          2A   2A N   CA      6    7  -34.06  -40.90                  147.00
    2   1925   2A   3A C   N       9   11   57.57  -68.20  127.17   10.12  -68.20  127.17   10.12
    2          3A   3A N   CA     11   12  126.47  145.30                  145.30
    3   1938  15A  16A C   N      74   76   78.89   55.40   26.03    2.09  -62.50  156.84   31.88
    3         16A  16A N   CA     76   77   26.99   38.20                  -40.90
    4   1940  17A  18A C   N      84   86  -52.28  -62.50   10.23    1.99 -134.00 -168.93   11.79
    4         18A  18A N   CA     86   87  -40.29  -40.90                  147.00
    5   1941  18A  19A C   N      89   91 -138.23 -134.00   80.59    4.67  -62.50  131.43   19.79
    5         19A  19A N   CA     91   92   66.52  147.00                  -40.90
    6   1943  20A  21A C   N      99  101   57.09   55.40    6.22    0.25  -62.50  140.17   28.49
    6         21A  21A N   CA    101  102   32.21   38.20                  -40.90
    7   1944  21A  22A C   N     104  106   65.10   55.40   14.29    0.71  -62.50  144.87   29.46
    7         22A  22A N   CA    106  107   27.71   38.20                  -40.90
    8   1959  36A  37A C   N     179  181   64.76   55.40   12.17    0.73  -62.50  145.89   29.67
    8         37A  37A N   CA    181  182   30.43   38.20                  -40.90
    9   1960  37A  38A C   N     184  186   61.66   55.40   13.15    0.48  -62.50  141.34   28.75
    9         38A  38A N   CA    186  187   26.64   38.20                  -40.90
   10   1971  48A  49A C   N     239  241  152.34 -134.00   75.68    1.93  -62.50 -147.83   42.20
   10         49A  49A N   CA    241  242  164.37  147.00                  -40.90
   11   1972  49A  50A C   N     244  246   92.38 -134.00  134.19    3.99  -68.20  161.20   14.13
   11         50A  50A N   CA    246  247  159.38  147.00                  145.30
   12   1974  51A  52A C   N     254  256  -68.05  -62.50    6.29    1.28 -134.00 -178.44   11.19
   12         52A  52A N   CA    256  257  -43.84  -40.90                  147.00
   13   1979  56A  57A C   N     279  281 -168.59 -134.00   36.18    1.61  -62.50 -153.38   30.97
   13         57A  57A N   CA    281  282  136.40  147.00                  -40.90
   14   1980  57A  58A C   N     284  286  -54.14  -68.20   14.23    1.13  -62.50  176.23   28.48
   14         58A  58A N   CA    286  287  143.07  145.30                  -40.90
   15   1984  61A  62A C   N     304  306   55.84   55.40    7.01    0.39  -62.50  138.57   28.17
   15         62A  62A N   CA    306  307   31.21   38.20                  -40.90
   16   1987  64A  65A C   N     319  321   54.66   55.40   28.31    1.65  -62.50  158.94   31.91
   16         65A  65A N   CA    321  322   66.50   38.20                  -40.90
   17   1988  65A  66A C   N     324  326  -56.39  -68.20   15.21    1.50  -62.50  164.33   26.64
   17         66A  66A N   CA    326  327  154.89  145.30                  -40.90
   18   1989  66A  67A C   N     329  331   58.10  -68.20  137.38    9.72  -62.50  178.92   35.52
   18         67A  67A N   CA    331  332   91.27  145.30                  -40.90
   19   1990  67A  68A C   N     334  336  -79.62  -68.20   46.56    4.14  -62.50  142.10   22.51
   19         68A  68A N   CA    336  337  100.16  145.30                  -40.90
   20   1992  69A  70A C   N     344  346  -65.88  -62.50   21.05    3.62 -134.00  165.95   10.24
   20         70A  70A N   CA    346  347  -61.67  -40.90                  147.00
   21   1993  70A  71A C   N     349  351 -177.98  -62.50  116.96   21.63  -62.50  116.96   21.63
   21         71A  71A N   CA    351  352  -22.35  -40.90                  -40.90
   22   2017  94A  95A C   N     469  471   83.05 -134.00  158.80    3.61  -62.50  178.28   28.77
   22         95A  95A N   CA    471  472 -143.85  147.00                  -40.90
   23   2030 107A 108A C   N     534  536   53.30   55.40    6.64    0.26  -62.50  143.88   29.15
   23        108A 108A N   CA    536  537   44.50   38.20                  -40.90
   24   2039 116A 117A C   N     579  581   72.19   55.40   45.46    1.67  -62.50  139.64   28.04
   24        117A 117A N   CA    581  582   -4.05   38.20                  -40.90
   25   2041 118A 119A C   N     589  591   62.82   55.40   10.13    0.56  -62.50  144.63   29.41
   25        119A 119A N   CA    591  592   31.30   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    5    3   39   55   59   57   82  101   94   81


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
seq_ala.B99990001.pdb          997.45105
seq_ala.B99990002.pdb         1177.28442

In [11]:
pdb2img('seq_ala.B99990001.pdb', '1lmp.pdb')
pdb2img('seq_ala.B99990002.pdb', '1lmp.pdb')