В этом таске мы будем с помощью Modeller переносить известную структуру лизоцима форели (с лигандом) на какой-нибудь другой лизоцим.
Другой лизоцим мы возьмём в Uniprot'е.
Not enough spoons to write comprehensible commentary, so here's just code.
%%bash
# This is crystal structure of rainbow trout's lysozyme,
# together with some ligands
if ! [ -e 1lmp.pdb ];
then wget http://www.pdb.org/pdb/files/1lmp.pdb;
fi
# And this is sequence of Anas platyrhynchos' lysozyme.
if ! [ -e P00705.fasta ];
then wget http://www.uniprot.org/uniprot/P00705.fasta;
fi
import sys
import modeller
import _modeller
import modeller.automodel
env=modeller.environ()
env.io.hetatm=True
MODELLER 9.19, 2017/07/19, r11078
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 shadbox 3.2.0-29-generic x86_64
Date and time of compilation : 2017/07/19 14:40:43
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2017/12/03 23:21:50
alignm=modeller.alignment(env)
alignm.append(file='P00705.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
-what?
Aha. Those ligands are not known to modeller, and so it treats them in a less smart way than regular residues. Moving on.
## есть смысл поправить идентификаторы
# alignm[0].code = '.....'
alignm[0].code
'sp|P00705|LYSC1_ANAPL'
What do we need to do here? This is just a string description, does it even matter in any way but semantically? It could, but as far as I can tell, it doesn't.
For now we'll continue as-is.
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration 1
!cat all_in_one.ali
>P1;sp|P00705|LYSC1_ANAPL sequence:: : : : :::-1.00:-1.00 MKALLTLVFCLLPLAAQGKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESGFNTQATNRNTDGSTDYGILQ INSRWWCDNGKTPRSKNACGIPCSVLLRSDITEAVRCAKRIVSDGDGMNAWVAWRNRCRGTDVSKWIRGCRL---* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ------------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQ INSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Looks basically all right.
P00705 could use some metadata, but eh.
## Выбираем объект для моделирования
s = alignm[0]
pdb = alignm[1]
print s.code, pdb.code
## Создаем объект automodel
a = modeller.automodel.automodel(
env, alnfile='all_in_one.ali',
knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
sp|P00705|LYSC1_ANAPL 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL: 4
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 52 (type TYR)>
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: 12802 11800
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1143 1143
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11800 11800
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2328
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 : 742.9526
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 : 1164 0 0 0.006 0.006 11.185 1.000
2 Bond angle potential : 1574 0 5 2.067 2.067 137.33 1.000
3 Stereochemical cosine torsion poten: 737 0 29 47.935 47.935 264.18 1.000
4 Stereochemical improper torsion pot: 464 0 0 1.242 1.242 17.289 1.000
5 Soft-sphere overlap restraints : 2328 0 0 0.001 0.001 0.33987 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) : 2404 0 0 0.112 0.112 34.224 1.000
10 Distance restraints 2 (N-O) : 2562 0 3 0.173 0.173 87.313 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: 146 0 5 4.671 4.671 37.563 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 1 59.117 59.117 10.611 1.000
15 Sidechain Chi_2 dihedral restraints: 85 0 0 72.716 72.716 30.459 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 74.584 74.584 17.161 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 97.168 97.168 13.649 1.000
18 Disulfide distance restraints : 4 0 0 0.006 0.006 0.27900E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.692 1.692 0.50584 1.000
20 Disulfide dihedral angle restraints: 4 0 0 29.439 29.439 3.3521 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) : 1605 0 0 0.273 0.273 24.909 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: 145 17 14 19.076 60.776 17.072 1.000
26 Distance restraints 4 (SDCH-SDCH) : 724 0 0 0.556 0.556 35.781 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: sp|P00705|LYSC1_ANAPL.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: 14187.6914
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3956 1M 2K C N 7 9 -69.23 -70.20 5.12 0.39 -62.90 173.90 22.93
1 2K 2K N CA 9 10 145.42 140.40 -40.80
2 3957 2K 3A C N 16 18 -62.30 -68.20 21.23 1.51 -62.50 165.80 27.18
2 3A 3A N CA 18 19 124.91 145.30 -40.90
3 3959 4L 5L C N 29 31 -99.38 -108.50 23.37 1.15 -63.50 156.36 19.95
3 5L 5L N CA 31 32 110.98 132.50 -41.20
4 3960 5L 6T C N 37 39 -121.98 -124.80 18.11 0.69 -63.20 177.71 19.54
4 6T 6T N CA 39 40 125.61 143.50 -42.10
5 3961 6T 7L C N 44 46 -104.79 -108.50 16.12 0.83 -63.50 163.32 20.70
5 7L 7L N CA 46 47 116.81 132.50 -41.20
6 3963 8V 9F C N 59 61 -111.63 -124.20 15.16 0.39 -63.20 -174.44 22.76
6 9F 9F N CA 61 62 134.83 143.30 -44.30
7 3965 10C 11L C N 76 78 -105.84 -108.50 14.92 0.78 -63.50 164.56 20.83
7 11L 11L N CA 78 79 117.82 132.50 -41.20
8 3966 11L 12L C N 84 86 -93.24 -108.50 16.82 0.89 -63.50 -178.31 27.02
8 12L 12L N CA 86 87 139.56 132.50 -41.20
9 3968 13P 14L C N 99 101 -115.20 -108.50 6.91 0.31 -63.50 -177.13 22.99
9 14L 14L N CA 101 102 134.20 132.50 -41.20
10 3969 14L 15A C N 107 109 -145.14 -134.00 11.74 0.53 -62.50 -165.74 36.26
10 15A 15A N CA 109 110 143.30 147.00 -40.90
11 3970 15A 16A C N 112 114 -142.15 -134.00 11.07 0.64 -62.50 -163.53 36.47
11 16A 16A N CA 114 115 139.50 147.00 -40.90
12 3971 16A 17Q C N 117 119 -167.83 -121.10 59.75 1.87 -63.80 176.65 31.14
12 17Q 17Q N CA 119 120 176.93 139.70 -40.30
13 3972 17Q 18G C N 126 128 76.36 78.70 3.90 0.20 82.20 177.82 8.93
13 18G 18G N CA 128 129 -169.22 -166.10 8.50
14 3973 18G 19K C N 130 132 -117.43 -118.00 18.57 0.89 -62.90 170.31 19.86
14 19K 19K N CA 132 133 120.55 139.10 -40.80
15 4008 53E 54S C N 408 410 -136.78 -64.10 79.92 8.48 -64.10 79.92 8.48
15 54S 54S N CA 410 411 -1.76 -35.00 -35.00
16 4088 133C 134R C N 1027 1029 -51.90 -63.00 26.41 3.02 -72.10 154.36 12.30
16 134R 134R N CA 1029 1030 -65.06 -41.10 141.90
17 4089 134R 135G C N 1038 1040 -75.73 -62.40 16.65 2.44 82.20 162.85 12.12
17 135G 135G N CA 1040 1041 -31.22 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 2 9 41 63 109 98 131 166 179 175
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 147
Number of all, selected real atoms : 1143 1143
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 11800 11800
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2346
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 : 839.1613
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 : 1164 0 0 0.006 0.006 11.478 1.000
2 Bond angle potential : 1574 0 5 2.130 2.130 145.14 1.000
3 Stereochemical cosine torsion poten: 737 0 23 47.260 47.260 256.74 1.000
4 Stereochemical improper torsion pot: 464 0 0 1.390 1.390 20.633 1.000
5 Soft-sphere overlap restraints : 2346 0 0 0.001 0.001 0.42081 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) : 2404 0 0 0.114 0.114 36.318 1.000
10 Distance restraints 2 (N-O) : 2562 0 5 0.183 0.183 97.376 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: 146 0 5 5.012 5.012 43.254 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 1 64.039 64.039 18.977 1.000
15 Sidechain Chi_2 dihedral restraints: 85 0 0 73.829 73.829 39.600 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 67.125 67.125 17.362 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 99.734 99.734 13.321 1.000
18 Disulfide distance restraints : 4 0 0 0.009 0.009 0.50650E-01 1.000
19 Disulfide angle restraints : 8 0 0 1.988 1.988 0.69831 1.000
20 Disulfide dihedral angle restraints: 4 0 0 30.148 30.148 3.4783 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) : 1605 0 0 0.350 0.350 37.172 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: 145 18 15 21.543 61.276 47.945 1.000
26 Distance restraints 4 (SDCH-SDCH) : 724 0 0 0.670 0.670 49.196 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: sp|P00705|LYSC1_ANAPL.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: 15201.5635
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3956 1M 2K C N 7 9 -95.84 -118.00 22.25 0.81 -62.90 -179.04 21.91
1 2K 2K N CA 9 10 137.14 139.10 -40.80
2 3957 2K 3A C N 16 18 -72.84 -68.20 9.30 0.60 -62.50 166.06 27.73
2 3A 3A N CA 18 19 153.36 145.30 -40.90
3 3958 3A 4L C N 21 23 -72.89 -70.70 2.31 0.18 -63.50 176.70 25.08
3 4L 4L N CA 23 24 142.35 141.60 -41.20
4 3959 4L 5L C N 29 31 -73.00 -70.70 67.83 5.05 -63.50 109.81 15.81
4 5L 5L N CA 31 32 -150.60 141.60 -41.20
5 3960 5L 6T C N 37 39 -63.50 -78.10 14.63 0.86 -63.20 169.04 21.70
5 6T 6T N CA 39 40 148.86 149.80 -42.10
6 3961 6T 7L C N 44 46 -69.10 -70.70 2.53 0.25 -63.50 175.32 24.67
6 7L 7L N CA 46 47 143.57 141.60 -41.20
7 3963 8V 9F C N 59 61 -76.82 -71.40 23.11 1.70 -63.20 153.14 22.18
7 9F 9F N CA 61 62 163.17 140.70 -44.30
8 3965 10C 11L C N 76 78 -77.14 -70.70 14.52 0.91 -63.50 164.75 23.68
8 11L 11L N CA 78 79 154.62 141.60 -41.20
9 3966 11L 12L C N 84 86 -79.53 -70.70 8.90 0.77 -63.50 176.84 25.50
9 12L 12L N CA 86 87 142.68 141.60 -41.20
10 3967 12L 13P C N 92 94 -51.06 -58.70 14.31 0.85 -64.50 170.74 13.46
10 13P 13P N CA 94 95 -42.59 -30.50 147.20
11 3968 13P 14L C N 99 101 -121.75 -108.50 31.75 1.81 -63.50 156.12 19.27
11 14L 14L N CA 101 102 103.65 132.50 -41.20
12 3969 14L 15A C N 107 109 162.49 -134.00 65.32 1.66 -62.50 -153.05 40.90
12 15A 15A N CA 109 110 162.26 147.00 -40.90
13 3970 15A 16A C N 112 114 -77.74 -68.20 12.80 0.81 -62.50 165.97 27.97
13 16A 16A N CA 114 115 153.83 145.30 -40.90
14 3973 18G 19K C N 130 132 -142.59 -118.00 30.12 1.46 -62.90 -179.00 20.80
14 19K 19K N CA 132 133 121.71 139.10 -40.80
15 4008 53E 54S C N 408 410 -138.15 -64.10 81.99 8.62 -64.10 81.99 8.62
15 54S 54S N CA 410 411 0.21 -35.00 -35.00
16 4074 119D 120G C N 914 916 58.01 82.20 88.76 5.47 -62.40 125.59 20.71
16 120G 120G N CA 916 917 -76.89 8.50 -41.20
17 4088 133C 134R C N 1027 1029 -50.90 -63.00 28.84 3.29 -72.10 152.30 12.16
17 134R 134R N CA 1029 1030 -67.28 -41.10 141.90
18 4089 134R 135G C N 1038 1040 -75.21 -62.40 16.33 2.38 82.20 162.31 12.07
18 135G 135G N CA 1040 1041 -31.07 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 5 12 49 66 113 107 119 153 182 190
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
sp|P00705|LYSC1_ANAPL.B99990001.pdb 742.95264
sp|P00705|LYSC1_ANAPL.B99990002.pdb 839.16125
3/132 residues do not have a CA atom. That's correct; we have three ligands.
Constraint violations are possibly relevant.
import nglview
import ipywidgets
nglview.show_structure_file('sp|P00705|LYSC1_ANAPL.B99990001.pdb')
Comparing to the original structure:
nglview.show_structure_file('1lmp.pdb')
Eh. It could be worse.
But! Ligands are missing.
Let's go rescue them.
To do that, we need to force modeller to read HETATMs (env.io.hetatm = True) and add .-type residues to the sequence. For this, we'll create a separate alignment from the unchanged 1lmp.pdb and a custom sequence, that is, the sequence of P00705.fasta with additional symbols.
alignm2 = modeller.alignment(env)
sequence = "".join(r.code for r in alignm[0].residues) + \
"".join(r.code for r in alignm[1].residues if r.type>20)
alignm2.append_sequence(sequence)
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm2.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm2[0].code = 'ligand_enabled'
alignm2.salign()
alignm2.write(file='all_in_one_2.ali', alignment_format='PIR')
!cat all_in_one_2.ali
SALIGN_____> adding the next group to the alignment; iteration 1 >P1;ligand_enabled sequence::1 : :+150 : :undefined:undefined:-1.00:-1.00 MKALLTLVFCLLPLAAQGKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESGFNTQATNRNTDGSTDYGILQ INSRWWCDNGKTPRSKNACGIPCSVLLRSDITEAVRCAKRIVSDGDGMNAWVAWRNRCRGTDVSKWIRGCRL...* >P1;1lmp structureX:1lmp.pdb: 1 :A:+132 :A:MOL_ID 1; MOLECULE LYSOZYME; CHAIN A; SYNONYM MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC 3.2.1.17:MOL_ID 1; ORGANISM_SCIENTIFIC ONCORHYNCHUS MYKISS; ORGANISM_COMMON RAINBOW TROUT; ORGANISM_TAXID 8022; ORGAN KIDNEY: 2.00: 0.16 ------------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQ INSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*
Aha! That's what was wrong with the first alignment: there were no . residues in the P00705.fasta that could match those in 1lmp, and those residues were matched to a deletion.
s = alignm2[0]
pdb = alignm2[1]
a = modeller.automodel.automodel(
env, alnfile='all_in_one_2.ali',
knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 129 residues out of 132 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C +N
atom indices : 1141 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 10 147
atom names : C CA +N O
atom indices : 1141 1136 0 1142
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: 4
The following 1 residues contain 6-membered rings with poor geometries
after transfer from templates. Rebuilding rings from internal coordinates:
<Residue 52 (type TYR)>
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: 14203 13201
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 : 150
Number of all, selected real atoms : 1186 1186
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13201 13201
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2582
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 : 885.1557
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 : 1164 0 0 0.007 0.007 14.385 1.000
2 Bond angle potential : 1574 0 7 2.186 2.186 152.27 1.000
3 Stereochemical cosine torsion poten: 737 0 24 47.948 47.948 267.36 1.000
4 Stereochemical improper torsion pot: 464 0 1 1.585 1.585 25.472 1.000
5 Soft-sphere overlap restraints : 2582 2 2 0.008 0.008 18.348 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) : 2404 0 0 0.103 0.103 32.120 1.000
10 Distance restraints 2 (N-O) : 2562 0 4 0.179 0.179 97.285 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: 146 0 2 4.340 4.340 32.432 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 2 71.962 71.962 34.028 1.000
15 Sidechain Chi_2 dihedral restraints: 85 0 0 66.220 66.220 32.873 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 93.924 93.924 24.583 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 100.579 100.579 14.921 1.000
18 Disulfide distance restraints : 4 0 0 0.013 0.013 0.11434 1.000
19 Disulfide angle restraints : 8 0 0 2.672 2.672 1.2615 1.000
20 Disulfide dihedral angle restraints: 4 0 0 27.137 27.137 2.6444 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) : 1605 0 0 0.292 0.292 28.188 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: 145 15 12 21.181 60.016 37.114 1.000
26 Distance restraints 4 (SDCH-SDCH) : 724 0 1 0.700 0.700 56.778 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.031 0.031 12.969 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: ligand_enabled.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: 16001.0684
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3956 1M 2K C N 7 9 -75.32 -70.20 8.16 0.49 -62.90 172.90 23.15
1 2K 2K N CA 9 10 146.75 140.40 -40.80
2 3957 2K 3A C N 16 18 -130.18 -134.00 10.22 0.63 -62.50 176.14 32.49
2 3A 3A N CA 18 19 156.48 147.00 -40.90
3 3958 3A 4L C N 21 23 -65.88 -70.70 4.90 0.42 -63.50 178.07 24.86
3 4L 4L N CA 23 24 140.74 141.60 -41.20
4 3959 4L 5L C N 29 31 -72.02 -70.70 21.74 1.70 -63.50 161.33 21.93
4 5L 5L N CA 31 32 119.90 141.60 -41.20
5 3960 5L 6T C N 37 39 -68.03 -78.10 10.58 0.55 -63.20 171.41 22.30
5 6T 6T N CA 39 40 146.56 149.80 -42.10
6 3961 6T 7L C N 44 46 -84.14 -70.70 23.79 2.29 -63.50 164.48 21.74
6 7L 7L N CA 46 47 121.97 141.60 -41.20
7 3963 8V 9F C N 59 61 -101.62 -124.20 34.39 0.96 -63.20 166.17 20.65
7 9F 9F N CA 61 62 117.36 143.30 -44.30
8 3965 10C 11L C N 76 78 -125.19 -108.50 22.54 1.01 -63.50 -178.08 29.08
8 11L 11L N CA 78 79 147.65 132.50 -41.20
9 3968 13P 14L C N 99 101 -109.01 -108.50 29.90 1.62 -63.50 150.83 18.88
9 14L 14L N CA 101 102 102.60 132.50 -41.20
10 3969 14L 15A C N 107 109 -151.68 -134.00 17.82 0.51 -62.50 -168.14 36.21
10 15A 15A N CA 109 110 149.23 147.00 -40.90
11 3970 15A 16A C N 112 114 -139.53 -134.00 8.25 0.26 -62.50 -177.01 34.12
11 16A 16A N CA 114 115 153.11 147.00 -40.90
12 3971 16A 17Q C N 117 119 -108.84 -121.10 12.28 0.48 -63.80 -175.11 29.59
12 17Q 17Q N CA 119 120 140.37 139.70 -40.30
13 3973 18G 19K C N 130 132 -109.91 -118.00 12.73 0.47 -62.90 176.45 20.83
13 19K 19K N CA 132 133 129.27 139.10 -40.80
14 4097 142I 143R C N 1101 1103 28.84 -72.10 129.75 11.24 -72.10 129.75 11.24
14 143R 143R N CA 1103 1104 -136.58 141.90 141.90
15 4098 143R 144G C N 1112 1114 -60.07 -62.40 31.08 4.76 82.20 143.49 10.25
15 144G 144G N CA 1114 1115 -10.21 -41.20 8.50
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 5 16 45 89 127 124 133 166 203 196
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_484W> Dihedral still outside +-90: -90.5716
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 : 150
Number of all, selected real atoms : 1186 1186
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13201 13201
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2544
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 : 915.6344
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 : 1164 0 0 0.007 0.007 13.967 1.000
2 Bond angle potential : 1574 0 6 2.132 2.132 145.19 1.000
3 Stereochemical cosine torsion poten: 737 0 30 48.409 48.409 273.16 1.000
4 Stereochemical improper torsion pot: 464 0 0 1.362 1.362 20.206 1.000
5 Soft-sphere overlap restraints : 2544 2 2 0.008 0.008 17.572 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) : 2404 0 0 0.097 0.097 28.254 1.000
10 Distance restraints 2 (N-O) : 2562 0 8 0.188 0.188 105.38 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 146 0 2 4.169 4.169 29.929 1.000
14 Sidechain Chi_1 dihedral restraints: 120 0 0 66.229 66.229 25.803 1.000
15 Sidechain Chi_2 dihedral restraints: 85 0 0 77.324 77.324 39.292 1.000
16 Sidechain Chi_3 dihedral restraints: 33 0 0 94.950 94.950 20.602 1.000
17 Sidechain Chi_4 dihedral restraints: 21 0 0 112.566 112.566 14.129 1.000
18 Disulfide distance restraints : 4 0 0 0.014 0.014 0.13333 1.000
19 Disulfide angle restraints : 8 0 0 3.258 3.258 1.8753 1.000
20 Disulfide dihedral angle restraints: 4 0 0 22.580 22.580 2.0468 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) : 1605 0 0 0.417 0.417 45.352 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: 145 19 16 26.542 64.204 53.461 1.000
26 Distance restraints 4 (SDCH-SDCH) : 724 0 2 0.782 0.782 67.710 1.000
27 Distance restraints 5 (X-Y) : 1401 0 0 0.028 0.028 11.575 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: ligand_enabled.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: 16481.4590
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 3956 1M 2K C N 7 9 -65.79 -70.20 5.06 0.31 -62.90 178.74 23.05
1 2K 2K N CA 9 10 137.92 140.40 -40.80
2 3957 2K 3A C N 16 18 -121.08 -134.00 13.18 0.35 -62.50 -175.71 33.33
2 3A 3A N CA 18 19 144.38 147.00 -40.90
3 3958 3A 4L C N 21 23 -86.76 -108.50 24.06 1.06 -63.50 165.04 21.69
3 4L 4L N CA 23 24 122.19 132.50 -41.20
4 3959 4L 5L C N 29 31 -130.03 -108.50 42.11 2.00 -63.50 164.19 26.92
4 5L 5L N CA 31 32 168.69 132.50 -41.20
5 3960 5L 6T C N 37 39 -77.38 -78.10 1.66 0.10 -63.20 167.20 22.38
5 6T 6T N CA 39 40 151.30 149.80 -42.10
6 3961 6T 7L C N 44 46 -68.86 -70.70 9.60 0.66 -63.50 173.46 23.78
6 7L 7L N CA 46 47 132.18 141.60 -41.20
7 3963 8V 9F C N 59 61 -115.39 -124.20 27.10 1.03 -63.20 170.18 20.47
7 9F 9F N CA 61 62 117.68 143.30 -44.30
8 3965 10C 11L C N 76 78 -128.81 -108.50 30.89 1.41 -63.50 175.61 28.43
8 11L 11L N CA 78 79 155.78 132.50 -41.20
9 3966 11L 12L C N 84 86 -116.40 -108.50 44.66 2.49 -63.50 140.12 17.29
9 12L 12L N CA 86 87 88.55 132.50 -41.20
10 3967 12L 13P C N 92 94 -74.68 -58.70 23.10 1.59 -64.50 161.35 12.58
10 13P 13P N CA 94 95 -13.83 -30.50 147.20
11 3968 13P 14L C N 99 101 83.05 -70.70 162.74 12.80 -63.50 -164.48 35.54
11 14L 14L N CA 101 102 88.23 141.60 -41.20
12 3969 14L 15A C N 107 109 171.70 -134.00 54.42 1.67 -62.50 -149.69 41.07
12 15A 15A N CA 109 110 150.56 147.00 -40.90
13 3970 15A 16A C N 112 114 -168.78 -134.00 39.28 0.90 -62.50 -173.00 36.26
13 16A 16A N CA 114 115 165.24 147.00 -40.90
14 3971 16A 17Q C N 117 119 -76.69 -73.00 3.71 0.27 -63.80 179.82 27.12
14 17Q 17Q N CA 119 120 140.35 140.70 -40.30
15 3972 17Q 18G C N 126 128 155.03 -167.20 38.04 0.84 82.20 177.24 11.96
15 18G 18G N CA 128 129 170.09 174.60 8.50
16 3973 18G 19K C N 130 132 -136.11 -118.00 25.80 0.91 -62.90 177.52 27.44
16 19K 19K N CA 132 133 157.48 139.10 -40.80
17 4008 53E 54S C N 408 410 -136.91 -64.10 80.86 8.47 -64.10 80.86 8.47
17 54S 54S N CA 410 411 0.18 -35.00 -35.00
18 4042 87T 88P C N 676 678 -44.21 -58.70 64.14 4.24 -64.50 121.53 10.17
18 88P 88P N CA 678 679 -92.98 -30.50 147.20
19 4043 88P 89R C N 683 685 -99.17 -125.20 66.26 2.54 57.30 161.92 16.64
19 89R 89R N CA 685 686 79.67 140.60 38.00
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 1 4 12 43 87 117 112 133 200 191 210
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf
----------------------------------------
ligand_enabled.B99990001.pdb 885.15570
ligand_enabled.B99990002.pdb 915.63440
nglview.show_structure_file('ligand_enabled.B99990001.pdb')
Not bad!