Revision 491b9a4d
| example/modeller_cox3.md | ||
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```python |
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import sys |
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sys.path.append('/usr/lib/modeller9.12/modlib/')
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sys.path.append('/usr/lib/modeller9.12/lib/x86_64-intel8/python2.5/')
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import modeller |
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import _modeller |
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import modeller.automodel |
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#impo modeller.automodel import * |
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``` |
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```python |
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env=modeller.environ() |
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env.io.hetatm=False #True |
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``` |
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```python |
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cd /home/domain/anur/work/cox3 |
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``` |
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/home/domain/anur/work/cox3 |
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```python |
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alignm=modeller.alignment(env) |
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alignm.append(file='COX3.fasta', align_codes='all',alignment_format='FASTA') |
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mdl1 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'C', 'LAST:'+'C'))
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mdl2 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'P', 'LAST:'+'P'))
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alignm.append_model(mdl1, atom_files='1v55.pdb', align_codes='1v55_C') |
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alignm.append_model(mdl2, atom_files='1v55.pdb', align_codes='1v55_P') |
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``` |
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```python |
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alignm.salign() |
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s= alignm[0] |
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for i in range(len(alignm)): |
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print "%s identical to wt in %4.1f perc" %(alignm[i].code,s.get_sequence_identity(alignm[i])) |
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aln.write(file='all_in_one.ali', alignment_format='PIR') |
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``` |
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SALIGN_____> adding the next group to the alignment; iteration 1 |
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SALIGN_____> adding the next group to the alignment; iteration 2 |
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SALIGN_____> adding the next group to the alignment; iteration 3 |
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SALIGN_____> adding the next group to the alignment; iteration 4 |
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SALIGN_____> adding the next group to the alignment; iteration 5 |
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SALIGN_____> adding the next group to the alignment; iteration 6 |
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SALIGN_____> adding the next group to the alignment; iteration 7 |
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SALIGN_____> adding the next group to the alignment; iteration 8 |
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SALIGN_____> adding the next group to the alignment; iteration 9 |
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SALIGN_____> adding the next group to the alignment; iteration 10 |
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SALIGN_____> adding the next group to the alignment; iteration 11 |
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9913 identical to wt in 100.0 perc |
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9606_V identical to wt in 87.7 perc |
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9606_A identical to wt in 87.4 perc |
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9606_I identical to wt in 87.4 perc |
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9606_F identical to wt in 87.4 perc |
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9606_S identical to wt in 87.4 perc |
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9606_L identical to wt in 87.4 perc |
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9606_M identical to wt in 87.4 perc |
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9606_E identical to wt in 87.4 perc |
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9606_T identical to wt in 87.4 perc |
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1v55_C identical to wt in 100.0 perc |
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1v55_P identical to wt in 100.0 perc |
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```python |
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for s in aln[:-2]: |
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print s.code |
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a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= ('1v55_C','1v55_P'), sequence = s.code )
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a.name='mod'+s.code |
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a.starting_model = 1 |
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a.ending_model = 1 |
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a.make() |
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``` |
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9913 |
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automodel__W> Topology and/or parameter libraries already in memory. These will |
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be used instead of the automodel defaults. If this is not what you |
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want, clear them before creating the automodel object with |
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env.libs.topology.clear() and env.libs.parameters.clear() |
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check_ali___> Checking pairwise structural superpositions. |
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Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
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ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
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---------------------------------------------------- |
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END OF TABLE |
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check_ali___> Checking the sequence-structure alignment. |
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Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
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ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
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---------------------------------------------- |
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END OF TABLE |
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getf_______W> RTF restraint not found in the atoms list: |
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residue type, indices: 16 261 |
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atom names : C +N |
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atom indices : 2123 0 |
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getf_______W> RTF restraint not found in the atoms list: |
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residue type, indices: 16 261 |
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atom names : C CA +N O |
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atom indices : 2123 2120 0 2124 |
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mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
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least one known structure available. MDT, not library, potential is used. |
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0 atoms in HETATM/BLK residues constrained |
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to protein atoms within 2.30 angstroms |
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and protein CA atoms within 10.00 angstroms |
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0 atoms in residues without defined topology |
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constrained to be rigid bodies |
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condens_443_> Restraints marked for deletion were removed. |
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Total number of restraints before, now: 26595 24757 |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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>> ENERGY; Differences between the model's features and restraints: |
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Number of all residues in MODEL : 261 |
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Number of all, selected real atoms : 2125 2125 |
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Number of all, selected pseudo atoms : 0 0 |
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Number of all static, selected restraints : 24757 24757 |
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COVALENT_CYS : F |
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NONBONDED_SEL_ATOMS : 1 |
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Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4695 |
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Dynamic pairs routine : 2, NATM x NATM cell sorting |
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Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
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LENNARD_JONES_SWITCH : 6.500 7.500 |
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COULOMB_JONES_SWITCH : 6.500 7.500 |
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RESIDUE_SPAN_RANGE : 0 99999 |
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NLOGN_USE : 15 |
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CONTACT_SHELL : 4.000 |
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DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
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SPHERE_STDV : 0.050 |
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RADII_FACTOR : 0.820 |
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Current energy : 7158.1758 |
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Summary of the restraint violations: |
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NUM ... number of restraints. |
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NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
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RVIOL ... relative difference from the best value. |
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NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
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RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
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RMS_2 ... RMS(feature, best_value, NUMB). |
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MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
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# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
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------------------------------------------------------------------------------------------------------ |
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1 Bond length potential : 2212 0 0 0.004 0.004 11.948 1.000 |
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2 Bond angle potential : 3027 0 2 1.873 1.873 208.11 1.000 |
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3 Stereochemical cosine torsion poten: 1709 0 19 38.273 38.273 369.73 1.000 |
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4 Stereochemical improper torsion pot: 1048 0 1 1.125 1.125 25.935 1.000 |
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5 Soft-sphere overlap restraints : 4695 0 0 0.001 0.001 0.43761 1.000 |
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6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
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8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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9 Distance restraints 1 (CA-CA) : 4433 0 2 0.120 0.120 586.51 1.000 |
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10 Distance restraints 2 (N-O) : 4608 0 0 0.133 0.133 869.96 1.000 |
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11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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13 Mainchain Omega dihedral restraints: 260 0 2 3.409 3.409 34.801 1.000 |
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14 Sidechain Chi_1 dihedral restraints: 226 0 1 46.061 46.061 13.243 1.000 |
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15 Sidechain Chi_2 dihedral restraints: 165 0 2 63.301 63.301 33.559 1.000 |
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16 Sidechain Chi_3 dihedral restraints: 46 0 0 69.837 69.837 26.999 1.000 |
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17 Sidechain Chi_4 dihedral restraints: 8 0 0 125.128 125.128 7.1805 1.000 |
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18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
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21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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23 Distance restraints 3 (SDCH-MNCH) : 4161 0 0 0.334 0.334 2942.5 1.000 |
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24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
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25 Phi/Psi pair of dihedral restraints: 259 3 9 15.024 19.220 -172.15 1.000 |
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26 Distance restraints 4 (SDCH-SDCH) : 2595 0 12 0.772 0.772 2199.4 1.000 |
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27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
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36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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# Heavy relative violation of each residue is written to: 9913.V99990001 |
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# The profile is NOT normalized by the number of restraints. |
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# The profiles are smoothed over a window of residues: 1 |
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# The sum of all numbers in the file: 18744.2441 |
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List of the violated restraints: |
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A restraint is violated when the relative difference |
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from the best value (RVIOL) is larger than CUTOFF. |
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ICSR ... index of a restraint in the current set. |
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RESNO ... residue numbers of the first two atoms. |
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ATM ... IUPAC atom names of the first two atoms. |
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FEAT ... the value of the feature in the model. |
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restr ... the mean of the basis restraint with the smallest |
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difference from the model (local minimum). |
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viol ... difference from the local minimum. |
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rviol ... relative difference from the local minimum. |
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RESTR ... the best value (global minimum). |
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VIOL ... difference from the best value. |
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RVIOL ... relative difference from the best value. |
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------------------------------------------------------------------------------------------------- |
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Feature 25 : Phi/Psi pair of dihedral restraints |
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List of the RVIOL violations larger than : 6.5000 |
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# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
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1 7997 1M 2T C N 7 9 -90.07 -78.10 21.48 0.71 -63.20 152.65 21.37 |
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1 2T 2T N CA 9 10 167.63 149.80 -42.10 |
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2 8123 127L 128E C N 1023 1025 -85.08 -63.60 83.66 12.37 -69.30 97.63 6.89 |
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2 128E 128E N CA 1025 1026 -121.16 -40.30 142.50 |
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3 8227 231H 232H C N 1849 1851 -111.37 -63.20 75.39 8.23 -63.20 75.39 8.23 |
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3 232H 232H N CA 1851 1852 15.69 -42.30 -42.30 |
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report______> Distribution of short non-bonded contacts: |
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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 |
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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 |
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FREQUENCY: 0 0 0 0 0 7 11 61 168 215 199 279 378 411 383 |
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<< end of ENERGY. |
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>> Summary of successfully produced models: |
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Filename molpdf |
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---------------------------------------- |
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9913.B99990001.pdb 7158.17578 |
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9606_V |
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automodel__W> Topology and/or parameter libraries already in memory. These will |
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be used instead of the automodel defaults. If this is not what you |
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want, clear them before creating the automodel object with |
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env.libs.topology.clear() and env.libs.parameters.clear() |
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check_ali___> Checking pairwise structural superpositions. |
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Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
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ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
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---------------------------------------------------- |
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END OF TABLE |
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check_ali___> Checking the sequence-structure alignment. |
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Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
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ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
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---------------------------------------------- |
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END OF TABLE |
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getf_______W> RTF restraint not found in the atoms list: |
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residue type, indices: 16 261 |
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atom names : C +N |
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atom indices : 2125 0 |
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getf_______W> RTF restraint not found in the atoms list: |
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residue type, indices: 16 261 |
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atom names : C CA +N O |
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atom indices : 2125 2122 0 2126 |
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mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
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least one known structure available. MDT, not library, potential is used. |
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0 atoms in HETATM/BLK residues constrained |
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to protein atoms within 2.30 angstroms |
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and protein CA atoms within 10.00 angstroms |
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0 atoms in residues without defined topology |
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constrained to be rigid bodies |
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condens_443_> Restraints marked for deletion were removed. |
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Total number of restraints before, now: 26187 24337 |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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>> ENERGY; Differences between the model's features and restraints: |
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Number of all residues in MODEL : 261 |
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Number of all, selected real atoms : 2127 2127 |
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Number of all, selected pseudo atoms : 0 0 |
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Number of all static, selected restraints : 24337 24337 |
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COVALENT_CYS : F |
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NONBONDED_SEL_ATOMS : 1 |
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Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4811 |
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Dynamic pairs routine : 2, NATM x NATM cell sorting |
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Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
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LENNARD_JONES_SWITCH : 6.500 7.500 |
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COULOMB_JONES_SWITCH : 6.500 7.500 |
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RESIDUE_SPAN_RANGE : 0 99999 |
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NLOGN_USE : 15 |
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CONTACT_SHELL : 4.000 |
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DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
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SPHERE_STDV : 0.050 |
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RADII_FACTOR : 0.820 |
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Current energy : 6565.6021 |
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Summary of the restraint violations: |
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NUM ... number of restraints. |
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NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
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RVIOL ... relative difference from the best value. |
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NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
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RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
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RMS_2 ... RMS(feature, best_value, NUMB). |
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MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 360 |
|
|
| 361 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 362 |
------------------------------------------------------------------------------------------------------ |
|
| 363 |
1 Bond length potential : 2214 0 0 0.004 0.004 10.728 1.000 |
|
| 364 |
2 Bond angle potential : 3030 0 2 1.780 1.780 190.34 1.000 |
|
| 365 |
3 Stereochemical cosine torsion poten: 1707 0 16 38.781 38.781 372.96 1.000 |
|
| 366 |
4 Stereochemical improper torsion pot: 1045 0 0 1.058 1.058 23.385 1.000 |
|
| 367 |
5 Soft-sphere overlap restraints : 4811 0 0 0.001 0.001 1.0434 1.000 |
|
| 368 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 369 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 370 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 371 |
9 Distance restraints 1 (CA-CA) : 4433 0 0 0.094 0.094 588.07 1.000 |
|
| 372 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.117 0.117 689.60 1.000 |
|
| 373 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 374 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 375 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.209 3.209 30.726 1.000 |
|
| 376 |
14 Sidechain Chi_1 dihedral restraints: 227 0 1 54.523 54.523 23.232 1.000 |
|
| 377 |
15 Sidechain Chi_2 dihedral restraints: 168 0 1 61.214 61.214 40.466 1.000 |
|
| 378 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 58.055 58.055 24.592 1.000 |
|
| 379 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 120.815 120.815 4.9296 1.000 |
|
| 380 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 381 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 382 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 383 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 384 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 385 |
23 Distance restraints 3 (SDCH-MNCH) : 3900 0 0 0.332 0.332 2735.1 1.000 |
|
| 386 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 387 |
25 Phi/Psi pair of dihedral restraints: 259 3 10 14.794 19.369 -174.12 1.000 |
|
| 388 |
26 Distance restraints 4 (SDCH-SDCH) : 2430 0 11 0.714 0.714 2004.5 1.000 |
|
| 389 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 390 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 391 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 392 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 393 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 394 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 395 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 396 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 397 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 398 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 399 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 400 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 401 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 402 |
|
|
| 403 |
|
|
| 404 |
|
|
| 405 |
# Heavy relative violation of each residue is written to: 9606_V.V99990001 |
|
| 406 |
# The profile is NOT normalized by the number of restraints. |
|
| 407 |
# The profiles are smoothed over a window of residues: 1 |
|
| 408 |
# The sum of all numbers in the file: 18410.9668 |
|
| 409 |
|
|
| 410 |
|
|
| 411 |
|
|
| 412 |
List of the violated restraints: |
|
| 413 |
A restraint is violated when the relative difference |
|
| 414 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 415 |
|
|
| 416 |
ICSR ... index of a restraint in the current set. |
|
| 417 |
RESNO ... residue numbers of the first two atoms. |
|
| 418 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 419 |
FEAT ... the value of the feature in the model. |
|
| 420 |
restr ... the mean of the basis restraint with the smallest |
|
| 421 |
difference from the model (local minimum). |
|
| 422 |
viol ... difference from the local minimum. |
|
| 423 |
rviol ... relative difference from the local minimum. |
|
| 424 |
RESTR ... the best value (global minimum). |
|
| 425 |
VIOL ... difference from the best value. |
|
| 426 |
RVIOL ... relative difference from the best value. |
|
| 427 |
|
|
| 428 |
|
|
| 429 |
------------------------------------------------------------------------------------------------- |
|
| 430 |
|
|
| 431 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 432 |
List of the RVIOL violations larger than : 6.5000 |
|
| 433 |
|
|
| 434 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 435 |
1 7997 1M 2T C N 7 9 -73.89 -78.10 5.52 0.36 -63.20 164.87 21.85 |
|
| 436 |
1 2T 2T N CA 9 10 153.38 149.80 -42.10 |
|
| 437 |
2 8123 127L 128E C N 1026 1028 -86.32 -63.60 82.64 12.30 -69.30 99.21 6.96 |
|
| 438 |
2 128E 128E N CA 1028 1029 -119.76 -40.30 142.50 |
|
| 439 |
3 8227 231H 232H C N 1851 1853 -113.42 -63.20 79.87 8.68 -63.20 79.87 8.68 |
|
| 440 |
3 232H 232H N CA 1853 1854 19.80 -42.30 -42.30 |
|
| 441 |
|
|
| 442 |
|
|
| 443 |
report______> Distribution of short non-bonded contacts: |
|
| 444 |
|
|
| 445 |
|
|
| 446 |
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 |
|
| 447 |
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 |
|
| 448 |
FREQUENCY: 0 0 0 0 0 9 17 72 217 228 179 284 367 429 353 |
|
| 449 |
|
|
| 450 |
|
|
| 451 |
<< end of ENERGY. |
|
| 452 |
|
|
| 453 |
>> Summary of successfully produced models: |
|
| 454 |
Filename molpdf |
|
| 455 |
---------------------------------------- |
|
| 456 |
9606_V.B99990001.pdb 6565.60205 |
|
| 457 |
|
|
| 458 |
9606_A |
|
| 459 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 460 |
be used instead of the automodel defaults. If this is not what you |
|
| 461 |
want, clear them before creating the automodel object with |
|
| 462 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 463 |
|
|
| 464 |
|
|
| 465 |
check_ali___> Checking pairwise structural superpositions. |
|
| 466 |
|
|
| 467 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 468 |
|
|
| 469 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 470 |
---------------------------------------------------- |
|
| 471 |
END OF TABLE |
|
| 472 |
|
|
| 473 |
check_ali___> Checking the sequence-structure alignment. |
|
| 474 |
|
|
| 475 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 476 |
|
|
| 477 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 478 |
---------------------------------------------- |
|
| 479 |
END OF TABLE |
|
| 480 |
|
|
| 481 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 482 |
residue type, indices: 16 261 |
|
| 483 |
atom names : C +N |
|
| 484 |
atom indices : 2123 0 |
|
| 485 |
|
|
| 486 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 487 |
residue type, indices: 16 261 |
|
| 488 |
atom names : C CA +N O |
|
| 489 |
atom indices : 2123 2120 0 2124 |
|
| 490 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 491 |
least one known structure available. MDT, not library, potential is used. |
|
| 492 |
0 atoms in HETATM/BLK residues constrained |
|
| 493 |
to protein atoms within 2.30 angstroms |
|
| 494 |
and protein CA atoms within 10.00 angstroms |
|
| 495 |
0 atoms in residues without defined topology |
|
| 496 |
constrained to be rigid bodies |
|
| 497 |
condens_443_> Restraints marked for deletion were removed. |
|
| 498 |
Total number of restraints before, now: 26163 24314 |
|
| 499 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 500 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 501 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 502 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 503 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 504 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 505 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 506 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 507 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 508 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 509 |
iupac_m_484W> Dihedral still outside +-90: 90.0977 |
|
| 510 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 511 |
|
|
| 512 |
|
|
| 513 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 514 |
Number of all residues in MODEL : 261 |
|
| 515 |
Number of all, selected real atoms : 2125 2125 |
|
| 516 |
Number of all, selected pseudo atoms : 0 0 |
|
| 517 |
Number of all static, selected restraints : 24314 24314 |
|
| 518 |
COVALENT_CYS : F |
|
| 519 |
NONBONDED_SEL_ATOMS : 1 |
|
| 520 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4761 |
|
| 521 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 522 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 523 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 524 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 525 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 526 |
NLOGN_USE : 15 |
|
| 527 |
CONTACT_SHELL : 4.000 |
|
| 528 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 529 |
SPHERE_STDV : 0.050 |
|
| 530 |
RADII_FACTOR : 0.820 |
|
| 531 |
Current energy : 6569.2383 |
|
| 532 |
|
|
| 533 |
|
|
| 534 |
|
|
| 535 |
|
|
| 536 |
|
|
| 537 |
Summary of the restraint violations: |
|
| 538 |
|
|
| 539 |
NUM ... number of restraints. |
|
| 540 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 541 |
RVIOL ... relative difference from the best value. |
|
| 542 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 543 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 544 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 545 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 546 |
|
|
| 547 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 548 |
------------------------------------------------------------------------------------------------------ |
|
| 549 |
1 Bond length potential : 2212 0 0 0.004 0.004 11.764 1.000 |
|
| 550 |
2 Bond angle potential : 3027 0 3 1.803 1.803 193.50 1.000 |
|
| 551 |
3 Stereochemical cosine torsion poten: 1704 0 17 38.650 38.650 371.69 1.000 |
|
| 552 |
4 Stereochemical improper torsion pot: 1044 0 0 1.071 1.071 24.081 1.000 |
|
| 553 |
5 Soft-sphere overlap restraints : 4761 0 0 0.001 0.001 0.95893 1.000 |
|
| 554 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 555 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 556 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 557 |
9 Distance restraints 1 (CA-CA) : 4433 0 0 0.094 0.094 588.59 1.000 |
|
| 558 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.118 0.118 687.22 1.000 |
|
| 559 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 560 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 561 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.305 3.305 32.628 1.000 |
|
| 562 |
14 Sidechain Chi_1 dihedral restraints: 226 0 0 51.035 51.035 11.649 1.000 |
|
| 563 |
15 Sidechain Chi_2 dihedral restraints: 168 0 1 60.161 60.161 31.284 1.000 |
|
| 564 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 48.215 48.215 25.921 1.000 |
|
| 565 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 71.145 71.145 6.3579 1.000 |
|
| 566 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 567 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 568 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 569 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 570 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 571 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.350 0.350 2733.9 1.000 |
|
| 572 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 573 |
25 Phi/Psi pair of dihedral restraints: 259 3 8 14.878 19.641 -174.12 1.000 |
|
| 574 |
26 Distance restraints 4 (SDCH-SDCH) : 2426 0 7 0.754 0.754 2023.8 1.000 |
|
| 575 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 576 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 577 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 578 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 579 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 580 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 581 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 582 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 583 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 584 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 585 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 586 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 587 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 588 |
|
|
| 589 |
|
|
| 590 |
|
|
| 591 |
# Heavy relative violation of each residue is written to: 9606_A.V99990001 |
|
| 592 |
# The profile is NOT normalized by the number of restraints. |
|
| 593 |
# The profiles are smoothed over a window of residues: 1 |
|
| 594 |
# The sum of all numbers in the file: 17983.2812 |
|
| 595 |
|
|
| 596 |
|
|
| 597 |
|
|
| 598 |
List of the violated restraints: |
|
| 599 |
A restraint is violated when the relative difference |
|
| 600 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 601 |
|
|
| 602 |
ICSR ... index of a restraint in the current set. |
|
| 603 |
RESNO ... residue numbers of the first two atoms. |
|
| 604 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 605 |
FEAT ... the value of the feature in the model. |
|
| 606 |
restr ... the mean of the basis restraint with the smallest |
|
| 607 |
difference from the model (local minimum). |
|
| 608 |
viol ... difference from the local minimum. |
|
| 609 |
rviol ... relative difference from the local minimum. |
|
| 610 |
RESTR ... the best value (global minimum). |
|
| 611 |
VIOL ... difference from the best value. |
|
| 612 |
RVIOL ... relative difference from the best value. |
|
| 613 |
|
|
| 614 |
|
|
| 615 |
------------------------------------------------------------------------------------------------- |
|
| 616 |
|
|
| 617 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 618 |
List of the RVIOL violations larger than : 6.5000 |
|
| 619 |
|
|
| 620 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 621 |
1 7988 1M 2T C N 7 9 -133.19 -124.80 17.39 0.55 -63.20 173.88 26.89 |
|
| 622 |
1 2T 2T N CA 9 10 158.73 143.50 -42.10 |
|
| 623 |
2 8114 127L 128E C N 1024 1026 -86.72 -63.60 84.50 12.57 -69.30 97.50 6.82 |
|
| 624 |
2 128E 128E N CA 1026 1027 -121.57 -40.30 142.50 |
|
| 625 |
3 8218 231H 232H C N 1849 1851 -114.73 -63.20 81.73 8.89 -63.20 81.73 8.89 |
|
| 626 |
3 232H 232H N CA 1851 1852 21.13 -42.30 -42.30 |
|
| 627 |
|
|
| 628 |
|
|
| 629 |
report______> Distribution of short non-bonded contacts: |
|
| 630 |
|
|
| 631 |
|
|
| 632 |
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 |
|
| 633 |
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 |
|
| 634 |
FREQUENCY: 0 0 0 0 0 8 13 55 183 249 221 279 367 400 354 |
|
| 635 |
|
|
| 636 |
|
|
| 637 |
<< end of ENERGY. |
|
| 638 |
|
|
| 639 |
>> Summary of successfully produced models: |
|
| 640 |
Filename molpdf |
|
| 641 |
---------------------------------------- |
|
| 642 |
9606_A.B99990001.pdb 6569.23828 |
|
| 643 |
|
|
| 644 |
9606_I |
|
| 645 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 646 |
be used instead of the automodel defaults. If this is not what you |
|
| 647 |
want, clear them before creating the automodel object with |
|
| 648 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 649 |
|
|
| 650 |
|
|
| 651 |
check_ali___> Checking pairwise structural superpositions. |
|
| 652 |
|
|
| 653 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 654 |
|
|
| 655 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 656 |
---------------------------------------------------- |
|
| 657 |
END OF TABLE |
|
| 658 |
|
|
| 659 |
check_ali___> Checking the sequence-structure alignment. |
|
| 660 |
|
|
| 661 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 662 |
|
|
| 663 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 664 |
---------------------------------------------- |
|
| 665 |
END OF TABLE |
|
| 666 |
|
|
| 667 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 668 |
residue type, indices: 16 261 |
|
| 669 |
atom names : C +N |
|
| 670 |
atom indices : 2126 0 |
|
| 671 |
|
|
| 672 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 673 |
residue type, indices: 16 261 |
|
| 674 |
atom names : C CA +N O |
|
| 675 |
atom indices : 2126 2123 0 2127 |
|
| 676 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 677 |
least one known structure available. MDT, not library, potential is used. |
|
| 678 |
0 atoms in HETATM/BLK residues constrained |
|
| 679 |
to protein atoms within 2.30 angstroms |
|
| 680 |
and protein CA atoms within 10.00 angstroms |
|
| 681 |
0 atoms in residues without defined topology |
|
| 682 |
constrained to be rigid bodies |
|
| 683 |
condens_443_> Restraints marked for deletion were removed. |
|
| 684 |
Total number of restraints before, now: 26179 24328 |
|
| 685 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 686 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 687 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 688 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 689 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 690 |
|
|
| 691 |
|
|
| 692 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 693 |
Number of all residues in MODEL : 261 |
|
| 694 |
Number of all, selected real atoms : 2128 2128 |
|
| 695 |
Number of all, selected pseudo atoms : 0 0 |
|
| 696 |
Number of all static, selected restraints : 24328 24328 |
|
| 697 |
COVALENT_CYS : F |
|
| 698 |
NONBONDED_SEL_ATOMS : 1 |
|
| 699 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4871 |
|
| 700 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 701 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 702 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 703 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 704 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 705 |
NLOGN_USE : 15 |
|
| 706 |
CONTACT_SHELL : 4.000 |
|
| 707 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 708 |
SPHERE_STDV : 0.050 |
|
| 709 |
RADII_FACTOR : 0.820 |
|
| 710 |
Current energy : 6929.7739 |
|
| 711 |
|
|
| 712 |
|
|
| 713 |
|
|
| 714 |
|
|
| 715 |
|
|
| 716 |
Summary of the restraint violations: |
|
| 717 |
|
|
| 718 |
NUM ... number of restraints. |
|
| 719 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 720 |
RVIOL ... relative difference from the best value. |
|
| 721 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 722 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 723 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 724 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 725 |
|
|
| 726 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 727 |
------------------------------------------------------------------------------------------------------ |
|
| 728 |
1 Bond length potential : 2215 0 1 0.006 0.006 18.748 1.000 |
|
| 729 |
2 Bond angle potential : 3031 7 9 3.444 3.444 511.68 1.000 |
|
| 730 |
3 Stereochemical cosine torsion poten: 1708 0 16 38.513 38.513 368.84 1.000 |
|
| 731 |
4 Stereochemical improper torsion pot: 1045 0 0 1.028 1.028 21.971 1.000 |
|
| 732 |
5 Soft-sphere overlap restraints : 4871 1 1 0.004 0.004 11.126 1.000 |
|
| 733 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 734 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 735 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 736 |
9 Distance restraints 1 (CA-CA) : 4433 0 0 0.095 0.095 588.96 1.000 |
|
| 737 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.119 0.119 684.27 1.000 |
|
| 738 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 739 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 740 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.259 3.259 31.709 1.000 |
|
| 741 |
14 Sidechain Chi_1 dihedral restraints: 227 0 0 53.884 53.884 19.977 1.000 |
|
| 742 |
15 Sidechain Chi_2 dihedral restraints: 169 0 2 65.492 65.492 43.653 1.000 |
|
| 743 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 64.926 64.926 28.202 1.000 |
|
| 744 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 80.914 80.914 5.9267 1.000 |
|
| 745 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 746 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 747 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 748 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 749 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 750 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.340 0.340 2729.0 1.000 |
|
| 751 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 752 |
25 Phi/Psi pair of dihedral restraints: 259 3 9 15.002 18.434 -174.51 1.000 |
|
| 753 |
26 Distance restraints 4 (SDCH-SDCH) : 2426 0 14 0.785 0.785 2040.2 1.000 |
|
| 754 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 755 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 756 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 757 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 758 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 759 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 760 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 761 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 762 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 763 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 764 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 765 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 766 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 767 |
|
|
| 768 |
|
|
| 769 |
|
|
| 770 |
# Heavy relative violation of each residue is written to: 9606_I.V99990001 |
|
| 771 |
# The profile is NOT normalized by the number of restraints. |
|
| 772 |
# The profiles are smoothed over a window of residues: 1 |
|
| 773 |
# The sum of all numbers in the file: 18748.8809 |
|
| 774 |
|
|
| 775 |
|
|
| 776 |
|
|
| 777 |
List of the violated restraints: |
|
| 778 |
A restraint is violated when the relative difference |
|
| 779 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 780 |
|
|
| 781 |
ICSR ... index of a restraint in the current set. |
|
| 782 |
RESNO ... residue numbers of the first two atoms. |
|
| 783 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 784 |
FEAT ... the value of the feature in the model. |
|
| 785 |
restr ... the mean of the basis restraint with the smallest |
|
| 786 |
difference from the model (local minimum). |
|
| 787 |
viol ... difference from the local minimum. |
|
| 788 |
rviol ... relative difference from the local minimum. |
|
| 789 |
RESTR ... the best value (global minimum). |
|
| 790 |
VIOL ... difference from the best value. |
|
| 791 |
RVIOL ... relative difference from the best value. |
|
| 792 |
|
|
| 793 |
|
|
| 794 |
------------------------------------------------------------------------------------------------- |
|
| 795 |
|
|
| 796 |
Feature 2 : Bond angle potential |
|
| 797 |
List of the RVIOL violations larger than : 4.5000 |
|
| 798 |
|
|
| 799 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 800 |
1 5103 251F 251F CB CG 2028 2029 152.26 122.30 29.96 6.51 122.30 29.96 6.51 |
|
| 801 |
|
|
| 802 |
------------------------------------------------------------------------------------------------- |
|
| 803 |
|
|
| 804 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 805 |
List of the RVIOL violations larger than : 6.5000 |
|
| 806 |
|
|
| 807 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 808 |
1 8000 1M 2T C N 7 9 -78.13 -78.10 12.53 0.53 -63.20 156.29 21.03 |
|
| 809 |
1 2T 2T N CA 9 10 162.32 149.80 -42.10 |
|
| 810 |
2 8126 127L 128E C N 1027 1029 -80.62 -63.60 87.36 12.61 -69.30 92.21 6.63 |
|
| 811 |
2 128E 128E N CA 1029 1030 -125.99 -40.30 142.50 |
|
| 812 |
3 8230 231H 232H C N 1852 1854 -114.01 -63.20 79.74 8.70 -63.20 79.74 8.70 |
|
| 813 |
3 232H 232H N CA 1854 1855 19.15 -42.30 -42.30 |
|
| 814 |
|
|
| 815 |
|
|
| 816 |
report______> Distribution of short non-bonded contacts: |
|
| 817 |
|
|
| 818 |
|
|
| 819 |
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 |
|
| 820 |
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 |
|
| 821 |
FREQUENCY: 0 0 0 0 0 10 16 74 185 265 204 297 367 415 381 |
|
| 822 |
|
|
| 823 |
|
|
| 824 |
<< end of ENERGY. |
|
| 825 |
|
|
| 826 |
>> Summary of successfully produced models: |
|
| 827 |
Filename molpdf |
|
| 828 |
---------------------------------------- |
|
| 829 |
9606_I.B99990001.pdb 6929.77393 |
|
| 830 |
|
|
| 831 |
9606_F |
|
| 832 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 833 |
be used instead of the automodel defaults. If this is not what you |
|
| 834 |
want, clear them before creating the automodel object with |
|
| 835 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 836 |
|
|
| 837 |
|
|
| 838 |
check_ali___> Checking pairwise structural superpositions. |
|
| 839 |
|
|
| 840 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 841 |
|
|
| 842 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 843 |
---------------------------------------------------- |
|
| 844 |
END OF TABLE |
|
| 845 |
|
|
| 846 |
check_ali___> Checking the sequence-structure alignment. |
|
| 847 |
|
|
| 848 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 849 |
|
|
| 850 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 851 |
---------------------------------------------- |
|
| 852 |
END OF TABLE |
|
| 853 |
|
|
| 854 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 855 |
residue type, indices: 16 261 |
|
| 856 |
atom names : C +N |
|
| 857 |
atom indices : 2129 0 |
|
| 858 |
|
|
| 859 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 860 |
residue type, indices: 16 261 |
|
| 861 |
atom names : C CA +N O |
|
| 862 |
atom indices : 2129 2126 0 2130 |
|
| 863 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 864 |
least one known structure available. MDT, not library, potential is used. |
|
| 865 |
0 atoms in HETATM/BLK residues constrained |
|
| 866 |
to protein atoms within 2.30 angstroms |
|
| 867 |
and protein CA atoms within 10.00 angstroms |
|
| 868 |
0 atoms in residues without defined topology |
|
| 869 |
constrained to be rigid bodies |
|
| 870 |
condens_443_> Restraints marked for deletion were removed. |
|
| 871 |
Total number of restraints before, now: 26199 24348 |
|
| 872 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 873 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 874 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 875 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 876 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 877 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 878 |
|
|
| 879 |
|
|
| 880 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 881 |
Number of all residues in MODEL : 261 |
|
| 882 |
Number of all, selected real atoms : 2131 2131 |
|
| 883 |
Number of all, selected pseudo atoms : 0 0 |
|
| 884 |
Number of all static, selected restraints : 24348 24348 |
|
| 885 |
COVALENT_CYS : F |
|
| 886 |
NONBONDED_SEL_ATOMS : 1 |
|
| 887 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4778 |
|
| 888 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 889 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 890 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 891 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 892 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 893 |
NLOGN_USE : 15 |
|
| 894 |
CONTACT_SHELL : 4.000 |
|
| 895 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 896 |
SPHERE_STDV : 0.050 |
|
| 897 |
RADII_FACTOR : 0.820 |
|
| 898 |
Current energy : 6458.9883 |
|
| 899 |
|
|
| 900 |
|
|
| 901 |
|
|
| 902 |
|
|
| 903 |
|
|
| 904 |
Summary of the restraint violations: |
|
| 905 |
|
|
| 906 |
NUM ... number of restraints. |
|
| 907 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 908 |
RVIOL ... relative difference from the best value. |
|
| 909 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 910 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 911 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 912 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 913 |
|
|
| 914 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 915 |
------------------------------------------------------------------------------------------------------ |
|
| 916 |
1 Bond length potential : 2219 0 0 0.004 0.004 10.494 1.000 |
|
| 917 |
2 Bond angle potential : 3036 0 2 1.731 1.731 180.53 1.000 |
|
| 918 |
3 Stereochemical cosine torsion poten: 1714 0 15 38.612 38.612 367.11 1.000 |
|
| 919 |
4 Stereochemical improper torsion pot: 1050 0 0 0.952 0.952 19.641 1.000 |
|
| 920 |
5 Soft-sphere overlap restraints : 4778 0 0 0.001 0.001 0.58739 1.000 |
|
| 921 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 922 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 923 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 924 |
9 Distance restraints 1 (CA-CA) : 4433 0 0 0.088 0.088 582.88 1.000 |
|
| 925 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.116 0.116 683.82 1.000 |
|
| 926 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 927 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 928 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.247 3.247 31.478 1.000 |
|
| 929 |
14 Sidechain Chi_1 dihedral restraints: 227 0 0 51.888 51.888 7.6842 1.000 |
|
| 930 |
15 Sidechain Chi_2 dihedral restraints: 169 0 1 64.007 64.007 31.177 1.000 |
|
| 931 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 65.360 65.360 28.065 1.000 |
|
| 932 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 76.540 76.540 4.6040 1.000 |
|
| 933 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 934 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 935 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 936 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 937 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 938 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.294 0.294 2710.2 1.000 |
|
| 939 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 940 |
25 Phi/Psi pair of dihedral restraints: 259 3 9 14.765 19.037 -178.33 1.000 |
|
| 941 |
26 Distance restraints 4 (SDCH-SDCH) : 2426 0 5 0.669 0.669 1979.0 1.000 |
|
| 942 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 943 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 944 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 945 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 946 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 947 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 948 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 949 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 950 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 951 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 952 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 953 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 954 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 955 |
|
|
| 956 |
|
|
| 957 |
|
|
| 958 |
# Heavy relative violation of each residue is written to: 9606_F.V99990001 |
|
| 959 |
# The profile is NOT normalized by the number of restraints. |
|
| 960 |
# The profiles are smoothed over a window of residues: 1 |
|
| 961 |
# The sum of all numbers in the file: 17361.5898 |
|
| 962 |
|
|
| 963 |
|
|
| 964 |
|
|
| 965 |
List of the violated restraints: |
|
| 966 |
A restraint is violated when the relative difference |
|
| 967 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 968 |
|
|
| 969 |
ICSR ... index of a restraint in the current set. |
|
| 970 |
RESNO ... residue numbers of the first two atoms. |
|
| 971 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 972 |
FEAT ... the value of the feature in the model. |
|
| 973 |
restr ... the mean of the basis restraint with the smallest |
|
| 974 |
difference from the model (local minimum). |
|
| 975 |
viol ... difference from the local minimum. |
|
| 976 |
rviol ... relative difference from the local minimum. |
|
| 977 |
RESTR ... the best value (global minimum). |
|
| 978 |
VIOL ... difference from the best value. |
|
| 979 |
RVIOL ... relative difference from the best value. |
|
| 980 |
|
|
| 981 |
|
|
| 982 |
------------------------------------------------------------------------------------------------- |
|
| 983 |
|
|
| 984 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 985 |
List of the RVIOL violations larger than : 6.5000 |
|
| 986 |
|
|
| 987 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 988 |
1 8020 1M 2T C N 7 9 -76.22 -78.10 9.41 0.47 -63.20 159.41 21.31 |
|
| 989 |
1 2T 2T N CA 9 10 159.02 149.80 -42.10 |
|
| 990 |
2 8146 127L 128E C N 1030 1032 -86.22 -63.60 82.68 12.30 -69.30 99.13 6.96 |
|
| 991 |
2 128E 128E N CA 1032 1033 -119.82 -40.30 142.50 |
|
| 992 |
3 8250 231H 232H C N 1855 1857 -112.98 -63.20 78.73 8.57 -63.20 78.73 8.57 |
|
| 993 |
3 232H 232H N CA 1857 1858 18.69 -42.30 -42.30 |
|
| 994 |
|
|
| 995 |
|
|
| 996 |
report______> Distribution of short non-bonded contacts: |
|
| 997 |
|
|
| 998 |
|
|
| 999 |
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 |
|
| 1000 |
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 |
|
| 1001 |
FREQUENCY: 0 0 0 0 0 5 20 66 185 232 194 296 363 405 376 |
|
| 1002 |
|
|
| 1003 |
|
|
| 1004 |
<< end of ENERGY. |
|
| 1005 |
|
|
| 1006 |
>> Summary of successfully produced models: |
|
| 1007 |
Filename molpdf |
|
| 1008 |
---------------------------------------- |
|
| 1009 |
9606_F.B99990001.pdb 6458.98828 |
|
| 1010 |
|
|
| 1011 |
9606_S |
|
| 1012 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 1013 |
be used instead of the automodel defaults. If this is not what you |
|
| 1014 |
want, clear them before creating the automodel object with |
|
| 1015 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 1016 |
|
|
| 1017 |
|
|
| 1018 |
check_ali___> Checking pairwise structural superpositions. |
|
| 1019 |
|
|
| 1020 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 1021 |
|
|
| 1022 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 1023 |
---------------------------------------------------- |
|
| 1024 |
END OF TABLE |
|
| 1025 |
|
|
| 1026 |
check_ali___> Checking the sequence-structure alignment. |
|
| 1027 |
|
|
| 1028 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 1029 |
|
|
| 1030 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 1031 |
---------------------------------------------- |
|
| 1032 |
END OF TABLE |
|
| 1033 |
|
|
| 1034 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1035 |
residue type, indices: 16 261 |
|
| 1036 |
atom names : C +N |
|
| 1037 |
atom indices : 2124 0 |
|
| 1038 |
|
|
| 1039 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1040 |
residue type, indices: 16 261 |
|
| 1041 |
atom names : C CA +N O |
|
| 1042 |
atom indices : 2124 2121 0 2125 |
|
| 1043 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 1044 |
least one known structure available. MDT, not library, potential is used. |
|
| 1045 |
0 atoms in HETATM/BLK residues constrained |
|
| 1046 |
to protein atoms within 2.30 angstroms |
|
| 1047 |
and protein CA atoms within 10.00 angstroms |
|
| 1048 |
0 atoms in residues without defined topology |
|
| 1049 |
constrained to be rigid bodies |
|
| 1050 |
condens_443_> Restraints marked for deletion were removed. |
|
| 1051 |
Total number of restraints before, now: 26168 24318 |
|
| 1052 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1053 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1054 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1055 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1056 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1057 |
|
|
| 1058 |
|
|
| 1059 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 1060 |
Number of all residues in MODEL : 261 |
|
| 1061 |
Number of all, selected real atoms : 2126 2126 |
|
| 1062 |
Number of all, selected pseudo atoms : 0 0 |
|
| 1063 |
Number of all static, selected restraints : 24318 24318 |
|
| 1064 |
COVALENT_CYS : F |
|
| 1065 |
NONBONDED_SEL_ATOMS : 1 |
|
| 1066 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4781 |
|
| 1067 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 1068 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 1069 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 1070 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 1071 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 1072 |
NLOGN_USE : 15 |
|
| 1073 |
CONTACT_SHELL : 4.000 |
|
| 1074 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 1075 |
SPHERE_STDV : 0.050 |
|
| 1076 |
RADII_FACTOR : 0.820 |
|
| 1077 |
Current energy : 6496.0596 |
|
| 1078 |
|
|
| 1079 |
|
|
| 1080 |
|
|
| 1081 |
|
|
| 1082 |
|
|
| 1083 |
Summary of the restraint violations: |
|
| 1084 |
|
|
| 1085 |
NUM ... number of restraints. |
|
| 1086 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 1087 |
RVIOL ... relative difference from the best value. |
|
| 1088 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 1089 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 1090 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 1091 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 1092 |
|
|
| 1093 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 1094 |
------------------------------------------------------------------------------------------------------ |
|
| 1095 |
1 Bond length potential : 2213 0 0 0.004 0.004 10.469 1.000 |
|
| 1096 |
2 Bond angle potential : 3028 0 3 1.765 1.765 185.98 1.000 |
|
| 1097 |
3 Stereochemical cosine torsion poten: 1705 0 16 38.623 38.623 370.38 1.000 |
|
| 1098 |
4 Stereochemical improper torsion pot: 1044 0 0 0.990 0.990 20.826 1.000 |
|
| 1099 |
5 Soft-sphere overlap restraints : 4781 0 0 0.001 0.001 0.59371 1.000 |
|
| 1100 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1101 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1102 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1103 |
9 Distance restraints 1 (CA-CA) : 4433 0 1 0.095 0.095 587.31 1.000 |
|
| 1104 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.117 0.117 682.60 1.000 |
|
| 1105 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1106 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1107 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.238 3.238 31.315 1.000 |
|
| 1108 |
14 Sidechain Chi_1 dihedral restraints: 227 0 0 46.690 46.690 2.9465 1.000 |
|
| 1109 |
15 Sidechain Chi_2 dihedral restraints: 168 0 2 61.521 61.521 38.612 1.000 |
|
| 1110 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 52.863 52.863 26.667 1.000 |
|
| 1111 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 99.049 99.049 5.3430 1.000 |
|
| 1112 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1113 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1114 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1115 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1116 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1117 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.308 0.308 2711.7 1.000 |
|
| 1118 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1119 |
25 Phi/Psi pair of dihedral restraints: 259 2 10 15.336 16.194 -173.24 1.000 |
|
| 1120 |
26 Distance restraints 4 (SDCH-SDCH) : 2426 0 8 0.704 0.704 1994.5 1.000 |
|
| 1121 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1122 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1123 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1124 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1125 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1126 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1127 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1128 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1129 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1130 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1131 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1132 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1133 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1134 |
|
|
| 1135 |
|
|
| 1136 |
|
|
| 1137 |
# Heavy relative violation of each residue is written to: 9606_S.V99990001 |
|
| 1138 |
# The profile is NOT normalized by the number of restraints. |
|
| 1139 |
# The profiles are smoothed over a window of residues: 1 |
|
| 1140 |
# The sum of all numbers in the file: 16972.8242 |
|
| 1141 |
|
|
| 1142 |
|
|
| 1143 |
|
|
| 1144 |
List of the violated restraints: |
|
| 1145 |
A restraint is violated when the relative difference |
|
| 1146 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 1147 |
|
|
| 1148 |
ICSR ... index of a restraint in the current set. |
|
| 1149 |
RESNO ... residue numbers of the first two atoms. |
|
| 1150 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 1151 |
FEAT ... the value of the feature in the model. |
|
| 1152 |
restr ... the mean of the basis restraint with the smallest |
|
| 1153 |
difference from the model (local minimum). |
|
| 1154 |
viol ... difference from the local minimum. |
|
| 1155 |
rviol ... relative difference from the local minimum. |
|
| 1156 |
RESTR ... the best value (global minimum). |
|
| 1157 |
VIOL ... difference from the best value. |
|
| 1158 |
RVIOL ... relative difference from the best value. |
|
| 1159 |
|
|
| 1160 |
|
|
| 1161 |
------------------------------------------------------------------------------------------------- |
|
| 1162 |
|
|
| 1163 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 1164 |
List of the RVIOL violations larger than : 6.5000 |
|
| 1165 |
|
|
| 1166 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 1167 |
1 8117 127L 128E C N 1025 1027 -86.68 -63.60 83.76 12.47 -69.30 98.23 6.87 |
|
| 1168 |
1 128E 128E N CA 1027 1028 -120.82 -40.30 142.50 |
|
| 1169 |
2 8221 231H 232H C N 1850 1852 -114.13 -63.20 81.80 8.88 -63.20 81.80 8.88 |
|
| 1170 |
2 232H 232H N CA 1852 1853 21.72 -42.30 -42.30 |
|
| 1171 |
|
|
| 1172 |
|
|
| 1173 |
report______> Distribution of short non-bonded contacts: |
|
| 1174 |
|
|
| 1175 |
|
|
| 1176 |
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 |
|
| 1177 |
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 |
|
| 1178 |
FREQUENCY: 0 0 0 0 0 9 17 61 175 237 197 299 355 418 379 |
|
| 1179 |
|
|
| 1180 |
|
|
| 1181 |
<< end of ENERGY. |
|
| 1182 |
|
|
| 1183 |
>> Summary of successfully produced models: |
|
| 1184 |
Filename molpdf |
|
| 1185 |
---------------------------------------- |
|
| 1186 |
9606_S.B99990001.pdb 6496.05957 |
|
| 1187 |
|
|
| 1188 |
9606_L |
|
| 1189 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 1190 |
be used instead of the automodel defaults. If this is not what you |
|
| 1191 |
want, clear them before creating the automodel object with |
|
| 1192 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 1193 |
|
|
| 1194 |
|
|
| 1195 |
check_ali___> Checking pairwise structural superpositions. |
|
| 1196 |
|
|
| 1197 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 1198 |
|
|
| 1199 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 1200 |
---------------------------------------------------- |
|
| 1201 |
END OF TABLE |
|
| 1202 |
|
|
| 1203 |
check_ali___> Checking the sequence-structure alignment. |
|
| 1204 |
|
|
| 1205 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 1206 |
|
|
| 1207 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 1208 |
---------------------------------------------- |
|
| 1209 |
END OF TABLE |
|
| 1210 |
|
|
| 1211 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1212 |
residue type, indices: 16 261 |
|
| 1213 |
atom names : C +N |
|
| 1214 |
atom indices : 2126 0 |
|
| 1215 |
|
|
| 1216 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1217 |
residue type, indices: 16 261 |
|
| 1218 |
atom names : C CA +N O |
|
| 1219 |
atom indices : 2126 2123 0 2127 |
|
| 1220 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 1221 |
least one known structure available. MDT, not library, potential is used. |
|
| 1222 |
0 atoms in HETATM/BLK residues constrained |
|
| 1223 |
to protein atoms within 2.30 angstroms |
|
| 1224 |
and protein CA atoms within 10.00 angstroms |
|
| 1225 |
0 atoms in residues without defined topology |
|
| 1226 |
constrained to be rigid bodies |
|
| 1227 |
condens_443_> Restraints marked for deletion were removed. |
|
| 1228 |
Total number of restraints before, now: 26177 24326 |
|
| 1229 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1230 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1231 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1232 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1233 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1234 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1235 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1236 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1237 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1238 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1239 |
|
|
| 1240 |
|
|
| 1241 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 1242 |
Number of all residues in MODEL : 261 |
|
| 1243 |
Number of all, selected real atoms : 2128 2128 |
|
| 1244 |
Number of all, selected pseudo atoms : 0 0 |
|
| 1245 |
Number of all static, selected restraints : 24326 24326 |
|
| 1246 |
COVALENT_CYS : F |
|
| 1247 |
NONBONDED_SEL_ATOMS : 1 |
|
| 1248 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4822 |
|
| 1249 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 1250 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 1251 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 1252 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 1253 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 1254 |
NLOGN_USE : 15 |
|
| 1255 |
CONTACT_SHELL : 4.000 |
|
| 1256 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 1257 |
SPHERE_STDV : 0.050 |
|
| 1258 |
RADII_FACTOR : 0.820 |
|
| 1259 |
Current energy : 6708.4106 |
|
| 1260 |
|
|
| 1261 |
|
|
| 1262 |
|
|
| 1263 |
|
|
| 1264 |
|
|
| 1265 |
Summary of the restraint violations: |
|
| 1266 |
|
|
| 1267 |
NUM ... number of restraints. |
|
| 1268 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 1269 |
RVIOL ... relative difference from the best value. |
|
| 1270 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 1271 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 1272 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 1273 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 1274 |
|
|
| 1275 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 1276 |
------------------------------------------------------------------------------------------------------ |
|
| 1277 |
1 Bond length potential : 2215 0 0 0.005 0.005 12.566 1.000 |
|
| 1278 |
2 Bond angle potential : 3031 0 3 1.867 1.867 206.95 1.000 |
|
| 1279 |
3 Stereochemical cosine torsion poten: 1706 0 18 39.086 39.086 379.94 1.000 |
|
| 1280 |
4 Stereochemical improper torsion pot: 1045 0 0 1.093 1.093 24.881 1.000 |
|
| 1281 |
5 Soft-sphere overlap restraints : 4822 0 0 0.001 0.001 0.90441 1.000 |
|
| 1282 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1283 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1284 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1285 |
9 Distance restraints 1 (CA-CA) : 4433 0 2 0.124 0.124 621.07 1.000 |
|
| 1286 |
10 Distance restraints 2 (N-O) : 4608 0 4 0.143 0.143 723.61 1.000 |
|
| 1287 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1288 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1289 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.542 3.542 37.629 1.000 |
|
| 1290 |
14 Sidechain Chi_1 dihedral restraints: 227 0 0 50.898 50.898 15.005 1.000 |
|
| 1291 |
15 Sidechain Chi_2 dihedral restraints: 169 0 1 62.237 62.237 40.949 1.000 |
|
| 1292 |
16 Sidechain Chi_3 dihedral restraints: 48 0 0 67.335 67.335 29.038 1.000 |
|
| 1293 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 76.220 76.220 6.3086 1.000 |
|
| 1294 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1295 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1296 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1297 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1298 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1299 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.335 0.335 2726.8 1.000 |
|
| 1300 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1301 |
25 Phi/Psi pair of dihedral restraints: 259 7 14 19.300 28.110 -152.14 1.000 |
|
| 1302 |
26 Distance restraints 4 (SDCH-SDCH) : 2426 0 14 0.775 0.775 2034.9 1.000 |
|
| 1303 |
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1304 |
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1305 |
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1306 |
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1307 |
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1308 |
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1309 |
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1310 |
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1311 |
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1312 |
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1313 |
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1314 |
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1315 |
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1316 |
|
|
| 1317 |
|
|
| 1318 |
|
|
| 1319 |
# Heavy relative violation of each residue is written to: 9606_L.V99990001 |
|
| 1320 |
# The profile is NOT normalized by the number of restraints. |
|
| 1321 |
# The profiles are smoothed over a window of residues: 1 |
|
| 1322 |
# The sum of all numbers in the file: 19367.4160 |
|
| 1323 |
|
|
| 1324 |
|
|
| 1325 |
|
|
| 1326 |
List of the violated restraints: |
|
| 1327 |
A restraint is violated when the relative difference |
|
| 1328 |
from the best value (RVIOL) is larger than CUTOFF. |
|
| 1329 |
|
|
| 1330 |
ICSR ... index of a restraint in the current set. |
|
| 1331 |
RESNO ... residue numbers of the first two atoms. |
|
| 1332 |
ATM ... IUPAC atom names of the first two atoms. |
|
| 1333 |
FEAT ... the value of the feature in the model. |
|
| 1334 |
restr ... the mean of the basis restraint with the smallest |
|
| 1335 |
difference from the model (local minimum). |
|
| 1336 |
viol ... difference from the local minimum. |
|
| 1337 |
rviol ... relative difference from the local minimum. |
|
| 1338 |
RESTR ... the best value (global minimum). |
|
| 1339 |
VIOL ... difference from the best value. |
|
| 1340 |
RVIOL ... relative difference from the best value. |
|
| 1341 |
|
|
| 1342 |
|
|
| 1343 |
------------------------------------------------------------------------------------------------- |
|
| 1344 |
|
|
| 1345 |
Feature 25 : Phi/Psi pair of dihedral restraints |
|
| 1346 |
List of the RVIOL violations larger than : 6.5000 |
|
| 1347 |
|
|
| 1348 |
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
|
| 1349 |
1 7998 1M 2T C N 7 9 -80.00 -78.10 7.10 0.25 -63.20 162.13 21.91 |
|
| 1350 |
1 2T 2T N CA 9 10 156.64 149.80 -42.10 |
|
| 1351 |
2 8007 10M 11V C N 84 86 -63.70 -62.40 2.01 0.23 -73.50 -179.80 15.52 |
|
| 1352 |
2 11V 11V N CA 86 87 -40.87 -42.40 139.20 |
|
| 1353 |
3 8008 11V 12K C N 91 93 84.34 -70.20 154.84 11.07 -70.20 154.84 11.07 |
|
| 1354 |
3 12K 12K N CA 93 94 130.79 140.40 140.40 |
|
| 1355 |
4 8119 122T 123P C N 989 991 -57.88 -58.70 24.55 1.96 -64.50 157.91 12.14 |
|
| 1356 |
4 123P 123P N CA 991 992 -55.03 -30.50 147.20 |
|
| 1357 |
5 8120 123P 124L C N 996 998 126.04 -108.50 125.73 5.89 -70.70 163.26 14.87 |
|
| 1358 |
5 124L 124L N CA 998 999 140.81 132.50 141.60 |
|
| 1359 |
6 8124 127L 128E C N 1027 1029 -87.12 -63.60 81.35 12.18 -69.30 100.90 7.06 |
|
| 1360 |
6 128E 128E N CA 1029 1030 -118.18 -40.30 142.50 |
|
| 1361 |
7 8228 231H 232H C N 1852 1854 -113.64 -63.20 79.29 8.64 -63.20 79.29 8.64 |
|
| 1362 |
7 232H 232H N CA 1854 1855 18.87 -42.30 -42.30 |
|
| 1363 |
|
|
| 1364 |
|
|
| 1365 |
report______> Distribution of short non-bonded contacts: |
|
| 1366 |
|
|
| 1367 |
|
|
| 1368 |
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 |
|
| 1369 |
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 |
|
| 1370 |
FREQUENCY: 0 0 0 0 0 8 15 81 183 233 198 284 381 403 371 |
|
| 1371 |
|
|
| 1372 |
|
|
| 1373 |
<< end of ENERGY. |
|
| 1374 |
|
|
| 1375 |
>> Summary of successfully produced models: |
|
| 1376 |
Filename molpdf |
|
| 1377 |
---------------------------------------- |
|
| 1378 |
9606_L.B99990001.pdb 6708.41064 |
|
| 1379 |
|
|
| 1380 |
9606_M |
|
| 1381 |
automodel__W> Topology and/or parameter libraries already in memory. These will |
|
| 1382 |
be used instead of the automodel defaults. If this is not what you |
|
| 1383 |
want, clear them before creating the automodel object with |
|
| 1384 |
env.libs.topology.clear() and env.libs.parameters.clear() |
|
| 1385 |
|
|
| 1386 |
|
|
| 1387 |
check_ali___> Checking pairwise structural superpositions. |
|
| 1388 |
|
|
| 1389 |
Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
|
| 1390 |
|
|
| 1391 |
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
|
| 1392 |
---------------------------------------------------- |
|
| 1393 |
END OF TABLE |
|
| 1394 |
|
|
| 1395 |
check_ali___> Checking the sequence-structure alignment. |
|
| 1396 |
|
|
| 1397 |
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
|
| 1398 |
|
|
| 1399 |
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
|
| 1400 |
---------------------------------------------- |
|
| 1401 |
END OF TABLE |
|
| 1402 |
|
|
| 1403 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1404 |
residue type, indices: 16 261 |
|
| 1405 |
atom names : C +N |
|
| 1406 |
atom indices : 2126 0 |
|
| 1407 |
|
|
| 1408 |
getf_______W> RTF restraint not found in the atoms list: |
|
| 1409 |
residue type, indices: 16 261 |
|
| 1410 |
atom names : C CA +N O |
|
| 1411 |
atom indices : 2126 2123 0 2127 |
|
| 1412 |
mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
|
| 1413 |
least one known structure available. MDT, not library, potential is used. |
|
| 1414 |
0 atoms in HETATM/BLK residues constrained |
|
| 1415 |
to protein atoms within 2.30 angstroms |
|
| 1416 |
and protein CA atoms within 10.00 angstroms |
|
| 1417 |
0 atoms in residues without defined topology |
|
| 1418 |
constrained to be rigid bodies |
|
| 1419 |
condens_443_> Restraints marked for deletion were removed. |
|
| 1420 |
Total number of restraints before, now: 26177 24324 |
|
| 1421 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1422 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1423 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1424 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1425 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1426 |
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
|
| 1427 |
|
|
| 1428 |
|
|
| 1429 |
>> ENERGY; Differences between the model's features and restraints: |
|
| 1430 |
Number of all residues in MODEL : 261 |
|
| 1431 |
Number of all, selected real atoms : 2128 2128 |
|
| 1432 |
Number of all, selected pseudo atoms : 0 0 |
|
| 1433 |
Number of all static, selected restraints : 24324 24324 |
|
| 1434 |
COVALENT_CYS : F |
|
| 1435 |
NONBONDED_SEL_ATOMS : 1 |
|
| 1436 |
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4830 |
|
| 1437 |
Dynamic pairs routine : 2, NATM x NATM cell sorting |
|
| 1438 |
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
|
| 1439 |
LENNARD_JONES_SWITCH : 6.500 7.500 |
|
| 1440 |
COULOMB_JONES_SWITCH : 6.500 7.500 |
|
| 1441 |
RESIDUE_SPAN_RANGE : 0 99999 |
|
| 1442 |
NLOGN_USE : 15 |
|
| 1443 |
CONTACT_SHELL : 4.000 |
|
| 1444 |
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
|
| 1445 |
SPHERE_STDV : 0.050 |
|
| 1446 |
RADII_FACTOR : 0.820 |
|
| 1447 |
Current energy : 6481.8320 |
|
| 1448 |
|
|
| 1449 |
|
|
| 1450 |
|
|
| 1451 |
|
|
| 1452 |
|
|
| 1453 |
Summary of the restraint violations: |
|
| 1454 |
|
|
| 1455 |
NUM ... number of restraints. |
|
| 1456 |
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
|
| 1457 |
RVIOL ... relative difference from the best value. |
|
| 1458 |
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
|
| 1459 |
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
|
| 1460 |
RMS_2 ... RMS(feature, best_value, NUMB). |
|
| 1461 |
MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
|
| 1462 |
|
|
| 1463 |
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
|
| 1464 |
------------------------------------------------------------------------------------------------------ |
|
| 1465 |
1 Bond length potential : 2215 0 0 0.004 0.004 10.731 1.000 |
|
| 1466 |
2 Bond angle potential : 3030 0 3 1.777 1.777 188.35 1.000 |
|
| 1467 |
3 Stereochemical cosine torsion poten: 1705 0 16 38.765 38.765 371.22 1.000 |
|
| 1468 |
4 Stereochemical improper torsion pot: 1044 0 0 1.009 1.009 21.571 1.000 |
|
| 1469 |
5 Soft-sphere overlap restraints : 4830 0 0 0.001 0.001 0.79378 1.000 |
|
| 1470 |
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1471 |
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1472 |
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1473 |
9 Distance restraints 1 (CA-CA) : 4433 0 0 0.088 0.088 582.13 1.000 |
|
| 1474 |
10 Distance restraints 2 (N-O) : 4608 0 0 0.118 0.118 684.87 1.000 |
|
| 1475 |
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1476 |
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1477 |
13 Mainchain Omega dihedral restraints: 260 0 1 3.280 3.280 32.136 1.000 |
|
| 1478 |
14 Sidechain Chi_1 dihedral restraints: 227 0 1 51.328 51.328 10.403 1.000 |
|
| 1479 |
15 Sidechain Chi_2 dihedral restraints: 169 0 1 60.299 60.299 30.779 1.000 |
|
| 1480 |
16 Sidechain Chi_3 dihedral restraints: 49 0 0 66.051 66.051 29.338 1.000 |
|
| 1481 |
17 Sidechain Chi_4 dihedral restraints: 8 0 0 86.862 86.862 5.4540 1.000 |
|
| 1482 |
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1483 |
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1484 |
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1485 |
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1486 |
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1487 |
23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.318 0.318 2721.0 1.000 |
|
| 1488 |
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
|
| 1489 |
25 Phi/Psi pair of dihedral restraints: 259 3 8 14.925 19.469 -174.50 1.000 |
|
Also available in: Unified diff