nelse003
commented
6 years ago NUDT7A-x0299 multistate-merge-conformations:
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Validating input parameters and input files
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----------------------------------------------- ------------------------------------------------ --- Processed merging parameters --- ----------------------------------------------- ------------------------------------------------
input { major = "/dls/labxchem/data/2017/lb18145-49/processing/analysis/initial_model/NUDT7A-x0299/refine.split.ground-state.pdb" minor = "refine.modified.pdb" pdb = None } options { minor_occupancy = 1 major_occupancy = 1 prune_duplicates_rmsd = 0.05 reset_all_occupancies = False } output { pdb = "multi-state-model.pdb" log = "multi-state-merge-conformations.log" make_restraints = True } settings { overwrite = True verbose = False }
----------------------------------------------- ------------------------------------------------ --- Reading input files --- ----------------------------------------------- ------------------------------------------------
----------------------------------------------- ------------------------------------------------ --- Updating input occupancies prior to merging --- ----------------------------------------------- ------------------------------------------------
Multiplying occupancies of input.major by 1.0 Multiplying occupancies of input.minor by 1.0
----------------------------------------------- ------------------------------------------------ --- Post-processing occupancies --- ----------------------------------------------- ------------------------------------------------
Sanitising occupancies so that residue occupancies are between 0 and 1
Setting all main-conf occupancies to 1.0
----------------------------------------------- ------------------------------------------------ --- Writing output structure --- ----------------------------------------------- ------------------------------------------------
Writing output structure to multi-state-model.pdb
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Parameters for generating restraints
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restraints { output { phenix = "multi-state-restraints.phenix.params" refmac = "multi-state-restraints.refmac.params" log = "multi-state-merge-conformations.log" } modes { all = False peptide_bond_links = True duplicated_atom_restraints = True local_structure_restraints = False occupancy_groups = True b_factor_restraints = False } duplicates { make_for = *all protein het rmsd_cutoff = 0.1 sigma_xyz = 0.02 } peptide_bonds { suffix = ".link.pdb" } local_restraints { altlocs = "B" max_distance = 4.2 min_distance = 1.6 sigma_xyz = 0.1 } occupancy { resname = "DRG,FRG,LIG,UNK,UNL" group_dist = 5 overlap_dist = 2 complete_groups = True simple_groups = False exclude_altlocs = None } b_factors { resname = None contact_dist = 4 sigma_b = 1 } }
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Generating restraints
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----------------------------------------------- ------------------------------------------------ --- Checking the continuity of the protein backbone --- ----------------------------------------------- ------------------------------------------------
No breaks in the backbone - hooray! (nothing needs to be done here)
----------------------------------------------- ------------------------------------------------ --- Generating restraints for duplicated conformers --- ----------------------------------------------- ------------------------------------------------
No duplicated conformers (no restraints created)
----------------------------------------------- ------------------------------------------------ --- Generating occupancy-constrained groups --- ----------------------------------------------- ------------------------------------------------
------------------------------------->>>
Created 1 occupancy groups for overlapping conformers
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FINISHED
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Final Parameters
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input { major = "/dls/labxchem/data/2017/lb18145-49/processing/analysis/initial_model/NUDT7A-x0299/refine.split.ground-state.pdb" minor = "refine.modified.pdb" pdb = None } options { minor_occupancy = 1 major_occupancy = 1 prune_duplicates_rmsd = 0.05 reset_all_occupancies = False } output { pdb = "multi-state-model.pdb" log = "multi-state-merge-conformations.log" make_restraints = True } restraints { output { phenix = "multi-state-restraints.phenix.params" refmac = "multi-state-restraints.refmac.params" log = "multi-state-merge-conformations.log" } modes { all = False peptide_bond_links = True duplicated_atom_restraints = True local_structure_restraints = False occupancy_groups = True b_factor_restraints = False } duplicates { make_for = *all protein het rmsd_cutoff = 0.1 sigma_xyz = 0.02 } peptide_bonds { suffix = ".link.pdb" } local_restraints { altlocs = "B" max_distance = 4.2 min_distance = 1.6 sigma_xyz = 0.1 } occupancy { resname = "DRG,FRG,LIG,UNK,UNL" group_dist = 5 overlap_dist = 2 complete_groups = True simple_groups = False exclude_altlocs = None } b_factors { resname = None contact_dist = 4 sigma_b = 1 } } settings { overwrite = True verbose = False }
NUDT7A-x0299 with two copies of the ligand:
The ground state selection in select_occupancy_groups() is reading in coincident as empty list []. Thus the select state method is failing.
This relates to having no coincident groups being processed in the giant.merge_conformations.
Compare to other cases with two ligands:
/dls/labxchem/data/2017/lb18145-12/processing/analysis/initial_model/NUDT21A-x0203 /dls/labxchem/data/2017/lb18145-25/processing/analysis/initial_model/NUDT21A-x0368 /dls/labxchem/data/2017/lb18145-25/processing/analysis/initial_model/NUDT21A-x0498 /dls/labxchem/data/2017/lb18145-25/processing/analysis/initial_model/NUDT21A-x0502 /dls/labxchem/data/2017/lb18145-25/processing/analysis/initial_model/NUDT21A-x0798 /dls/labxchem/data/2017/lb18145-25/processing/analysis/initial_model/NUDT21A-x0896