Starting phenix.real_space_refine on Sat Dec 16 00:42:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m52_30083/12_2023/6m52_30083_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 168 5.16 5 C 20978 2.51 5 N 5886 2.21 5 O 6344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ASP 151": "OD1" <-> "OD2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H ASP 151": "OD1" <-> "OD2" Residue "H ASP 172": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I ASP 172": "OD1" <-> "OD2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J ASP 151": "OD1" <-> "OD2" Residue "J ASP 172": "OD1" <-> "OD2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ASP 151": "OD1" <-> "OD2" Residue "K ASP 172": "OD1" <-> "OD2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L ASP 151": "OD1" <-> "OD2" Residue "L ASP 172": "OD1" <-> "OD2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M ASP 151": "OD1" <-> "OD2" Residue "M ASP 172": "OD1" <-> "OD2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N ASP 172": "OD1" <-> "OD2" Residue "O ASP 151": "OD1" <-> "OD2" Residue "O ASP 172": "OD1" <-> "OD2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P ASP 151": "OD1" <-> "OD2" Residue "P ASP 172": "OD1" <-> "OD2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q ASP 172": "OD1" <-> "OD2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R ASP 151": "OD1" <-> "OD2" Residue "R ASP 172": "OD1" <-> "OD2" Residue "S ASP 151": "OD1" <-> "OD2" Residue "S ASP 172": "OD1" <-> "OD2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T ASP 151": "OD1" <-> "OD2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U GLU 95": "OE1" <-> "OE2" Residue "U ASP 151": "OD1" <-> "OD2" Residue "U ASP 172": "OD1" <-> "OD2" Residue "V ASP 151": "OD1" <-> "OD2" Residue "V ASP 172": "OD1" <-> "OD2" Residue "W ASP 151": "OD1" <-> "OD2" Residue "W ASP 172": "OD1" <-> "OD2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X ASP 151": "OD1" <-> "OD2" Residue "X ASP 172": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33382 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "B" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "D" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "E" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "G" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "H" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "J" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "M" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "N" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "O" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1395 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1407 Chain: "R" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.70, per 1000 atoms: 0.68 Number of scatterers: 33382 At special positions: 0 Unit cell: (136.59, 136.59, 136.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 168 16.00 O 6344 8.00 N 5886 7.00 C 20978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 8.5 seconds 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 73.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.833A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 77 removed outlier: 3.697A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.641A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.735A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'B' and resid 15 through 41 removed outlier: 3.766A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.823A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 125 removed outlier: 3.553A pdb=" N MET B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.756A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'C' and resid 15 through 41 removed outlier: 3.760A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 77 removed outlier: 3.833A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 125 removed outlier: 3.609A pdb=" N ASN C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 139 through 159 removed outlier: 3.773A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'D' and resid 15 through 41 removed outlier: 3.759A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 77 removed outlier: 3.804A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 125 removed outlier: 3.560A pdb=" N MET D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 Processing helix chain 'D' and resid 139 through 159 removed outlier: 3.765A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'E' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 77 removed outlier: 3.829A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 125 removed outlier: 3.553A pdb=" N MET E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 110 " --> pdb=" O HIS E 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 Processing helix chain 'E' and resid 139 through 159 removed outlier: 3.752A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'F' and resid 15 through 41 removed outlier: 3.759A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 125 removed outlier: 3.616A pdb=" N ASN F 110 " --> pdb=" O HIS F 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 Processing helix chain 'F' and resid 139 through 159 removed outlier: 3.771A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'G' and resid 15 through 41 removed outlier: 3.760A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 77 removed outlier: 3.831A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 125 removed outlier: 3.554A pdb=" N MET G 101 " --> pdb=" O GLY G 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN G 110 " --> pdb=" O HIS G 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 137 Processing helix chain 'G' and resid 139 through 159 removed outlier: 3.767A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'H' and resid 15 through 41 removed outlier: 3.767A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 77 removed outlier: 3.820A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 125 removed outlier: 3.550A pdb=" N MET H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN H 110 " --> pdb=" O HIS H 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 137 Processing helix chain 'H' and resid 139 through 159 removed outlier: 3.756A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'I' and resid 15 through 41 removed outlier: 3.761A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 77 removed outlier: 3.830A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 125 removed outlier: 3.522A pdb=" N MET I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN I 110 " --> pdb=" O HIS I 106 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 137 Processing helix chain 'I' and resid 139 through 159 removed outlier: 3.785A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 174 Processing helix chain 'J' and resid 15 through 41 removed outlier: 3.766A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 125 removed outlier: 3.554A pdb=" N MET J 101 " --> pdb=" O GLY J 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN J 110 " --> pdb=" O HIS J 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 137 Processing helix chain 'J' and resid 139 through 159 removed outlier: 3.751A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'K' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 125 removed outlier: 3.554A pdb=" N MET K 101 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN K 110 " --> pdb=" O HIS K 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 137 Processing helix chain 'K' and resid 139 through 159 removed outlier: 3.751A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'L' and resid 15 through 41 removed outlier: 3.760A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 77 removed outlier: 3.831A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 125 removed outlier: 3.522A pdb=" N MET L 101 " --> pdb=" O GLY L 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN L 110 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 Processing helix chain 'L' and resid 139 through 159 removed outlier: 3.772A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'M' and resid 15 through 41 removed outlier: 3.760A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 77 removed outlier: 3.833A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 125 removed outlier: 3.560A pdb=" N MET M 101 " --> pdb=" O GLY M 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN M 110 " --> pdb=" O HIS M 106 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'M' and resid 139 through 159 removed outlier: 3.767A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 174 Processing helix chain 'N' and resid 15 through 41 removed outlier: 3.760A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 77 removed outlier: 3.833A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 125 removed outlier: 3.562A pdb=" N MET N 101 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 137 Processing helix chain 'N' and resid 139 through 159 removed outlier: 3.773A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'O' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 77 removed outlier: 3.821A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 125 removed outlier: 3.553A pdb=" N MET O 101 " --> pdb=" O GLY O 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN O 110 " --> pdb=" O HIS O 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 137 Processing helix chain 'O' and resid 139 through 159 removed outlier: 3.752A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 174 Processing helix chain 'P' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 77 removed outlier: 3.822A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 125 removed outlier: 3.552A pdb=" N MET P 101 " --> pdb=" O GLY P 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN P 110 " --> pdb=" O HIS P 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 137 Processing helix chain 'P' and resid 139 through 159 removed outlier: 3.751A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'Q' and resid 15 through 41 removed outlier: 3.759A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 125 removed outlier: 3.544A pdb=" N MET Q 101 " --> pdb=" O GLY Q 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN Q 110 " --> pdb=" O HIS Q 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 137 Processing helix chain 'Q' and resid 139 through 159 removed outlier: 3.787A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 174 Processing helix chain 'R' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 125 removed outlier: 3.554A pdb=" N MET R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 137 Processing helix chain 'R' and resid 139 through 159 removed outlier: 3.751A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 Processing helix chain 'S' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 77 removed outlier: 3.822A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 125 removed outlier: 3.618A pdb=" N ASN S 110 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 137 Processing helix chain 'S' and resid 139 through 159 removed outlier: 3.759A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 174 Processing helix chain 'T' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 77 removed outlier: 3.827A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 125 removed outlier: 3.550A pdb=" N MET T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN T 110 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 137 Processing helix chain 'T' and resid 139 through 159 removed outlier: 3.775A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 174 Processing helix chain 'U' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 77 removed outlier: 3.824A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 125 removed outlier: 3.613A pdb=" N ASN U 110 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 137 Processing helix chain 'U' and resid 139 through 159 removed outlier: 3.752A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 174 Processing helix chain 'V' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 77 removed outlier: 3.821A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 125 removed outlier: 3.628A pdb=" N ASN V 110 " --> pdb=" O HIS V 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 137 Processing helix chain 'V' and resid 139 through 159 removed outlier: 3.751A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 174 Processing helix chain 'W' and resid 15 through 41 removed outlier: 3.766A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 77 removed outlier: 3.821A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 125 removed outlier: 3.626A pdb=" N ASN W 110 " --> pdb=" O HIS W 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 137 Processing helix chain 'W' and resid 139 through 159 removed outlier: 3.755A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 174 Processing helix chain 'X' and resid 15 through 41 removed outlier: 3.765A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 77 removed outlier: 3.825A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 125 removed outlier: 3.610A pdb=" N ASN X 110 " --> pdb=" O HIS X 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 137 Processing helix chain 'X' and resid 139 through 159 removed outlier: 3.753A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 174 2241 hydrogen bonds defined for protein. 6723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.23 Time building geometry restraints manager: 12.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9779 1.33 - 1.45: 5585 1.45 - 1.57: 18446 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34074 Sorted by residual: bond pdb=" CB GLU F 65 " pdb=" CG GLU F 65 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB GLU Q 65 " pdb=" CG GLU Q 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB GLU N 65 " pdb=" CG GLU N 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLU M 65 " pdb=" CG GLU M 65 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 ... (remaining 34069 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.88: 660 106.88 - 113.66: 18271 113.66 - 120.43: 14966 120.43 - 127.20: 11733 127.20 - 133.97: 340 Bond angle restraints: 45970 Sorted by residual: angle pdb=" N GLU I 95 " pdb=" CA GLU I 95 " pdb=" CB GLU I 95 " ideal model delta sigma weight residual 114.17 107.88 6.29 1.14e+00 7.69e-01 3.05e+01 angle pdb=" N GLU L 95 " pdb=" CA GLU L 95 " pdb=" CB GLU L 95 " ideal model delta sigma weight residual 114.17 107.90 6.27 1.14e+00 7.69e-01 3.02e+01 angle pdb=" C TRP F 94 " pdb=" N GLU F 95 " pdb=" CA GLU F 95 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N GLU U 95 " pdb=" CA GLU U 95 " pdb=" C GLU U 95 " ideal model delta sigma weight residual 110.80 119.33 -8.53 2.13e+00 2.20e-01 1.60e+01 angle pdb=" N GLU S 95 " pdb=" CA GLU S 95 " pdb=" C GLU S 95 " ideal model delta sigma weight residual 110.80 119.31 -8.51 2.13e+00 2.20e-01 1.60e+01 ... (remaining 45965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 18044 17.12 - 34.24: 2012 34.24 - 51.36: 365 51.36 - 68.48: 100 68.48 - 85.60: 41 Dihedral angle restraints: 20562 sinusoidal: 8354 harmonic: 12208 Sorted by residual: dihedral pdb=" CA TRP Q 94 " pdb=" C TRP Q 94 " pdb=" N GLU Q 95 " pdb=" CA GLU Q 95 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP E 94 " pdb=" C TRP E 94 " pdb=" N GLU E 95 " pdb=" CA GLU E 95 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 20559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3333 0.055 - 0.110: 1183 0.110 - 0.164: 312 0.164 - 0.219: 17 0.219 - 0.274: 13 Chirality restraints: 4858 Sorted by residual: chirality pdb=" CG LEU K 73 " pdb=" CB LEU K 73 " pdb=" CD1 LEU K 73 " pdb=" CD2 LEU K 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU R 73 " pdb=" CB LEU R 73 " pdb=" CD1 LEU R 73 " pdb=" CD2 LEU R 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU E 73 " pdb=" CB LEU E 73 " pdb=" CD1 LEU E 73 " pdb=" CD2 LEU E 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4855 not shown) Planarity restraints: 6068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 33 " -0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR W 33 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR W 33 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR W 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR W 33 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR W 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR W 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR W 33 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 33 " 0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR S 33 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR S 33 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR S 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR S 33 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR S 33 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 33 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 33 " -0.031 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR V 33 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR V 33 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR V 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR V 33 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR V 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR V 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR V 33 " -0.008 2.00e-02 2.50e+03 ... (remaining 6065 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 10841 2.89 - 3.39: 30125 3.39 - 3.90: 52134 3.90 - 4.40: 62009 4.40 - 4.90: 103418 Nonbonded interactions: 258527 Sorted by model distance: nonbonded pdb=" N ASP E 46 " pdb=" OD1 ASP E 46 " model vdw 2.390 2.520 nonbonded pdb=" N ASP R 46 " pdb=" OD1 ASP R 46 " model vdw 2.391 2.520 nonbonded pdb=" N ASP T 46 " pdb=" OD1 ASP T 46 " model vdw 2.391 2.520 nonbonded pdb=" N ASP W 46 " pdb=" OD1 ASP W 46 " model vdw 2.392 2.520 nonbonded pdb=" N ASP S 46 " pdb=" OD1 ASP S 46 " model vdw 2.392 2.520 ... (remaining 258522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'B' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'C' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'D' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'E' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'F' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'G' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'H' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'I' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'J' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'K' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'L' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'M' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'N' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'O' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'P' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'Q' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'R' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'S' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'T' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'U' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'V' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'W' and (resid 6 through 63 or resid 65 through 176)) selection = (chain 'X' and (resid 6 through 63 or resid 65 through 176)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.930 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 90.930 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 34074 Z= 0.600 Angle : 0.942 8.625 45970 Z= 0.568 Chirality : 0.059 0.274 4858 Planarity : 0.005 0.042 6068 Dihedral : 15.324 85.598 12670 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 4066 helix: 0.61 (0.08), residues: 3106 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP Q 94 HIS 0.006 0.001 HIS J 61 PHE 0.013 0.003 PHE L 171 TYR 0.055 0.004 TYR W 33 ARG 0.003 0.001 ARG U 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 4.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 2.5301 time to fit residues: 1102.2464 Evaluate side-chains 326 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 4.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN B 51 ASN C 51 ASN D 51 ASN E 51 ASN H 51 ASN J 51 ASN K 51 ASN L 51 ASN O 51 ASN Q 51 ASN T 51 ASN U 51 ASN V 51 ASN V 110 ASN W 51 ASN W 110 ASN X 51 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34074 Z= 0.179 Angle : 0.512 5.870 45970 Z= 0.293 Chirality : 0.037 0.116 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.248 22.694 4494 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.99 % Allowed : 4.52 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.12), residues: 4066 helix: 2.72 (0.09), residues: 3058 sheet: None (None), residues: 0 loop : -1.99 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 94 HIS 0.003 0.001 HIS D 58 PHE 0.010 0.001 PHE N 133 TYR 0.018 0.002 TYR U 33 ARG 0.001 0.000 ARG F 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 411 time to evaluate : 3.879 Fit side-chains outliers start: 35 outliers final: 0 residues processed: 443 average time/residue: 2.2399 time to fit residues: 1117.3828 Evaluate side-chains 293 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 0.0670 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 3.9990 chunk 126 optimal weight: 0.0370 chunk 297 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN I 51 ASN M 51 ASN P 51 ASN R 51 ASN S 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34074 Z= 0.197 Angle : 0.512 7.632 45970 Z= 0.292 Chirality : 0.038 0.156 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.192 22.454 4494 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 7.57 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.13), residues: 4066 helix: 3.37 (0.09), residues: 3058 sheet: None (None), residues: 0 loop : -1.72 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 94 HIS 0.003 0.001 HIS Q 58 PHE 0.009 0.002 PHE L 133 TYR 0.016 0.002 TYR B 33 ARG 0.004 0.000 ARG O 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 315 time to evaluate : 3.881 Fit side-chains outliers start: 60 outliers final: 23 residues processed: 350 average time/residue: 2.1313 time to fit residues: 845.1632 Evaluate side-chains 318 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 295 time to evaluate : 3.862 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4158 time to fit residues: 20.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34074 Z= 0.198 Angle : 0.509 7.489 45970 Z= 0.290 Chirality : 0.038 0.133 4858 Planarity : 0.003 0.026 6068 Dihedral : 4.162 21.967 4494 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.53 % Allowed : 10.32 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.13), residues: 4066 helix: 3.54 (0.09), residues: 3058 sheet: None (None), residues: 0 loop : -1.60 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 94 HIS 0.003 0.001 HIS N 58 PHE 0.009 0.002 PHE U 133 TYR 0.013 0.002 TYR B 33 ARG 0.004 0.000 ARG T 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 360 time to evaluate : 3.991 Fit side-chains outliers start: 54 outliers final: 21 residues processed: 379 average time/residue: 2.0803 time to fit residues: 898.0548 Evaluate side-chains 375 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 354 time to evaluate : 3.819 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 2 residues processed: 19 average time/residue: 0.4004 time to fit residues: 17.7822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34074 Z= 0.192 Angle : 0.500 7.159 45970 Z= 0.284 Chirality : 0.038 0.132 4858 Planarity : 0.003 0.026 6068 Dihedral : 4.122 21.743 4494 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.32 % Allowed : 10.06 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.13), residues: 4066 helix: 3.57 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.47 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 94 HIS 0.003 0.001 HIS F 58 PHE 0.009 0.002 PHE L 133 TYR 0.010 0.001 TYR U 33 ARG 0.003 0.000 ARG U 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 396 time to evaluate : 4.169 Fit side-chains outliers start: 82 outliers final: 40 residues processed: 449 average time/residue: 1.8159 time to fit residues: 941.4859 Evaluate side-chains 419 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 379 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 23 residues processed: 17 average time/residue: 0.6889 time to fit residues: 21.5858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN D 110 ASN G 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.213 Angle : 0.518 6.880 45970 Z= 0.294 Chirality : 0.039 0.134 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.167 22.131 4494 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.69 % Allowed : 9.78 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.13), residues: 4066 helix: 3.50 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.52 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP T 94 HIS 0.003 0.001 HIS G 58 PHE 0.008 0.002 PHE I 133 TYR 0.010 0.002 TYR V 40 ARG 0.003 0.000 ARG W 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 399 time to evaluate : 3.916 Fit side-chains outliers start: 95 outliers final: 62 residues processed: 477 average time/residue: 1.7425 time to fit residues: 965.0925 Evaluate side-chains 456 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 394 time to evaluate : 3.913 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 48 residues processed: 14 average time/residue: 0.4185 time to fit residues: 14.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 110 ASN D 110 ASN F 110 ASN I 110 ASN L 110 ASN N 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34074 Z= 0.245 Angle : 0.552 6.986 45970 Z= 0.311 Chirality : 0.040 0.141 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.233 21.414 4494 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.54 % Allowed : 10.68 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.13), residues: 4066 helix: 3.39 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.56 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP Q 94 HIS 0.003 0.001 HIS C 58 PHE 0.009 0.002 PHE U 133 TYR 0.011 0.002 TYR X 40 ARG 0.003 0.000 ARG J 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 357 time to evaluate : 3.838 Fit side-chains outliers start: 90 outliers final: 63 residues processed: 426 average time/residue: 1.9806 time to fit residues: 967.1321 Evaluate side-chains 413 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 350 time to evaluate : 3.740 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 49 residues processed: 14 average time/residue: 0.4248 time to fit residues: 15.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 110 ASN D 110 ASN F 99 ASN F 110 ASN I 110 ASN L 110 ASN M 110 ASN N 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34074 Z= 0.314 Angle : 0.613 7.114 45970 Z= 0.342 Chirality : 0.043 0.162 4858 Planarity : 0.003 0.028 6068 Dihedral : 4.349 21.401 4494 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.23 % Allowed : 11.16 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.13), residues: 4066 helix: 3.16 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.63 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP T 94 HIS 0.002 0.001 HIS R 14 PHE 0.010 0.002 PHE B 133 TYR 0.013 0.002 TYR B 40 ARG 0.003 0.001 ARG O 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 325 time to evaluate : 4.195 Fit side-chains outliers start: 79 outliers final: 39 residues processed: 388 average time/residue: 2.0826 time to fit residues: 919.6159 Evaluate side-chains 353 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 314 time to evaluate : 3.884 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 25 residues processed: 14 average time/residue: 0.4150 time to fit residues: 14.6776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN I 110 ASN L 110 ASN M 110 ASN N 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34074 Z= 0.246 Angle : 0.558 6.746 45970 Z= 0.313 Chirality : 0.040 0.136 4858 Planarity : 0.003 0.028 6068 Dihedral : 4.252 21.176 4494 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.61 % Allowed : 12.07 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.13), residues: 4066 helix: 3.35 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.56 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 94 HIS 0.003 0.001 HIS G 58 PHE 0.010 0.002 PHE L 133 TYR 0.012 0.002 TYR B 40 ARG 0.003 0.000 ARG W 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 332 time to evaluate : 4.052 Fit side-chains outliers start: 57 outliers final: 39 residues processed: 374 average time/residue: 2.1564 time to fit residues: 914.4769 Evaluate side-chains 364 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 325 time to evaluate : 3.896 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 25 residues processed: 14 average time/residue: 0.5328 time to fit residues: 16.4093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 0.4980 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 110 ASN I 110 ASN L 110 ASN M 110 ASN N 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34074 Z= 0.197 Angle : 0.507 6.404 45970 Z= 0.287 Chirality : 0.038 0.131 4858 Planarity : 0.003 0.027 6068 Dihedral : 4.142 21.077 4494 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.44 % Allowed : 12.21 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.13), residues: 4066 helix: 3.64 (0.09), residues: 3058 sheet: None (None), residues: 0 loop : -1.55 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 94 HIS 0.003 0.001 HIS F 58 PHE 0.011 0.002 PHE P 133 TYR 0.010 0.001 TYR K 40 ARG 0.003 0.000 ARG O 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 329 time to evaluate : 4.021 Fit side-chains outliers start: 51 outliers final: 48 residues processed: 364 average time/residue: 2.0452 time to fit residues: 853.2729 Evaluate side-chains 367 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 319 time to evaluate : 3.832 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 34 residues processed: 14 average time/residue: 0.4599 time to fit residues: 16.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 4.9990 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 110 ASN F 110 ASN I 110 ASN L 110 ASN M 110 ASN N 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111253 restraints weight = 85176.662| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.04 r_work: 0.3172 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34074 Z= 0.210 Angle : 0.522 8.324 45970 Z= 0.294 Chirality : 0.039 0.132 4858 Planarity : 0.003 0.028 6068 Dihedral : 4.167 21.028 4494 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.47 % Allowed : 12.30 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.13), residues: 4066 helix: 3.55 (0.09), residues: 3082 sheet: None (None), residues: 0 loop : -1.45 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 94 HIS 0.003 0.001 HIS C 58 PHE 0.011 0.002 PHE G 133 TYR 0.010 0.001 TYR X 40 ARG 0.008 0.000 ARG W 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13739.22 seconds wall clock time: 243 minutes 37.61 seconds (14617.61 seconds total)