Starting phenix.real_space_refine (version: dev) on Fri Dec 16 19:40:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/12_2022/6k43_9913_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.030 sd= 1.242 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "M TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "N ASP 4": "OD1" <-> "OD2" Residue "N ASP 33": "OD1" <-> "OD2" Residue "N TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "O TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O ASP 132": "OD1" <-> "OD2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "P GLU 18": "OE1" <-> "OE2" Residue "P TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "Q ASP 33": "OD1" <-> "OD2" Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q ASP 139": "OD1" <-> "OD2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "R GLU 146": "OE1" <-> "OE2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ASP 160": "OD1" <-> "OD2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "T GLU 146": "OE1" <-> "OE2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "V ASP 33": "OD1" <-> "OD2" Residue "V TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 50": "OD1" <-> "OD2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ASP 132": "OD1" <-> "OD2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 50": "OD1" <-> "OD2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X ASP 33": "OD1" <-> "OD2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X GLU 127": "OE1" <-> "OE2" Residue "X ASP 139": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X ASP 160": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 31808 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" 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: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.62, per 1000 atoms: 0.55 Number of scatterers: 31808 At special positions: 0 Unit cell: (132.09, 132.09, 132.09, 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 36 26.01 S 96 16.00 O 6116 8.00 N 5428 7.00 C 20132 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.91 Conformation dependent library (CDL) restraints added in 4.8 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 114 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.695A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.810A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.832A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 removed outlier: 3.698A pdb=" N LYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 64 Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 4.683A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.851A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 109 Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.618A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.518A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.817A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.642A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.845A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 144 Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.690A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.723A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 64 Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.825A pdb=" N LYS G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.681A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 removed outlier: 3.715A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 64 Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.814A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 144 Processing helix chain 'H' and resid 146 through 152 removed outlier: 3.905A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.720A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 64 Processing helix chain 'I' and resid 83 through 109 Processing helix chain 'I' and resid 114 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.896A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 3.707A pdb=" N LYS J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 64 Processing helix chain 'J' and resid 83 through 109 Processing helix chain 'J' and resid 114 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.698A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.842A pdb=" N LYS K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 144 Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.826A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.699A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.834A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.685A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.827A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 109 Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 removed outlier: 3.708A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.815A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.680A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 removed outlier: 3.709A pdb=" N LYS O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 64 Processing helix chain 'O' and resid 83 through 109 Processing helix chain 'O' and resid 114 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 3.878A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.737A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.815A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 144 Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.805A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 64 Processing helix chain 'Q' and resid 83 through 109 Processing helix chain 'Q' and resid 114 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.845A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.820A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 removed outlier: 3.683A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 64 removed outlier: 3.598A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.677A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 removed outlier: 3.685A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 64 Processing helix chain 'T' and resid 83 through 109 Processing helix chain 'T' and resid 114 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 3.876A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.746A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.749A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 144 Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.850A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 removed outlier: 3.682A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.829A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 144 Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 3.742A pdb=" N LYS W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.814A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 4.626A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.586A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.822A pdb=" N LYS X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 4.671A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2415 hydrogen bonds defined for protein. 7245 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: 9.11 Time building geometry restraints manager: 14.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13491 1.39 - 1.56: 18653 1.56 - 1.73: 0 1.73 - 1.90: 192 1.90 - 2.07: 48 Bond restraints: 32384 Sorted by residual: bond pdb=" C ASP R 99 " pdb=" O ASP R 99 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.60e+00 bond pdb=" C ASP W 99 " pdb=" O ASP W 99 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C ASP A 99 " pdb=" O ASP A 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP T 99 " pdb=" O ASP T 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP O 99 " pdb=" O ASP O 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 ... (remaining 32379 not shown) Histogram of bond angle deviations from ideal: 85.34 - 104.16: 285 104.16 - 122.98: 41844 122.98 - 141.80: 1783 141.80 - 160.62: 0 160.62 - 179.44: 24 Bond angle restraints: 43936 Sorted by residual: angle pdb=" C TYR R 25 " pdb=" N PHE R 26 " pdb=" CA PHE R 26 " ideal model delta sigma weight residual 120.29 116.11 4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" C TYR W 25 " pdb=" N PHE W 26 " pdb=" CA PHE W 26 " ideal model delta sigma weight residual 120.29 116.25 4.04 1.42e+00 4.96e-01 8.09e+00 angle pdb=" C TYR I 25 " pdb=" N PHE I 26 " pdb=" CA PHE I 26 " ideal model delta sigma weight residual 120.29 116.26 4.03 1.42e+00 4.96e-01 8.05e+00 angle pdb=" C TYR G 25 " pdb=" N PHE G 26 " pdb=" CA PHE G 26 " ideal model delta sigma weight residual 120.29 116.33 3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" C TYR N 25 " pdb=" N PHE N 26 " pdb=" CA PHE N 26 " ideal model delta sigma weight residual 120.29 116.34 3.95 1.42e+00 4.96e-01 7.74e+00 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 16963 18.74 - 37.48: 2063 37.48 - 56.22: 259 56.22 - 74.95: 61 74.95 - 93.69: 38 Dihedral angle restraints: 19384 sinusoidal: 8064 harmonic: 11320 Sorted by residual: dihedral pdb=" C2B HEM K 301 " pdb=" C3B HEM K 301 " pdb=" CAB HEM K 301 " pdb=" CBB HEM K 301 " ideal model delta sinusoidal sigma weight residual -0.00 -39.28 39.28 2 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA PRO T 159 " pdb=" C PRO T 159 " pdb=" N ASP T 160 " pdb=" CA ASP T 160 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C2C HEM X 201 " pdb=" C3C HEM X 201 " pdb=" CAC HEM X 201 " pdb=" CBC HEM X 201 " ideal model delta sinusoidal sigma weight residual 0.00 37.74 -37.74 2 1.00e+01 1.00e-02 1.80e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2435 0.024 - 0.049: 1594 0.049 - 0.073: 595 0.073 - 0.097: 161 0.097 - 0.121: 91 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CA PRO J 159 " pdb=" N PRO J 159 " pdb=" C PRO J 159 " pdb=" CB PRO J 159 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA PRO L 161 " pdb=" N PRO L 161 " pdb=" C PRO L 161 " pdb=" CB PRO L 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA PRO Q 161 " pdb=" N PRO Q 161 " pdb=" C PRO Q 161 " pdb=" CB PRO Q 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 4873 not shown) Planarity restraints: 5680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM K 301 " 0.002 2.00e-02 2.50e+03 1.07e-02 2.58e+00 pdb=" C1B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" C2B HEM K 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3B HEM K 301 " -0.019 2.00e-02 2.50e+03 pdb=" C4B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" CAB HEM K 301 " 0.016 2.00e-02 2.50e+03 pdb=" CHB HEM K 301 " 0.011 2.00e-02 2.50e+03 pdb=" CHC HEM K 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMB HEM K 301 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " -0.016 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP G 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM O 202 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.37e+00 pdb=" C1B HEM O 202 " 0.005 2.00e-02 2.50e+03 pdb=" C2B HEM O 202 " 0.006 2.00e-02 2.50e+03 pdb=" C3B HEM O 202 " -0.005 2.00e-02 2.50e+03 pdb=" C4B HEM O 202 " 0.000 2.00e-02 2.50e+03 pdb=" CAB HEM O 202 " -0.001 2.00e-02 2.50e+03 pdb=" CHB HEM O 202 " 0.010 2.00e-02 2.50e+03 pdb=" CHC HEM O 202 " 0.013 2.00e-02 2.50e+03 pdb=" CMB HEM O 202 " -0.004 2.00e-02 2.50e+03 ... (remaining 5677 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 26 1.99 - 2.72: 2837 2.72 - 3.45: 46904 3.45 - 4.17: 62780 4.17 - 4.90: 122129 Nonbonded interactions: 234676 Sorted by model distance: nonbonded pdb=" OE1 GLU J 18 " pdb=" OE1 GLU J 51 " model vdw 1.266 3.040 nonbonded pdb=" OE1 GLU B 18 " pdb=" OE1 GLU B 51 " model vdw 1.287 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.303 3.040 nonbonded pdb=" OE1 GLU P 18 " pdb=" OE1 GLU P 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU L 18 " pdb=" OE1 GLU L 51 " model vdw 1.319 3.040 ... (remaining 234671 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 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 20132 2.51 5 N 5428 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.140 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: 0.030 Extract box with map and model: 6.430 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.280 Process input model: 76.520 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.082 32384 Z= 0.485 Angle : 0.716 15.729 43936 Z= 0.393 Chirality : 0.037 0.121 4876 Planarity : 0.003 0.027 5680 Dihedral : 15.849 93.692 12000 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.11), residues: 3792 helix: -0.37 (0.08), residues: 2888 sheet: None (None), residues: 0 loop : -4.43 (0.15), residues: 904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1011 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 1015 average time/residue: 0.4469 time to fit residues: 709.2486 Evaluate side-chains 669 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 665 time to evaluate : 3.802 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.2513 time to fit residues: 7.1384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 219 optimal weight: 0.1980 chunk 341 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 130 HIS C 24 GLN D 24 GLN D 156 GLN F 24 GLN F 118 ASN F 156 GLN E 24 GLN E 130 HIS G 24 GLN H 24 GLN I 24 GLN J 24 GLN K 24 GLN L 24 GLN M 24 GLN M 156 GLN N 24 GLN N 118 ASN O 24 GLN P 129 HIS Q 24 GLN R 24 GLN S 24 GLN S 118 ASN S 130 HIS S 156 GLN T 24 GLN U 24 GLN U 130 HIS V 24 GLN W 24 GLN W 156 GLN X 118 ASN X 156 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 32384 Z= 0.216 Angle : 0.625 11.589 43936 Z= 0.300 Chirality : 0.034 0.134 4876 Planarity : 0.003 0.020 5680 Dihedral : 6.770 87.115 4272 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.13), residues: 3792 helix: 3.15 (0.08), residues: 2900 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 819 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 65 residues processed: 824 average time/residue: 0.3881 time to fit residues: 521.5321 Evaluate side-chains 710 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 645 time to evaluate : 3.685 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 65 outliers final: 4 residues processed: 65 average time/residue: 0.2548 time to fit residues: 37.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 369 optimal weight: 7.9990 chunk 304 optimal weight: 0.3980 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 158 GLN B 28 HIS B 137 GLN C 28 HIS C 72 GLN D 72 GLN F 72 GLN E 28 HIS G 28 HIS H 28 HIS H 137 GLN I 28 HIS I 137 GLN J 158 GLN K 137 GLN L 28 HIS M 72 GLN N 72 GLN O 137 GLN P 28 HIS Q 28 HIS Q 72 GLN R 72 GLN S 137 GLN T 137 GLN T 158 GLN U 28 HIS V 28 HIS V 72 GLN W 72 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 32384 Z= 0.363 Angle : 0.707 22.980 43936 Z= 0.348 Chirality : 0.036 0.128 4876 Planarity : 0.003 0.027 5680 Dihedral : 6.932 89.848 4272 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.72 (0.13), residues: 3792 helix: 3.17 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : -3.35 (0.21), residues: 888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 688 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 72 residues processed: 750 average time/residue: 0.4040 time to fit residues: 488.9353 Evaluate side-chains 700 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 628 time to evaluate : 3.884 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 72 outliers final: 4 residues processed: 72 average time/residue: 0.2656 time to fit residues: 41.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 363 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 97 optimal weight: 0.0010 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS C 28 HIS E 28 HIS G 28 HIS H 28 HIS I 28 HIS K 137 GLN L 28 HIS P 28 HIS Q 28 HIS S 137 GLN U 28 HIS V 28 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 32384 Z= 0.217 Angle : 0.590 20.275 43936 Z= 0.279 Chirality : 0.033 0.128 4876 Planarity : 0.002 0.015 5680 Dihedral : 6.955 88.655 4272 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.49 (0.14), residues: 3792 helix: 3.73 (0.08), residues: 2940 sheet: None (None), residues: 0 loop : -3.45 (0.19), residues: 852 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 595 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 40 residues processed: 628 average time/residue: 0.3854 time to fit residues: 391.5294 Evaluate side-chains 592 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 552 time to evaluate : 3.743 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 4 residues processed: 40 average time/residue: 0.2589 time to fit residues: 24.9325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN F 137 GLN M 156 GLN N 156 GLN R 137 GLN S 137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 32384 Z= 0.198 Angle : 0.573 21.099 43936 Z= 0.268 Chirality : 0.032 0.135 4876 Planarity : 0.002 0.028 5680 Dihedral : 6.842 84.508 4272 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3792 helix: 3.91 (0.08), residues: 2956 sheet: None (None), residues: 0 loop : -3.46 (0.20), residues: 836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 554 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 38 residues processed: 571 average time/residue: 0.4075 time to fit residues: 376.5282 Evaluate side-chains 579 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 541 time to evaluate : 3.864 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 38 outliers final: 4 residues processed: 38 average time/residue: 0.2569 time to fit residues: 23.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 2.9990 chunk 327 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 0.0570 chunk 363 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN M 137 GLN N 156 GLN Q 156 GLN R 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 32384 Z= 0.223 Angle : 0.576 18.215 43936 Z= 0.275 Chirality : 0.033 0.135 4876 Planarity : 0.002 0.017 5680 Dihedral : 6.803 89.340 4272 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.76 (0.14), residues: 3792 helix: 3.89 (0.08), residues: 2952 sheet: None (None), residues: 0 loop : -3.30 (0.21), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 554 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 74 outliers final: 49 residues processed: 589 average time/residue: 0.4497 time to fit residues: 434.0525 Evaluate side-chains 593 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 544 time to evaluate : 3.778 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 49 outliers final: 4 residues processed: 49 average time/residue: 0.2899 time to fit residues: 32.6515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN J 54 HIS M 137 GLN N 156 GLN X 54 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 32384 Z= 0.205 Angle : 0.583 21.503 43936 Z= 0.274 Chirality : 0.032 0.133 4876 Planarity : 0.002 0.027 5680 Dihedral : 6.851 88.136 4272 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.92 (0.14), residues: 3792 helix: 4.00 (0.08), residues: 2944 sheet: None (None), residues: 0 loop : -3.16 (0.21), residues: 848 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 533 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 557 average time/residue: 0.4185 time to fit residues: 376.0761 Evaluate side-chains 539 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 519 time to evaluate : 3.642 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 4 residues processed: 20 average time/residue: 0.2584 time to fit residues: 15.0115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN N 156 GLN P 54 HIS R 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 32384 Z= 0.199 Angle : 0.571 20.341 43936 Z= 0.273 Chirality : 0.032 0.133 4876 Planarity : 0.002 0.020 5680 Dihedral : 6.871 88.935 4272 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.07 (0.14), residues: 3792 helix: 4.08 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 844 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 541 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 25 residues processed: 555 average time/residue: 0.4242 time to fit residues: 378.6876 Evaluate side-chains 540 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 515 time to evaluate : 3.799 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 25 outliers final: 4 residues processed: 25 average time/residue: 0.2665 time to fit residues: 18.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 337 optimal weight: 0.0670 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 305 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN M 137 GLN N 156 GLN R 137 GLN R 156 GLN U 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 32384 Z= 0.290 Angle : 0.639 13.100 43936 Z= 0.320 Chirality : 0.034 0.142 4876 Planarity : 0.003 0.039 5680 Dihedral : 6.980 87.362 4272 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3792 helix: 3.75 (0.08), residues: 2928 sheet: None (None), residues: 0 loop : -2.91 (0.22), residues: 864 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 558 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 35 residues processed: 566 average time/residue: 0.4505 time to fit residues: 407.9661 Evaluate side-chains 570 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 535 time to evaluate : 3.808 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 35 outliers final: 4 residues processed: 35 average time/residue: 0.2583 time to fit residues: 22.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 374 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN F 54 HIS G 54 HIS L 54 HIS M 54 HIS M 137 GLN N 156 GLN O 54 HIS R 137 GLN W 54 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 32384 Z= 0.206 Angle : 0.604 20.836 43936 Z= 0.293 Chirality : 0.033 0.149 4876 Planarity : 0.003 0.093 5680 Dihedral : 6.958 88.246 4272 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.12 (0.14), residues: 3792 helix: 4.17 (0.08), residues: 2916 sheet: None (None), residues: 0 loop : -2.93 (0.21), residues: 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 509 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 513 average time/residue: 0.4059 time to fit residues: 339.0179 Evaluate side-chains 502 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 496 time to evaluate : 3.952 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.2980 time to fit residues: 9.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN E 137 GLN K 156 GLN M 137 GLN N 156 GLN R 137 GLN W 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126648 restraints weight = 49097.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130148 restraints weight = 29082.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132539 restraints weight = 19689.389| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 32384 Z= 0.257 Angle : 0.651 21.160 43936 Z= 0.314 Chirality : 0.033 0.165 4876 Planarity : 0.003 0.062 5680 Dihedral : 6.893 89.252 4272 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.92 (0.14), residues: 3792 helix: 3.93 (0.08), residues: 2928 sheet: None (None), residues: 0 loop : -2.70 (0.22), residues: 864 =============================================================================== Job complete usr+sys time: 6974.19 seconds wall clock time: 126 minutes 57.56 seconds (7617.56 seconds total)