Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 06:57:01 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/01_2021/7a6b_11669_updated.pdb" } resolution = 1.33 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= 0.000 sd= 0.017 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 41494 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "1" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "K" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "a" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "B" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "E" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "e" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "r" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "G" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "I" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "M" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "O" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "Q" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "S" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "U" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "W" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "Y" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "2" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "4" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "F" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "H" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "P" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "X" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "6" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 169, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1284 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} 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: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} 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: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "1" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "K" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "a" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "E" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "e" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "r" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "I" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "O" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "U" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "W" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "Y" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "2" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "4" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "6" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Residues with excluded nonbonded symmetry interactions: 432 residue: pdb=" N ALYS A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 49 " occ=0.50 residue: pdb=" N ALYS A 53 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 53 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N ALYS A 71 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 71 " occ=0.50 residue: pdb=" N ALEU A 72 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 72 " occ=0.50 residue: pdb=" N AGLN A 75 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 75 " occ=0.50 residue: pdb=" N ALYS A 87 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 87 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 113 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 ... (remaining 420 not shown) Time building chain proxies: 26.04, per 1000 atoms: 0.63 Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) } Number of scatterers: 41494 At special positions: 0 Unit cell: (131.364, 131.364, 131.364, 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) S 120 16.00 Na 32 11.00 O 11150 8.00 N 6672 7.00 C 23520 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.04 Conformation dependent library (CDL) restraints added in 8.6 seconds 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 76 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 76 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 76 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 76 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 76 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 76 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 76 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 76 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 76 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 76 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 76 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 76 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 76 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 76 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 76 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 76 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 2808 hydrogen bonds defined for protein. 8688 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: 12.21 Time building geometry restraints manager: 17.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8432 1.32 - 1.45: 8657 1.45 - 1.58: 21335 1.58 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 38640 Sorted by residual: bond pdb=" C BSER a 163 " pdb=" O BSER a 163 " ideal model delta sigma weight residual 1.236 1.357 -0.122 1.32e-02 5.74e+03 8.50e+01 bond pdb=" C BSER K 163 " pdb=" O BSER K 163 " ideal model delta sigma weight residual 1.236 1.353 -0.117 1.32e-02 5.74e+03 7.83e+01 bond pdb=" C BSER A 163 " pdb=" O BSER A 163 " ideal model delta sigma weight residual 1.236 1.330 -0.094 1.32e-02 5.74e+03 5.09e+01 bond pdb=" C BSER 1 163 " pdb=" O BSER 1 163 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" C BSER B 163 " pdb=" O BSER B 163 " ideal model delta sigma weight residual 1.236 1.309 -0.074 1.32e-02 5.74e+03 3.11e+01 ... (remaining 38635 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.70: 475 105.70 - 112.81: 17464 112.81 - 119.92: 18193 119.92 - 127.03: 15972 127.03 - 134.13: 360 Bond angle restraints: 52464 Sorted by residual: angle pdb=" CA ASP W 150 " pdb=" CB ASP W 150 " pdb=" CG ASP W 150 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" CA ASP K 150 " pdb=" CB ASP K 150 " pdb=" CG ASP K 150 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA ASP 1 150 " pdb=" CB ASP 1 150 " pdb=" CG ASP 1 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP Q 150 " pdb=" CB ASP Q 150 " pdb=" CG ASP Q 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP O 150 " pdb=" CB ASP O 150 " pdb=" CG ASP O 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 ... (remaining 52459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 20885 15.57 - 31.13: 1917 31.13 - 46.70: 622 46.70 - 62.27: 264 62.27 - 77.84: 72 Dihedral angle restraints: 23760 sinusoidal: 9864 harmonic: 13896 Sorted by residual: dihedral pdb=" C TYR 2 39 " pdb=" N TYR 2 39 " pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C TYR P 39 " pdb=" N TYR P 39 " pdb=" CA TYR P 39 " pdb=" CB TYR P 39 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C TYR G 39 " pdb=" N TYR G 39 " pdb=" CA TYR G 39 " pdb=" CB TYR G 39 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 23757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2957 0.087 - 0.175: 1584 0.175 - 0.262: 685 0.262 - 0.350: 126 0.350 - 0.437: 48 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA TYR 2 39 " pdb=" N TYR 2 39 " pdb=" C TYR 2 39 " pdb=" CB TYR 2 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 5397 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 137 " 0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR K 137 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR K 137 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR K 137 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR K 137 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR K 137 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR K 137 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR K 137 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR r 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR r 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR r 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR r 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR r 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR r 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR r 137 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR a 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.086 2.00e-02 2.50e+03 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.62: 927 2.62 - 3.35: 61215 3.35 - 4.08: 129381 4.08 - 4.81: 201860 4.81 - 5.54: 277643 Nonbonded interactions: 671026 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU 1 101 " pdb=" NH2BARG 1 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU U 101 " pdb=" NH2BARG U 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU O 101 " pdb=" NH2BARG O 156 " model vdw 1.893 2.520 ... (remaining 671021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 41494 True True 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 S 120 5.16 5 Na 32 4.78 5 C 23520 2.51 5 N 6672 2.21 5 O 11150 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=0.50 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set model interpretation parameters: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 26.990 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.140 Process input model: 123.240 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.830 Internal consistency checks: 0.000 Total: 164.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.015 0.122 38640 Angle : 1.603 9.077 52464 Chirality : 0.124 0.437 5400 Planarity : 0.011 0.061 7128 Dihedral : 15.327 77.836 14976 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 25.00 % 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: 2.52 (0.11), residues: 5136 helix: 1.91 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.84 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 72 poor density : 744 time to evaluate : 3.393 Fit side-chains outliers start: 72 outliers final: 0 residues processed: 768 average time/residue: 1.3391 time to fit residues: 1034.2937 Evaluate side-chains 538 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 538 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 75 GLN B A 86 GLN A 98 ASN A 125 ASN A 136 HIS 1 60 HIS 1 75 GLN B 1 83 GLN 1 86 GLN 1 98 ASN 1 125 ASN 1 136 HIS K 60 HIS K 75 GLN B K 83 GLN K 86 GLN K 98 ASN K 125 ASN K 136 HIS a 60 HIS a 75 GLN B a 83 GLN a 86 GLN a 98 ASN a 125 ASN a 136 HIS B 60 HIS B 75 GLN B B 83 GLN B 86 GLN B 98 ASN B 125 ASN B 136 HIS E 60 HIS E 75 GLN B E 83 GLN E 86 GLN E 98 ASN E 125 ASN E 136 HIS e 60 HIS e 75 GLN B e 83 GLN e 86 GLN e 98 ASN e 125 ASN e 136 HIS r 60 HIS r 75 GLN B r 83 GLN r 86 GLN r 98 ASN r 125 ASN r 136 HIS G 60 HIS G 75 GLN B G 83 GLN G 86 GLN G 98 ASN G 125 ASN G 136 HIS I 60 HIS I 75 GLN B I 83 GLN I 86 GLN I 98 ASN I 125 ASN I 136 HIS M 60 HIS M 75 GLN B M 86 GLN M 98 ASN M 125 ASN M 136 HIS O 60 HIS O 75 GLN B O 83 GLN O 86 GLN O 98 ASN O 125 ASN O 136 HIS Q 60 HIS Q 75 GLN B Q 83 GLN Q 86 GLN Q 98 ASN Q 125 ASN Q 136 HIS S 60 HIS S 75 GLN B S 83 GLN S 86 GLN S 98 ASN S 125 ASN S 136 HIS U 60 HIS U 75 GLN B U 83 GLN U 86 GLN U 98 ASN U 125 ASN U 136 HIS W 60 HIS W 75 GLN B W 83 GLN W 86 GLN W 98 ASN W 125 ASN W 136 HIS Y 60 HIS Y 75 GLN B Y 83 GLN Y 86 GLN Y 98 ASN Y 125 ASN Y 136 HIS 2 60 HIS 2 75 GLN B 2 83 GLN 2 86 GLN 2 98 ASN 2 125 ASN 2 136 HIS 4 60 HIS 4 75 GLN B 4 83 GLN 4 86 GLN 4 98 ASN 4 125 ASN 4 136 HIS F 60 HIS F 75 GLN B F 83 GLN F 86 GLN F 98 ASN F 125 ASN F 136 HIS H 60 HIS H 75 GLN B H 83 GLN H 86 GLN H 98 ASN H 125 ASN H 136 HIS P 60 HIS P 75 GLN B P 83 GLN P 86 GLN P 98 ASN P 125 ASN P 136 HIS X 60 HIS X 75 GLN B X 83 GLN X 86 GLN X 98 ASN X 125 ASN X 136 HIS 6 60 HIS 6 75 GLN B 6 83 GLN 6 86 GLN 6 98 ASN 6 125 ASN 6 136 HIS Total number of N/Q/H flips: 166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 38640 Angle : 0.642 6.072 52464 Chirality : 0.039 0.155 5400 Planarity : 0.004 0.034 7128 Dihedral : 4.726 19.181 5328 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.34 (0.11), residues: 5136 helix: 3.29 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.83 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 672 time to evaluate : 3.336 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 1.4029 time to fit residues: 948.1780 Evaluate side-chains 548 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 548 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 0.9980 chunk 126 optimal weight: 0.0970 chunk 297 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN A 139 ASN 1 86 GLN 1 125 ASN 1 139 ASN K 86 GLN K 125 ASN K 139 ASN a 86 GLN a 125 ASN a 139 ASN B 86 GLN B 125 ASN B 139 ASN E 86 GLN E 125 ASN E 139 ASN e 86 GLN e 125 ASN e 139 ASN r 86 GLN r 125 ASN r 139 ASN G 86 GLN G 125 ASN G 139 ASN I 86 GLN I 125 ASN I 139 ASN M 86 GLN M 125 ASN M 139 ASN O 86 GLN O 125 ASN O 139 ASN Q 86 GLN Q 125 ASN Q 139 ASN S 86 GLN S 125 ASN S 139 ASN U 86 GLN U 125 ASN U 139 ASN W 86 GLN W 125 ASN W 139 ASN Y 86 GLN Y 125 ASN Y 139 ASN 2 86 GLN 2 125 ASN 2 139 ASN 4 86 GLN 4 125 ASN 4 139 ASN F 86 GLN F 125 ASN F 139 ASN H 86 GLN H 125 ASN H 139 ASN P 86 GLN P 125 ASN P 139 ASN X 86 GLN X 125 ASN X 139 ASN 6 86 GLN 6 125 ASN 6 139 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.023 38640 Angle : 0.619 5.550 52464 Chirality : 0.037 0.141 5400 Planarity : 0.003 0.019 7128 Dihedral : 4.580 19.006 5328 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.62 (0.11), residues: 5136 helix: 3.50 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.84 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 588 time to evaluate : 3.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 1.4436 time to fit residues: 854.3604 Evaluate side-chains 549 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 549 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 0.3980 chunk 177 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 0.6980 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 83 GLN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.025 38640 Angle : 0.566 5.652 52464 Chirality : 0.035 0.134 5400 Planarity : 0.003 0.026 7128 Dihedral : 4.392 19.156 5328 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.12 (0.12), residues: 5136 helix: 3.86 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.95 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 636 time to evaluate : 3.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 1.4016 time to fit residues: 897.2050 Evaluate side-chains 553 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 553 time to evaluate : 3.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.027 38640 Angle : 0.697 7.574 52464 Chirality : 0.039 0.137 5400 Planarity : 0.005 0.042 7128 Dihedral : 4.597 18.913 5328 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.51 (0.11), residues: 5136 helix: 3.44 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.73 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 573 time to evaluate : 3.315 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 1.4469 time to fit residues: 834.7016 Evaluate side-chains 499 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 499 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.025 38640 Angle : 0.609 7.529 52464 Chirality : 0.036 0.135 5400 Planarity : 0.006 0.089 7128 Dihedral : 4.478 19.311 5328 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.95 (0.12), residues: 5136 helix: 3.75 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.87 (0.23), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 557 time to evaluate : 3.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 1.4252 time to fit residues: 799.4957 Evaluate side-chains 526 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 526 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 50.0000 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.029 38640 Angle : 0.673 10.415 52464 Chirality : 0.037 0.136 5400 Planarity : 0.008 0.126 7128 Dihedral : 4.569 19.427 5328 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.78 (0.11), residues: 5136 helix: 3.62 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.80 (0.23), residues: 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 573 time to evaluate : 4.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 1.4251 time to fit residues: 823.0065 Evaluate side-chains 522 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 522 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 250 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 86 GLN A 125 ASN 1 60 HIS 1 86 GLN 1 125 ASN K 60 HIS K 86 GLN K 125 ASN a 60 HIS a 86 GLN a 125 ASN B 60 HIS B 86 GLN B 125 ASN E 60 HIS E 86 GLN E 125 ASN e 60 HIS e 86 GLN e 125 ASN r 60 HIS r 86 GLN r 125 ASN G 60 HIS G 86 GLN G 125 ASN I 60 HIS I 86 GLN I 125 ASN M 60 HIS M 86 GLN M 125 ASN O 60 HIS O 86 GLN O 125 ASN Q 60 HIS Q 86 GLN Q 125 ASN S 60 HIS S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 60 HIS W 86 GLN W 125 ASN Y 60 HIS Y 86 GLN Y 125 ASN 2 60 HIS 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 60 HIS F 86 GLN F 125 ASN H 60 HIS H 86 GLN H 125 ASN P 60 HIS P 86 GLN P 125 ASN X 60 HIS X 86 GLN X 125 ASN 6 60 HIS 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.035 38640 Angle : 0.795 15.448 52464 Chirality : 0.039 0.136 5400 Planarity : 0.005 0.072 7128 Dihedral : 4.651 19.007 5328 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.42 (0.11), residues: 5136 helix: 3.38 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.65 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 548 time to evaluate : 3.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 1.4761 time to fit residues: 814.8605 Evaluate side-chains 475 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 475 time to evaluate : 3.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 86 GLN A 125 ASN 1 60 HIS 1 86 GLN 1 125 ASN K 60 HIS K 86 GLN K 125 ASN a 60 HIS a 86 GLN a 125 ASN B 60 HIS B 86 GLN B 125 ASN E 60 HIS E 86 GLN E 125 ASN e 60 HIS e 86 GLN e 125 ASN r 60 HIS r 86 GLN r 125 ASN G 60 HIS G 86 GLN G 125 ASN I 60 HIS I 86 GLN I 125 ASN M 60 HIS M 86 GLN M 125 ASN O 60 HIS O 86 GLN O 125 ASN Q 60 HIS Q 86 GLN Q 125 ASN S 60 HIS S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 60 HIS W 86 GLN W 125 ASN Y 60 HIS Y 86 GLN Y 125 ASN 2 60 HIS 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 60 HIS F 86 GLN F 125 ASN H 60 HIS H 86 GLN H 125 ASN P 60 HIS P 86 GLN P 125 ASN X 60 HIS X 86 GLN X 125 ASN 6 60 HIS 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.035 38640 Angle : 0.726 6.463 52464 Chirality : 0.040 0.152 5400 Planarity : 0.004 0.023 7128 Dihedral : 4.701 18.423 5328 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.14 (0.11), residues: 5136 helix: 3.19 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.56 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 578 time to evaluate : 3.471 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 1.4811 time to fit residues: 861.6177 Evaluate side-chains 525 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 525 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 183 optimal weight: 0.7980 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 8.9990 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.032 38640 Angle : 0.646 8.241 52464 Chirality : 0.036 0.140 5400 Planarity : 0.005 0.078 7128 Dihedral : 4.572 19.275 5328 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.66 (0.11), residues: 5136 helix: 3.56 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.67 (0.22), residues: 960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield and 0 Emsley and 5136 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 573 time to evaluate : 3.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 1.4395 time to fit residues: 830.4823 Evaluate side-chains 549 residues out of total 3264 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 549 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.8980 chunk 344 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 50.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.163108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134741 restraints weight = 174628.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.134376 restraints weight = 52003.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.135214 restraints weight = 53006.082| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.031 38640 ANGLE : 0.676 13.382 52464 CHIRALITY : 0.036 0.140 5400 PLANARITY : 0.010 0.168 7128 DIHEDRAL : 4.567 19.315 5328 MIN NONBONDED DISTANCE : 2.177 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.36 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.79 % FAVORED : 98.21 % ROTAMER OUTLIERS : 1.79 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 25.00 % 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: 4.96 (0.12), RESIDUES: 5136 HELIX: 3.77 (0.07), RESIDUES: 4176 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.81 (0.23), RESIDUES: 960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.031 38640 Angle : 0.676 13.382 52464 Chirality : 0.036 0.140 5400 Planarity : 0.010 0.168 7128 Dihedral : 4.567 19.315 5328 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.96 (0.12), residues: 5136 helix: 3.77 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.81 (0.23), residues: 960 =============================================================================== Job complete usr+sys time: 13597.86 seconds wall clock time: 240 minutes 9.15 seconds (14409.15 seconds total)