Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 15:43:40 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/01_2021/6s61_10101.pdb" } resolution = 1.84 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 71060 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "B" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "C" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "D" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "E" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "F" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "G" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "H" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "I" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "J" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "K" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "L" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "M" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "N" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "O" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "P" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "Q" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "R" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "S" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "T" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "U" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "V" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "W" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "X" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' FE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} 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: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "D" 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: "F" 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: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "J" 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "L" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} 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: "N" 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "P" 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} 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: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "T" 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "V" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "W" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "X" 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: 56 residue: pdb=" N ASER A 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER A 113 " occ=0.30 residue: pdb=" N ASER B 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER B 113 " occ=0.30 residue: pdb=" N ASER C 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER C 113 " occ=0.30 residue: pdb=" N ASER D 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER D 113 " occ=0.30 residue: pdb=" N ASER E 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER E 113 " occ=0.30 residue: pdb=" N ASER F 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER F 113 " occ=0.30 residue: pdb=" N ASER G 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER G 113 " occ=0.30 residue: pdb=" N ASER H 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER H 113 " occ=0.30 residue: pdb=" N ASER I 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER I 113 " occ=0.30 residue: pdb=" N ASER J 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER J 113 " occ=0.30 residue: pdb=" N ASER K 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER K 113 " occ=0.30 residue: pdb=" N ASER L 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER L 113 " occ=0.30 ... (remaining 44 not shown) Time building chain proxies: 58.56, per 1000 atoms: 0.82 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'B' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'C' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'D' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'E' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'F' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'G' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'H' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'I' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'J' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'K' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'L' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'M' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'N' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'O' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'P' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'Q' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'R' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'S' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'T' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'U' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'V' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'W' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'X' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) } Number of scatterers: 71060 At special positions: 0 Unit cell: (134.48, 134.48, 134.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 24 29.99 Fe 6 26.01 S 192 16.00 O 10430 8.00 N 6048 7.00 C 21456 6.00 H 32904 1.00 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: 50.29 Conformation dependent library (CDL) restraints added in 11.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 8040 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: 28.84 Time building geometry restraints manager: 52.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32808 1.03 - 1.23: 2040 1.23 - 1.42: 13296 1.42 - 1.62: 19464 1.62 - 1.81: 312 Bond restraints: 67920 Sorted by residual: bond pdb=" CA ARG U 63 " pdb=" HA ARG U 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG E 63 " pdb=" HA ARG E 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG S 63 " pdb=" HA ARG S 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG G 63 " pdb=" HA ARG G 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG O 63 " pdb=" HA ARG O 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 67915 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.63: 528 104.63 - 111.94: 74376 111.94 - 119.26: 18312 119.26 - 126.57: 28512 126.57 - 133.88: 480 Bond angle restraints: 122208 Sorted by residual: angle pdb=" N ARG I 63 " pdb=" CA ARG I 63 " pdb=" C ARG I 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG N 63 " pdb=" CA ARG N 63 " pdb=" C ARG N 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG C 63 " pdb=" CA ARG C 63 " pdb=" C ARG C 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG G 63 " pdb=" CA ARG G 63 " pdb=" C ARG G 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG J 63 " pdb=" CA ARG J 63 " pdb=" C ARG J 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 ... (remaining 122203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 25848 17.50 - 34.99: 1296 34.99 - 52.48: 336 52.48 - 69.98: 264 69.98 - 87.47: 24 Dihedral angle restraints: 27768 sinusoidal: 12888 harmonic: 14880 Sorted by residual: dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL P 46 " pdb=" C VAL P 46 " pdb=" N ALA P 47 " pdb=" CA ALA P 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL W 46 " pdb=" C VAL W 46 " pdb=" N ALA W 47 " pdb=" CA ALA W 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 27765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3168 0.047 - 0.093: 1128 0.093 - 0.140: 408 0.140 - 0.186: 120 0.186 - 0.232: 96 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA ASN P 50 " pdb=" N ASN P 50 " pdb=" C ASN P 50 " pdb=" CB ASN P 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN W 50 " pdb=" N ASN W 50 " pdb=" C ASN W 50 " pdb=" CB ASN W 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4917 not shown) Planarity restraints: 10344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN V 75 " -0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN V 75 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN V 75 " 0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN V 75 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN V 75 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN V 75 " -0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN S 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN S 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN S 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN S 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN S 75 " 0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN O 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN O 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN O 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN O 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN O 75 " 0.495 2.00e-02 2.50e+03 ... (remaining 10341 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 168 1.17 - 2.03: 1776 2.03 - 2.88: 180624 2.88 - 3.74: 350652 3.74 - 4.60: 593820 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1127040 Sorted by model distance: nonbonded pdb=" NH2BARG E 63 " pdb=" NH2BARG U 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG H 63 " pdb=" NH2BARG S 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG O 63 " pdb=" NH2BARG V 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG F 63 " pdb=" NH2BARG Q 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG J 63 " pdb=" NH2BARG W 63 " model vdw 0.312 3.100 ... (remaining 1127035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 71060 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21456 2.51 5 N 6048 2.21 5 O 10430 1.98 5 H 32904 0.53 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=0.15 max=1.00 mean=0.99 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: 1.440 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: 0.400 Extract box with map and model: 11.300 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.230 Process input model: 262.850 Set up NCS constraints: 0.330 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:8.310 Internal consistency checks: 0.000 Total: 285.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.011 0.088 35016 Angle : 1.358 8.395 47160 Chirality : 0.063 0.232 4920 Planarity : 0.010 0.046 6216 Dihedral : 12.210 87.470 13344 Min Nonbonded Distance : 0.312 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.12), residues: 4224 helix: 2.89 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.60 (0.23), residues: 864 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 984 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 48 poor density : 936 time to evaluate : 4.681 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 984 average time/residue: 3.3872 time to fit residues: 3340.7442 Evaluate side-chains 792 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 792 time to evaluate : 4.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8482 ------------------------------------------------------------------------------- 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: 0.9980 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 370 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 83 GLN A 141 GLN B 75 GLN B 83 GLN B 141 GLN C 75 GLN C 83 GLN C 141 GLN D 75 GLN D 83 GLN D 141 GLN E 75 GLN E 83 GLN E 141 GLN F 75 GLN F 83 GLN F 141 GLN G 75 GLN G 83 GLN G 141 GLN H 75 GLN H 83 GLN H 141 GLN I 75 GLN I 83 GLN I 141 GLN J 75 GLN J 83 GLN J 141 GLN K 75 GLN K 83 GLN K 141 GLN L 75 GLN L 83 GLN L 141 GLN M 75 GLN M 83 GLN M 141 GLN N 75 GLN N 83 GLN N 141 GLN O 75 GLN O 83 GLN O 141 GLN P 75 GLN P 83 GLN P 141 GLN Q 75 GLN Q 83 GLN Q 141 GLN R 75 GLN R 83 GLN R 141 GLN S 75 GLN S 83 GLN S 141 GLN T 75 GLN T 83 GLN T 141 GLN U 75 GLN U 83 GLN U 141 GLN V 75 GLN V 83 GLN V 141 GLN W 75 GLN W 83 GLN W 141 GLN X 75 GLN X 83 GLN X 141 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.017 35016 Angle : 0.503 5.147 47160 Chirality : 0.032 0.120 4920 Planarity : 0.003 0.016 6216 Dihedral : 3.836 18.332 4632 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.51 (0.13), residues: 4224 helix: 4.25 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.86 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 816 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 816 time to evaluate : 5.023 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 816 average time/residue: 3.7821 time to fit residues: 3094.1951 Evaluate side-chains 718 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 718 time to evaluate : 4.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8152 ------------------------------------------------------------------------------- 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: 10.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 0.6980 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 105 HIS J 141 GLN K 141 GLN L 141 GLN M 105 HIS M 141 GLN N 105 HIS N 141 GLN O 141 GLN P 141 GLN Q 105 HIS Q 141 GLN R 141 GLN S 105 HIS S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.029 35016 Angle : 0.683 7.170 47160 Chirality : 0.038 0.128 4920 Planarity : 0.004 0.034 6216 Dihedral : 4.088 16.290 4632 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.12), residues: 4224 helix: 3.29 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 674 time to evaluate : 4.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 3.7053 time to fit residues: 2505.0897 Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 674 time to evaluate : 4.699 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8620 ------------------------------------------------------------------------------- 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: 10.0000 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 353 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN U 14 GLN V 14 GLN W 14 GLN X 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.029 35016 Angle : 0.677 7.100 47160 Chirality : 0.037 0.125 4920 Planarity : 0.005 0.030 6216 Dihedral : 4.134 16.993 4632 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.12), residues: 4224 helix: 3.01 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.63 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 722 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 48 poor density : 674 time to evaluate : 5.130 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 698 average time/residue: 3.6012 time to fit residues: 2521.6089 Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 650 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8489 ------------------------------------------------------------------------------- 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: 10.0000 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN U 14 GLN V 14 GLN W 14 GLN X 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.025 35016 Angle : 0.612 5.660 47160 Chirality : 0.035 0.124 4920 Planarity : 0.004 0.027 6216 Dihedral : 4.123 18.954 4632 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.13), residues: 4224 helix: 3.23 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.66 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 698 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 674 time to evaluate : 4.735 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 698 average time/residue: 3.5448 time to fit residues: 2482.0773 Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 650 time to evaluate : 4.671 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8667 ------------------------------------------------------------------------------- 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: 10.0000 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 125 ASN G 125 ASN I 125 ASN K 125 ASN N 125 ASN R 125 ASN V 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.023 35016 Angle : 0.619 5.516 47160 Chirality : 0.035 0.124 4920 Planarity : 0.004 0.029 6216 Dihedral : 4.142 19.079 4632 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.13), residues: 4224 helix: 3.18 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.62 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 678 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 654 time to evaluate : 4.733 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 678 average time/residue: 3.5818 time to fit residues: 2436.3438 Evaluate side-chains 694 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 670 time to evaluate : 4.732 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8728 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.026 35016 Angle : 0.634 5.517 47160 Chirality : 0.035 0.124 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.140 18.633 4632 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.13), residues: 4224 helix: 3.13 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.65 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 698 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 674 time to evaluate : 4.788 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 698 average time/residue: 3.6001 time to fit residues: 2520.6898 Evaluate side-chains 694 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 670 time to evaluate : 4.660 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8211 ------------------------------------------------------------------------------- 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: 9.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.026 35016 Angle : 0.618 5.445 47160 Chirality : 0.035 0.123 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.131 18.818 4632 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.13), residues: 4224 helix: 3.21 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.64 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 650 time to evaluate : 4.698 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 674 average time/residue: 3.6046 time to fit residues: 2437.3550 Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 650 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.022 35016 Angle : 0.558 5.369 47160 Chirality : 0.033 0.122 4920 Planarity : 0.003 0.023 6216 Dihedral : 4.061 19.797 4632 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.13), residues: 4224 helix: 3.63 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.69 (0.24), residues: 864 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 650 time to evaluate : 5.960 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 674 average time/residue: 3.6055 time to fit residues: 2437.9093 Evaluate side-chains 673 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 649 time to evaluate : 4.728 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.8255 ------------------------------------------------------------------------------- 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: 10.0000 chunk 387 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.4980 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.026 35016 Angle : 0.627 5.317 47160 Chirality : 0.036 0.122 4920 Planarity : 0.004 0.029 6216 Dihedral : 4.121 19.169 4632 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.13), residues: 4224 helix: 3.27 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.65 (0.24), residues: 864 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield and 0 Emsley and 4224 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 676 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 652 time to evaluate : 4.672 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 676 average time/residue: 3.5800 time to fit residues: 2427.8388 Evaluate side-chains 672 residues out of total 3600 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 648 time to evaluate : 4.683 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.7655 ------------------------------------------------------------------------------- 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: 9.9990 chunk 344 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.139433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.115530 restraints weight = 131669.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121781 restraints weight = 74004.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.126053 restraints weight = 47937.368| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.025 35016 ANGLE : 0.625 5.393 47160 CHIRALITY : 0.035 0.125 4920 PLANARITY : 0.004 0.030 6216 DIHEDRAL : 4.130 18.953 4632 MIN NONBONDED DISTANCE : 1.787 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 4.44 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.18 % FAVORED : 98.82 % ROTAMER OUTLIERS : 0.65 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 33.33 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 4.14 (0.13), RESIDUES: 4224 HELIX: 3.23 (0.08), RESIDUES: 3360 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.64 (0.24), RESIDUES: 864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.025 35016 Angle : 0.625 5.393 47160 Chirality : 0.035 0.125 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.130 18.953 4632 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.13), residues: 4224 helix: 3.23 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.64 (0.24), residues: 864 =============================================================================== Job complete usr+sys time: 31564.40 seconds wall clock time: 543 minutes 14.83 seconds (32594.83 seconds total)