Starting phenix.real_space_refine (version: dev) on Fri Apr 8 22:55:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/04_2022/7k3v_22657.pdb" } resolution = 1.34 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 38406 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "B" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "C" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "D" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "E" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "F" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "G" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "H" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "I" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "J" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "K" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "L" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "M" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "N" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "O" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "P" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "Q" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "R" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "S" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "T" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "U" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "V" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "W" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "X" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "G" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "H" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "L" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "N" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "O" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "P" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "S" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "T" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "U" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "W" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 50.39, per 1000 atoms: 1.31 Number of scatterers: 38406 At special positions: 0 Unit cell: (137.2, 137.2, 137.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 254 29.99 S 192 16.00 Na 80 11.00 O 9536 8.00 N 6096 7.00 C 22248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.00 Conformation dependent library (CDL) restraints added in 13.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 208 " pdb="ZN ZN F 208 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - 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 208 " pdb="ZN ZN J 208 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 204 " pdb="ZN ZN M 204 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 208 " pdb="ZN ZN N 208 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 204 " pdb="ZN ZN O 204 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 208 " pdb="ZN ZN P 208 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 209 " pdb="ZN ZN Q 209 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 209 " pdb="ZN ZN R 209 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 208 " pdb="ZN ZN S 208 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 209 " pdb="ZN ZN T 209 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 208 " pdb="ZN ZN U 208 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 209 " pdb="ZN ZN V 209 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 208 " pdb="ZN ZN W 208 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 208 " pdb="ZN ZN X 208 " - pdb=" ND1 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 2688 hydrogen bonds defined for protein. 8064 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: 16.39 Time building geometry restraints manager: 17.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11952 1.34 - 1.46: 6288 1.46 - 1.58: 17592 1.58 - 1.70: 0 1.70 - 1.81: 288 Bond restraints: 36120 Sorted by residual: bond pdb=" CB ARG N 79 " pdb=" CG ARG N 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG Q 79 " pdb=" CG ARG Q 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG P 79 " pdb=" CG ARG P 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG S 79 " pdb=" CG ARG S 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG O 79 " pdb=" CG ARG O 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 ... (remaining 36115 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.73: 384 105.73 - 112.77: 19272 112.77 - 119.81: 12816 119.81 - 126.85: 15792 126.85 - 133.89: 408 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP X 93 " pdb=" N GLU X 94 " pdb=" CA GLU X 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 19776 14.98 - 29.97: 1776 29.97 - 44.95: 528 44.95 - 59.94: 288 59.94 - 74.92: 48 Dihedral angle restraints: 22416 sinusoidal: 9576 harmonic: 12840 Sorted by residual: dihedral pdb=" CA TRP V 93 " pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TRP E 93 " pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TRP K 93 " pdb=" C TRP K 93 " pdb=" N GLU K 94 " pdb=" CA GLU K 94 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 22413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3240 0.033 - 0.065: 1296 0.065 - 0.098: 480 0.098 - 0.131: 120 0.131 - 0.164: 48 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CG LEU K 72 " pdb=" CB LEU K 72 " pdb=" CD1 LEU K 72 " pdb=" CD2 LEU K 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CG LEU J 72 " pdb=" CB LEU J 72 " pdb=" CD1 LEU J 72 " pdb=" CD2 LEU J 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CG LEU W 72 " pdb=" CB LEU W 72 " pdb=" CD1 LEU W 72 " pdb=" CD2 LEU W 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 5181 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU S 94 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU S 94 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU S 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER S 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU N 94 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU N 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER N 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 94 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU K 94 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU K 94 " 0.012 2.00e-02 2.50e+03 pdb=" N SER K 95 " 0.012 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 0.21 - 1.15: 84 1.15 - 2.09: 140 2.09 - 3.02: 26276 3.02 - 3.96: 124464 3.96 - 4.90: 223228 Warning: very small nonbonded interaction distances. Nonbonded interactions: 374192 Sorted by model distance: nonbonded pdb=" O HOH O 318 " pdb=" O HOH O 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH X 318 " pdb=" O HOH X 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH E 318 " pdb=" O HOH E 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH G 318 " pdb=" O HOH G 339 " model vdw 0.211 2.440 nonbonded pdb=" O HOH C 318 " pdb=" O HOH C 339 " model vdw 0.211 2.440 ... (remaining 374187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 254 6.06 5 S 192 5.16 5 Na 80 4.78 5 C 22248 2.51 5 N 6096 2.21 5 O 9536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 20.450 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.330 Process input model: 149.560 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 36120 Z= 0.315 Angle : 0.786 7.609 48672 Z= 0.442 Chirality : 0.044 0.164 5184 Planarity : 0.004 0.020 6360 Dihedral : 14.678 74.920 13920 Min Nonbonded Distance : 0.211 Molprobity Statistics. All-atom Clashscore : 2.71 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: 3.60 (0.13), residues: 4080 helix: 2.75 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.89 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.7883 time to fit residues: 1116.8711 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2576 ------------------------------------------------------------------------------- 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: 0.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 0.0670 chunk 370 optimal weight: 10.0000 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 105 HIS O 105 HIS P 105 HIS Q 105 HIS R 105 HIS S 105 HIS T 105 HIS U 105 HIS V 105 HIS W 105 HIS X 105 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 36120 Z= 0.174 Angle : 0.614 6.657 48672 Z= 0.339 Chirality : 0.038 0.148 5184 Planarity : 0.004 0.023 6360 Dihedral : 4.524 20.194 4536 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 4.35 (0.13), residues: 4080 helix: 3.30 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.02 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.6786 time to fit residues: 963.8409 Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7664 ------------------------------------------------------------------------------- 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: 20.0000 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 36120 Z= 0.172 Angle : 0.613 6.586 48672 Z= 0.338 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.023 6360 Dihedral : 4.502 20.155 4536 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.57 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: 4.42 (0.13), residues: 4080 helix: 3.36 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 1.6423 time to fit residues: 900.8346 Evaluate side-chains 456 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 4.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 36120 Z= 0.195 Angle : 0.650 6.811 48672 Z= 0.358 Chirality : 0.039 0.151 5184 Planarity : 0.004 0.026 6360 Dihedral : 4.531 19.970 4536 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.47 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: 4.29 (0.13), residues: 4080 helix: 3.26 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 1.7707 time to fit residues: 1085.7178 Evaluate side-chains 516 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2041 ------------------------------------------------------------------------------- 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: 9.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 36120 Z= 0.191 Angle : 0.644 7.187 48672 Z= 0.354 Chirality : 0.039 0.149 5184 Planarity : 0.004 0.025 6360 Dihedral : 4.526 19.973 4536 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.50 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: 4.35 (0.13), residues: 4080 helix: 3.30 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.7025 time to fit residues: 975.9323 Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7009 ------------------------------------------------------------------------------- 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: 6.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 36120 Z= 0.203 Angle : 0.663 7.899 48672 Z= 0.364 Chirality : 0.039 0.152 5184 Planarity : 0.004 0.026 6360 Dihedral : 4.542 19.936 4536 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.54 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: 4.29 (0.13), residues: 4080 helix: 3.26 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 1.7421 time to fit residues: 1007.6339 Evaluate side-chains 485 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9012 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 36120 Z= 0.198 Angle : 0.660 8.680 48672 Z= 0.362 Chirality : 0.039 0.151 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.536 19.947 4536 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.48 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: 4.32 (0.13), residues: 4080 helix: 3.28 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 5.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.7290 time to fit residues: 990.2658 Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6954 ------------------------------------------------------------------------------- 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: 20.0000 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 36120 Z= 0.230 Angle : 0.680 7.118 48672 Z= 0.376 Chirality : 0.041 0.156 5184 Planarity : 0.004 0.029 6360 Dihedral : 4.588 19.598 4536 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.61 % 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: 4080 helix: 3.11 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 528 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 528 average time/residue: 1.7898 time to fit residues: 1121.6981 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7179 ------------------------------------------------------------------------------- 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: 20.0000 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS B 60 HIS B 105 HIS C 60 HIS C 105 HIS D 60 HIS D 105 HIS E 60 HIS E 105 HIS F 60 HIS F 105 HIS G 60 HIS G 105 HIS H 60 HIS H 105 HIS I 60 HIS I 105 HIS J 60 HIS J 105 HIS K 60 HIS K 105 HIS L 60 HIS L 105 HIS M 60 HIS M 105 HIS N 60 HIS N 105 HIS O 60 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 36120 Z= 0.162 Angle : 0.586 6.594 48672 Z= 0.324 Chirality : 0.037 0.148 5184 Planarity : 0.003 0.023 6360 Dihedral : 4.517 20.005 4536 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.14 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: 4.46 (0.13), residues: 4080 helix: 3.38 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.7427 time to fit residues: 999.0711 Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0646 ------------------------------------------------------------------------------- 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: 4.9990 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 60 HIS F 105 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 60 HIS N 105 HIS O 60 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 36120 Z= 0.207 Angle : 0.648 6.917 48672 Z= 0.359 Chirality : 0.040 0.154 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.566 19.986 4536 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.81 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: 4.21 (0.13), residues: 4080 helix: 3.19 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.02 (0.26), residues: 816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 1.7195 time to fit residues: 962.6154 Evaluate side-chains 468 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 4.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6960 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS M 141 GLN N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.221084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156943 restraints weight = 33543.485| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 0.51 r_work: 0.3703 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work: 0.3354 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work: 0.3320 rms_B_bonded: 4.14 restraints_weight: 0.0625 r_work: 0.3267 rms_B_bonded: 4.40 restraints_weight: 0.0312 r_work: 0.3233 rms_B_bonded: 4.40 restraints_weight: 0.0156 r_work: 0.3213 rms_B_bonded: 4.64 restraints_weight: 0.0078 r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.0039 r_work: 0.3183 rms_B_bonded: 4.80 restraints_weight: 0.0020 r_work: 0.3172 rms_B_bonded: 4.84 restraints_weight: 0.0010 r_work: 0.3166 rms_B_bonded: 4.90 restraints_weight: 0.0005 r_work: 0.3163 rms_B_bonded: 4.97 restraints_weight: 0.0002 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4423 r_free = 0.4423 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 36120 Z= 0.298 Angle : 0.758 7.528 48672 Z= 0.419 Chirality : 0.044 0.172 5184 Planarity : 0.005 0.035 6360 Dihedral : 4.619 19.255 4536 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.80 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: 3.84 (0.13), residues: 4080 helix: 2.90 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.04 (0.26), residues: 816 =============================================================================== Job complete usr+sys time: 16439.66 seconds wall clock time: 293 minutes 33.06 seconds (17613.06 seconds total)