Starting phenix.real_space_refine on Tue Aug 26 12:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_22657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_22657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_22657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_22657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3v_22657/08_2025/7k3v_22657.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 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. Process input model Symmetric amino acids flipped. Time to flip 648 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} 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, 'GLU:plan': 2, 'ARG:plan': 1} 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: 20.25, per 1000 atoms: 0.53 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 - 3.00 Amino acid : True - 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: 2.95 Conformation dependent library (CDL) restraints added in 3.4 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal 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: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 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: 6.86 Time building geometry restraints manager: 3.77 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: 0.00 - 1.52: 45936 1.52 - 3.04: 2304 3.04 - 4.57: 264 4.57 - 6.09: 96 6.09 - 7.61: 72 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 - 35.98: 21816 35.98 - 71.96: 456 71.96 - 107.94: 24 107.94 - 143.92: 24 143.92 - 179.90: 96 Dihedral angle restraints: 22416 sinusoidal: 9576 harmonic: 12840 Sorted by residual: dihedral pdb=" CB CGLU C 162 " pdb=" CG CGLU C 162 " pdb=" CD CGLU C 162 " pdb=" OE1CGLU C 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CGLU H 162 " pdb=" CG CGLU H 162 " pdb=" CD CGLU H 162 " pdb=" OE1CGLU H 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CGLU I 162 " pdb=" CG CGLU I 162 " pdb=" CD CGLU I 162 " pdb=" OE1CGLU I 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+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 3.040 nonbonded pdb=" O HOH X 318 " pdb=" O HOH X 338 " model vdw 0.211 3.040 nonbonded pdb=" O HOH E 318 " pdb=" O HOH E 338 " model vdw 0.211 3.040 nonbonded pdb=" O HOH G 318 " pdb=" O HOH G 339 " model vdw 0.211 3.040 nonbonded pdb=" O HOH C 318 " pdb=" O HOH C 339 " model vdw 0.211 3.040 ... (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 Time spend for trying shortcut: 0.03 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 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: 4.620 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: 0.040 Extract box with map and model: 1.190 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 52.840 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.006 0.150 36144 Z= 0.271 Angle : 0.786 7.609 48672 Z= 0.442 Chirality : 0.044 0.164 5184 Planarity : 0.004 0.020 6360 Dihedral : 21.253 179.899 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 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG O 9 TYR 0.028 0.004 TYR B 39 PHE 0.027 0.004 PHE V 41 TRP 0.007 0.003 TRP R 93 HIS 0.005 0.002 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00492 (36120) covalent geometry : angle 0.78563 (48672) hydrogen bonds : bond 0.10432 ( 2688) hydrogen bonds : angle 4.24165 ( 8064) metal coordination : bond 0.14995 ( 24) *********************** 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 to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.547 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: 0.9499 time to fit residues: 586.9258 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 125 ASN A 141 GLN B 105 HIS B 125 ASN B 141 GLN C 105 HIS C 125 ASN C 141 GLN D 105 HIS D 125 ASN D 141 GLN E 105 HIS E 125 ASN E 141 GLN F 105 HIS F 125 ASN F 141 GLN G 105 HIS G 125 ASN G 141 GLN H 105 HIS H 125 ASN H 141 GLN I 105 HIS I 125 ASN I 141 GLN J 105 HIS J 125 ASN J 141 GLN K 105 HIS K 125 ASN K 141 GLN L 105 HIS L 125 ASN L 141 GLN M 105 HIS M 125 ASN M 141 GLN N 105 HIS N 125 ASN N 141 GLN O 105 HIS O 125 ASN O 141 GLN P 105 HIS P 125 ASN P 141 GLN Q 105 HIS Q 125 ASN Q 141 GLN R 105 HIS R 125 ASN R 141 GLN S 105 HIS S 125 ASN S 141 GLN T 105 HIS T 125 ASN T 141 GLN U 105 HIS U 125 ASN U 141 GLN V 105 HIS V 125 ASN V 141 GLN W 105 HIS W 125 ASN W 141 GLN X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.223401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158746 restraints weight = 34134.066| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 0.53 r_work: 0.3624 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work: 0.3242 rms_B_bonded: 3.29 restraints_weight: 0.1250 r_work: 0.3183 rms_B_bonded: 4.67 restraints_weight: 0.0625 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 36144 Z= 0.169 Angle : 0.664 6.879 48672 Z= 0.368 Chirality : 0.039 0.151 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.601 20.235 4536 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.61 % Allowed : 2.42 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.09 (0.13), residues: 4080 helix: 3.10 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 63 TYR 0.024 0.003 TYR Q 39 PHE 0.022 0.003 PHE C 41 TRP 0.008 0.002 TRP M 93 HIS 0.004 0.001 HIS O 118 Details of bonding type rmsd covalent geometry : bond 0.00337 (36120) covalent geometry : angle 0.66423 (48672) hydrogen bonds : bond 0.06711 ( 2688) hydrogen bonds : angle 3.92430 ( 8064) metal coordination : bond 0.00016 ( 24) *********************** 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 552 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 528 time to evaluate : 1.261 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: 552 average time/residue: 0.9688 time to fit residues: 622.8612 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 129 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 314 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 125 ASN A 141 GLN B 105 HIS B 125 ASN B 141 GLN C 105 HIS C 125 ASN C 141 GLN D 105 HIS D 125 ASN D 141 GLN E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 105 HIS G 125 ASN G 141 GLN H 105 HIS H 125 ASN H 141 GLN I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 105 HIS K 125 ASN K 141 GLN L 105 HIS L 125 ASN L 141 GLN M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.227688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164534 restraints weight = 34533.768| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 0.53 r_work: 0.3690 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3327 rms_B_bonded: 3.35 restraints_weight: 0.1250 r_work: 0.3275 rms_B_bonded: 4.57 restraints_weight: 0.0625 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 36144 Z= 0.117 Angle : 0.538 6.000 48672 Z= 0.296 Chirality : 0.036 0.140 5184 Planarity : 0.003 0.021 6360 Dihedral : 4.416 20.811 4536 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.80 (0.13), residues: 4080 helix: 3.59 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.20 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 63 TYR 0.019 0.002 TYR X 39 PHE 0.014 0.002 PHE A 41 TRP 0.010 0.002 TRP C 93 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00210 (36120) covalent geometry : angle 0.53786 (48672) hydrogen bonds : bond 0.05285 ( 2688) hydrogen bonds : angle 3.63667 ( 8064) metal coordination : bond 0.00175 ( 24) *********************** 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 576 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.605 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: 576 average time/residue: 1.0574 time to fit residues: 702.7079 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 361 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 406 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 125 ASN A 141 GLN B 105 HIS B 125 ASN B 141 GLN C 105 HIS C 125 ASN C 141 GLN D 105 HIS D 125 ASN D 141 GLN E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 105 HIS G 125 ASN G 141 GLN H 105 HIS H 125 ASN H 141 GLN I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 105 HIS K 125 ASN K 141 GLN L 105 HIS L 125 ASN L 141 GLN M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.222677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158156 restraints weight = 34610.056| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 0.53 r_work: 0.3618 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3240 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36144 Z= 0.185 Angle : 0.701 6.916 48672 Z= 0.387 Chirality : 0.041 0.156 5184 Planarity : 0.005 0.032 6360 Dihedral : 4.565 19.985 4536 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.25 (0.13), residues: 4080 helix: 3.22 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG N 79 TYR 0.026 0.003 TYR A 39 PHE 0.025 0.004 PHE A 41 TRP 0.005 0.002 TRP W 93 HIS 0.004 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00373 (36120) covalent geometry : angle 0.70102 (48672) hydrogen bonds : bond 0.06894 ( 2688) hydrogen bonds : angle 3.90431 ( 8064) metal coordination : bond 0.00223 ( 24) *********************** 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 528 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.573 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: 528 average time/residue: 0.8021 time to fit residues: 497.2932 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 110 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 chunk 152 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 305 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 125 ASN A 141 GLN B 105 HIS B 125 ASN B 141 GLN C 105 HIS C 125 ASN C 141 GLN D 105 HIS D 125 ASN D 141 GLN E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 105 HIS G 125 ASN G 141 GLN H 105 HIS H 125 ASN H 141 GLN I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 105 HIS K 125 ASN K 141 GLN L 105 HIS L 125 ASN L 141 GLN M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.224091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162192 restraints weight = 36346.498| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.54 r_work: 0.3678 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.3284 rms_B_bonded: 3.13 restraints_weight: 0.1250 r_work: 0.3229 rms_B_bonded: 4.15 restraints_weight: 0.0625 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36144 Z= 0.147 Angle : 0.625 6.877 48672 Z= 0.344 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.023 6360 Dihedral : 4.533 20.537 4536 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 3.03 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.44 (0.13), residues: 4080 helix: 3.37 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.023 0.003 TYR W 39 PHE 0.021 0.003 PHE K 41 TRP 0.007 0.002 TRP E 93 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00284 (36120) covalent geometry : angle 0.62497 (48672) hydrogen bonds : bond 0.06250 ( 2688) hydrogen bonds : angle 3.80518 ( 8064) metal coordination : bond 0.00068 ( 24) *********************** 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 552 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 528 time to evaluate : 1.527 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: 552 average time/residue: 0.9253 time to fit residues: 594.4324 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 239 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 275 optimal weight: 0.0570 chunk 249 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 358 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 385 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 125 ASN A 141 GLN B 105 HIS B 125 ASN B 141 GLN C 105 HIS C 125 ASN C 141 GLN D 105 HIS D 125 ASN D 141 GLN E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 105 HIS G 125 ASN G 141 GLN H 105 HIS H 125 ASN H 141 GLN I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 105 HIS K 125 ASN K 141 GLN L 105 HIS L 125 ASN L 141 GLN M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.224360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162170 restraints weight = 34995.042| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 0.53 r_work: 0.3653 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3281 rms_B_bonded: 3.28 restraints_weight: 0.1250 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36144 Z= 0.144 Angle : 0.621 7.842 48672 Z= 0.341 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.022 6360 Dihedral : 4.522 20.758 4536 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.51 (0.13), residues: 4080 helix: 3.42 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 63 TYR 0.021 0.003 TYR W 39 PHE 0.020 0.003 PHE D 41 TRP 0.007 0.002 TRP G 93 HIS 0.003 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00277 (36120) covalent geometry : angle 0.62114 (48672) hydrogen bonds : bond 0.06148 ( 2688) hydrogen bonds : angle 3.78891 ( 8064) metal coordination : bond 0.00018 ( 24) *********************** 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 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.8540 time to fit residues: 505.6852 Evaluate side-chains 480 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 57 optimal weight: 5.9990 chunk 353 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 219 optimal weight: 0.0980 chunk 332 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 297 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 A 125 ASN A 141 GLN B 60 HIS B 105 HIS B 125 ASN B 141 GLN C 60 HIS C 105 HIS C 125 ASN C 141 GLN D 60 HIS D 105 HIS D 125 ASN D 141 GLN E 60 HIS E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 60 HIS G 105 HIS G 125 ASN G 141 GLN H 60 HIS H 105 HIS H 125 ASN H 141 GLN I 60 HIS I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 60 HIS K 105 HIS K 125 ASN K 141 GLN L 60 HIS L 105 HIS L 125 ASN L 141 GLN M 60 HIS M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 60 HIS O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.225816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164409 restraints weight = 35230.916| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.51 r_work: 0.3716 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.3316 rms_B_bonded: 3.13 restraints_weight: 0.1250 r_work: 0.3259 rms_B_bonded: 4.17 restraints_weight: 0.0625 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 36144 Z= 0.127 Angle : 0.554 6.202 48672 Z= 0.306 Chirality : 0.036 0.145 5184 Planarity : 0.003 0.021 6360 Dihedral : 4.469 21.025 4536 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.73 (0.13), residues: 4080 helix: 3.53 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.25 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 63 TYR 0.020 0.002 TYR G 39 PHE 0.017 0.002 PHE R 41 TRP 0.008 0.002 TRP M 93 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00234 (36120) covalent geometry : angle 0.55406 (48672) hydrogen bonds : bond 0.05712 ( 2688) hydrogen bonds : angle 3.70723 ( 8064) metal coordination : bond 0.00137 ( 24) *********************** 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 528 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.536 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: 528 average time/residue: 1.0617 time to fit residues: 645.7820 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 211 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 404 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 A 125 ASN A 141 GLN B 60 HIS B 105 HIS B 125 ASN B 141 GLN C 60 HIS C 105 HIS C 125 ASN C 141 GLN D 60 HIS D 105 HIS D 125 ASN D 141 GLN E 60 HIS E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 60 HIS G 105 HIS G 125 ASN G 141 GLN H 60 HIS H 105 HIS H 125 ASN H 141 GLN I 60 HIS I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 60 HIS K 105 HIS K 125 ASN K 141 GLN L 60 HIS L 105 HIS L 125 ASN L 141 GLN M 60 HIS M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 60 HIS O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.225195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165892 restraints weight = 37527.946| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 0.53 r_work: 0.3692 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.3298 rms_B_bonded: 3.14 restraints_weight: 0.1250 r_work: 0.3240 rms_B_bonded: 4.23 restraints_weight: 0.0625 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 36144 Z= 0.133 Angle : 0.571 6.249 48672 Z= 0.316 Chirality : 0.037 0.145 5184 Planarity : 0.003 0.021 6360 Dihedral : 4.497 21.119 4536 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.65 (0.13), residues: 4080 helix: 3.47 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.25 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 63 TYR 0.021 0.002 TYR R 39 PHE 0.019 0.003 PHE K 41 TRP 0.007 0.002 TRP K 93 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00249 (36120) covalent geometry : angle 0.57143 (48672) hydrogen bonds : bond 0.05916 ( 2688) hydrogen bonds : angle 3.73613 ( 8064) metal coordination : bond 0.00077 ( 24) *********************** 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 528 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.619 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: 528 average time/residue: 1.0807 time to fit residues: 657.7144 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 279 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 A 125 ASN A 141 GLN B 60 HIS B 105 HIS B 125 ASN B 141 GLN C 60 HIS C 105 HIS C 125 ASN C 141 GLN D 60 HIS D 105 HIS D 125 ASN D 141 GLN E 60 HIS E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 60 HIS G 105 HIS G 125 ASN G 141 GLN H 60 HIS H 105 HIS H 125 ASN H 141 GLN I 60 HIS I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 60 HIS K 105 HIS K 125 ASN K 141 GLN L 60 HIS L 105 HIS L 125 ASN L 141 GLN M 60 HIS M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 60 HIS O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.226031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165317 restraints weight = 36556.989| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 0.51 r_work: 0.3726 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.3322 rms_B_bonded: 3.11 restraints_weight: 0.1250 r_work: 0.3261 rms_B_bonded: 4.24 restraints_weight: 0.0625 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 36144 Z= 0.126 Angle : 0.551 6.115 48672 Z= 0.305 Chirality : 0.036 0.145 5184 Planarity : 0.003 0.021 6360 Dihedral : 4.461 21.080 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.13), residues: 4080 helix: 3.55 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.30 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 63 TYR 0.020 0.002 TYR R 39 PHE 0.017 0.002 PHE V 41 TRP 0.008 0.002 TRP K 93 HIS 0.003 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00231 (36120) covalent geometry : angle 0.55116 (48672) hydrogen bonds : bond 0.05661 ( 2688) hydrogen bonds : angle 3.69057 ( 8064) metal coordination : bond 0.00096 ( 24) *********************** 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 528 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.614 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: 528 average time/residue: 1.0767 time to fit residues: 654.8497 Evaluate side-chains 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 22 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 320 optimal weight: 9.9990 chunk 280 optimal weight: 0.1980 chunk 86 optimal weight: 20.0000 chunk 361 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 237 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 A 125 ASN A 141 GLN B 60 HIS B 105 HIS B 125 ASN B 141 GLN C 60 HIS C 105 HIS C 125 ASN C 141 GLN D 60 HIS D 105 HIS D 125 ASN D 141 GLN E 60 HIS E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 60 HIS G 105 HIS G 125 ASN G 141 GLN H 60 HIS H 105 HIS H 125 ASN H 141 GLN I 60 HIS I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 60 HIS K 105 HIS K 125 ASN K 141 GLN L 60 HIS L 105 HIS L 125 ASN L 141 GLN M 60 HIS M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 60 HIS O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.224413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163345 restraints weight = 35688.665| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 0.55 r_work: 0.3692 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work: 0.3286 rms_B_bonded: 3.10 restraints_weight: 0.1250 r_work: 0.3225 rms_B_bonded: 4.17 restraints_weight: 0.0625 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 36144 Z= 0.147 Angle : 0.603 6.455 48672 Z= 0.334 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.022 6360 Dihedral : 4.522 21.040 4536 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.50 (0.13), residues: 4080 helix: 3.40 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.05 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 79 TYR 0.023 0.003 TYR R 39 PHE 0.021 0.003 PHE L 41 TRP 0.005 0.002 TRP T 93 HIS 0.003 0.001 HIS K 118 Details of bonding type rmsd covalent geometry : bond 0.00282 (36120) covalent geometry : angle 0.60333 (48672) hydrogen bonds : bond 0.06256 ( 2688) hydrogen bonds : angle 3.79847 ( 8064) metal coordination : bond 0.00038 ( 24) ********************** 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 504 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.652 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: 504 average time/residue: 0.9638 time to fit residues: 569.3458 Evaluate side-chains 480 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 7 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 353 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 A 125 ASN A 141 GLN B 60 HIS B 105 HIS B 125 ASN B 141 GLN C 60 HIS C 105 HIS C 125 ASN C 141 GLN D 60 HIS D 105 HIS D 125 ASN D 141 GLN E 60 HIS E 105 HIS E 125 ASN E 141 GLN F 60 HIS F 105 HIS F 125 ASN F 141 GLN G 60 HIS G 105 HIS G 125 ASN G 141 GLN H 60 HIS H 105 HIS H 125 ASN H 141 GLN I 60 HIS I 105 HIS I 125 ASN I 141 GLN J 60 HIS J 105 HIS J 125 ASN J 141 GLN K 60 HIS K 105 HIS K 125 ASN K 141 GLN L 60 HIS L 105 HIS L 125 ASN L 141 GLN M 60 HIS M 105 HIS M 125 ASN M 141 GLN N 60 HIS N 105 HIS N 125 ASN N 141 GLN O 60 HIS O 105 HIS O 125 ASN O 141 GLN P 60 HIS P 105 HIS P 125 ASN P 141 GLN Q 60 HIS Q 105 HIS Q 125 ASN Q 141 GLN R 60 HIS R 105 HIS R 125 ASN R 141 GLN S 60 HIS S 105 HIS S 125 ASN S 141 GLN T 60 HIS T 105 HIS T 125 ASN T 141 GLN U 60 HIS U 105 HIS U 125 ASN U 141 GLN V 60 HIS V 105 HIS V 125 ASN V 141 GLN W 60 HIS W 105 HIS W 125 ASN W 141 GLN X 60 HIS X 105 HIS X 125 ASN X 141 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.223356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161477 restraints weight = 35107.784| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 0.50 r_work: 0.3671 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work: 0.3262 rms_B_bonded: 3.09 restraints_weight: 0.1250 r_work: 0.3202 rms_B_bonded: 4.13 restraints_weight: 0.0625 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 36144 Z= 0.167 Angle : 0.647 6.730 48672 Z= 0.359 Chirality : 0.040 0.152 5184 Planarity : 0.004 0.026 6360 Dihedral : 4.570 20.626 4536 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.13), residues: 4080 helix: 3.25 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.06 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG S 79 TYR 0.025 0.003 TYR P 39 PHE 0.023 0.003 PHE C 41 TRP 0.004 0.001 TRP I 93 HIS 0.004 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00330 (36120) covalent geometry : angle 0.64738 (48672) hydrogen bonds : bond 0.06628 ( 2688) hydrogen bonds : angle 3.86913 ( 8064) metal coordination : bond 0.00105 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46557.73 seconds wall clock time: 786 minutes 42.04 seconds (47202.04 seconds total)