Starting phenix.real_space_refine on Sat May 2 08:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.map" model { file = "/net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nef_49307/05_2026/9nef_49307.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.258 sd= 0.999 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: 4 Type Number sf(0) Gaussians P 60 5.49 5 C 2520 2.51 5 N 540 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3960 Number of models: 1 Model: "" Number of chains: 60 Chain: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 8 1 " pdbres="LEU 8 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 9 1 " pdbres="LEU 9 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 A 1 " pdbres="LEU A 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 B 1 " pdbres="LEU B 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 C 1 " pdbres="LEU C 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 D 1 " pdbres="LEU D 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 E 1 " pdbres="LEU E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 F 1 " pdbres="LEU F 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 G 1 " pdbres="LEU G 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 H 1 " pdbres="LEU H 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 I 1 " pdbres="LEU I 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 J 1 " pdbres="LEU J 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 K 1 " pdbres="LEU K 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 L 1 " pdbres="LEU L 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 M 1 " pdbres="LEU M 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 N 1 " pdbres="LEU N 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 O 1 " pdbres="LEU O 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 P 1 " pdbres="LEU P 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 Q 1 " pdbres="LEU Q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 R 1 " pdbres="LEU R 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 S 1 " pdbres="LEU S 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 T 1 " pdbres="LEU T 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 U 1 " pdbres="LEU U 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 V 1 " pdbres="LEU V 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 W 1 " pdbres="LEU W 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 X 1 " pdbres="LEU X 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 Y 1 " pdbres="LEU Y 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 Z 1 " pdbres="LEU Z 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 0 1 " pdbres="LEU 0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 1 1 " pdbres="LEU 1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 2 1 " pdbres="LEU 2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 3 1 " pdbres="LEU 3 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 4 1 " pdbres="LEU 4 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 5 1 " pdbres="LEU 5 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 6 1 " pdbres="LEU 6 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 7 1 " pdbres="LEU 7 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 a 1 " pdbres="LEU a 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 b 1 " pdbres="LEU b 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 c 1 " pdbres="LEU c 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 d 1 " pdbres="LEU d 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 e 1 " pdbres="LEU e 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 f 1 " pdbres="LEU f 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 g 1 " pdbres="LEU g 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 h 1 " pdbres="LEU h 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 i 1 " pdbres="LEU i 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 j 1 " pdbres="LEU j 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 k 1 " pdbres="LEU k 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 l 1 " pdbres="LEU l 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 m 1 " pdbres="LEU m 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 n 1 " pdbres="LEU n 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 o 1 " pdbres="LEU o 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 p 1 " pdbres="LEU p 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 q 1 " pdbres="LEU q 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 r 1 " pdbres="LEU r 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 s 1 " pdbres="LEU s 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 t 1 " pdbres="LEU t 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 u 1 " pdbres="LEU u 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 v 1 " pdbres="LEU v 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 w 1 " pdbres="LEU w 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 x 1 " pdbres="LEU x 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.25 Number of scatterers: 3960 At special positions: 0 Unit cell: (138.75, 138.75, 34.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 60 15.00 O 840 8.00 N 540 7.00 C 2520 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 55.7 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.27: 480 1.27 - 1.36: 480 1.36 - 1.46: 1071 1.46 - 1.55: 1929 1.55 - 1.65: 60 Bond restraints: 4020 Sorted by residual: bond pdb=" C53 UQ4 K 1 " pdb=" N52 UQ4 K 1 " ideal model delta sigma weight residual 1.342 1.517 -0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C53 UQ4 W 1 " pdb=" N52 UQ4 W 1 " ideal model delta sigma weight residual 1.342 1.516 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C53 UQ4 4 1 " pdb=" N52 UQ4 4 1 " ideal model delta sigma weight residual 1.342 1.516 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C53 UQ4 Q 1 " pdb=" N52 UQ4 Q 1 " ideal model delta sigma weight residual 1.342 1.516 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C53 UQ4 k 1 " pdb=" N52 UQ4 k 1 " ideal model delta sigma weight residual 1.342 1.516 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 4015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 3660 2.70 - 5.40: 1230 5.40 - 8.10: 480 8.10 - 10.80: 90 10.80 - 13.50: 60 Bond angle restraints: 5520 Sorted by residual: angle pdb=" C LEU t 4 " pdb=" N LEU t 5 " pdb=" CA LEU t 5 " ideal model delta sigma weight residual 121.70 113.33 8.37 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C LEU r 4 " pdb=" N LEU r 5 " pdb=" CA LEU r 5 " ideal model delta sigma weight residual 121.70 113.36 8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C LEU V 4 " pdb=" N LEU V 5 " pdb=" CA LEU V 5 " ideal model delta sigma weight residual 121.70 113.36 8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C LEU 1 4 " pdb=" N LEU 1 5 " pdb=" CA LEU 1 5 " ideal model delta sigma weight residual 121.70 113.36 8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C LEU R 4 " pdb=" N LEU R 5 " pdb=" CA LEU R 5 " ideal model delta sigma weight residual 121.70 113.36 8.34 1.80e+00 3.09e-01 2.14e+01 ... (remaining 5515 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.21: 1244 16.21 - 32.41: 647 32.41 - 48.61: 149 48.61 - 64.82: 60 64.82 - 81.02: 180 Dihedral angle restraints: 2280 sinusoidal: 1440 harmonic: 840 Sorted by residual: dihedral pdb=" CA LEU j 3 " pdb=" C LEU j 3 " pdb=" N LEU j 4 " pdb=" CA LEU j 4 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LEU J 3 " pdb=" C LEU J 3 " pdb=" N LEU J 4 " pdb=" CA LEU J 4 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LEU D 3 " pdb=" C LEU D 3 " pdb=" N LEU D 4 " pdb=" CA LEU D 4 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.046: 240 0.046 - 0.089: 150 0.089 - 0.132: 90 0.132 - 0.175: 0 0.175 - 0.218: 60 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA LEU N 5 " pdb=" N LEU N 5 " pdb=" C LEU N 5 " pdb=" CB LEU N 5 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU 7 5 " pdb=" N LEU 7 5 " pdb=" C LEU 7 5 " pdb=" CB LEU 7 5 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU J 5 " pdb=" N LEU J 5 " pdb=" C LEU J 5 " pdb=" CB LEU J 5 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 537 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PTR x 6 " -0.008 2.00e-02 2.50e+03 5.11e-03 5.23e-01 pdb=" CG PTR x 6 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PTR x 6 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PTR x 6 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PTR x 6 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PTR x 6 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PTR x 6 " -0.007 2.00e-02 2.50e+03 pdb=" OH PTR x 6 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PTR 1 6 " 0.008 2.00e-02 2.50e+03 5.10e-03 5.20e-01 pdb=" CG PTR 1 6 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PTR 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PTR 1 6 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PTR 1 6 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PTR 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PTR 1 6 " 0.007 2.00e-02 2.50e+03 pdb=" OH PTR 1 6 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PTR R 6 " 0.008 2.00e-02 2.50e+03 5.08e-03 5.17e-01 pdb=" CG PTR R 6 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PTR R 6 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PTR R 6 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PTR R 6 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PTR R 6 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PTR R 6 " 0.008 2.00e-02 2.50e+03 pdb=" OH PTR R 6 " -0.000 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 1805 3.05 - 3.51: 3424 3.51 - 3.97: 4350 3.97 - 4.44: 5048 4.44 - 4.90: 7539 Nonbonded interactions: 22166 Sorted by model distance: nonbonded pdb=" O LEU X 4 " pdb=" CA LEU X 5 " model vdw 2.584 2.776 nonbonded pdb=" O LEU t 4 " pdb=" CA LEU t 5 " model vdw 2.584 2.776 nonbonded pdb=" O LEU Z 4 " pdb=" CA LEU Z 5 " model vdw 2.584 2.776 nonbonded pdb=" O LEU n 4 " pdb=" CA LEU n 5 " model vdw 2.584 2.776 nonbonded pdb=" O LEU 1 4 " pdb=" CA LEU 1 5 " model vdw 2.584 2.776 ... (remaining 22161 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: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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=1.00 max=1.00 mean=1.00 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: 2.370 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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 : 0.045 0.175 4080 Z= 2.502 Angle : 3.337 13.501 5520 Z= 1.229 Chirality : 0.090 0.218 540 Planarity : 0.004 0.007 480 Dihedral : 33.369 81.017 1680 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -7.72 (0.35), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.27), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.04358 ( 4020) covalent geometry : angle 3.33735 ( 5520) Misc. bond : bond 0.10591 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.115 Fit side-chains REVERT: u 2 LEU cc_start: 0.9052 (tp) cc_final: 0.8818 (tt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0352 time to fit residues: 3.2005 Evaluate side-chains 26 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.089345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.075692 restraints weight = 16823.254| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 6.85 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.098 4080 Z= 1.067 Angle : 3.212 24.513 5520 Z= 1.223 Chirality : 0.136 0.407 540 Planarity : 0.009 0.021 480 Dihedral : 34.691 89.776 1200 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 30.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 19.17 % Allowed : 32.08 % Favored : 48.75 % Cbeta Deviations : 2.67 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.20 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.25 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02487 ( 4020) covalent geometry : angle 3.21176 ( 5520) Misc. bond : bond 0.00228 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 4 time to evaluate : 0.127 Fit side-chains REVERT: a 5 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7333 (tp) outliers start: 46 outliers final: 33 residues processed: 49 average time/residue: 0.0291 time to fit residues: 2.2489 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 4 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.075275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.068916 restraints weight = 23842.212| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 4.68 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.093 4080 Z= 1.078 Angle : 3.404 26.212 5520 Z= 1.264 Chirality : 0.129 0.443 540 Planarity : 0.009 0.023 480 Dihedral : 32.409 89.983 1200 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 30.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 31.25 % Allowed : 15.83 % Favored : 52.92 % Cbeta Deviations : 3.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.57 (0.24), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.52 (0.18), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02511 ( 4020) covalent geometry : angle 3.40437 ( 5520) Misc. bond : bond 0.00228 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 2 time to evaluate : 0.071 Fit side-chains REVERT: Q 5 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8075 (tp) REVERT: 5 5 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (tt) REVERT: 6 5 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7567 (tt) REVERT: p 5 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8855 (tt) REVERT: q 5 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8461 (mp) outliers start: 75 outliers final: 44 residues processed: 76 average time/residue: 0.0341 time to fit residues: 3.9149 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 2 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain q residue 5 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.072186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.065905 restraints weight = 24538.849| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.65 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.110 4080 Z= 1.054 Angle : 3.345 28.078 5520 Z= 1.248 Chirality : 0.124 0.408 540 Planarity : 0.009 0.028 480 Dihedral : 33.980 89.550 1200 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 33.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 30.42 % Allowed : 16.67 % Favored : 52.92 % Cbeta Deviations : 2.67 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.91 (0.23), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.78 (0.18), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02474 ( 4020) covalent geometry : angle 3.34490 ( 5520) Misc. bond : bond 0.00204 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 2 time to evaluate : 0.112 Fit side-chains REVERT: F 5 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8359 (tt) REVERT: Q 5 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8137 (tp) REVERT: 5 5 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8490 (tt) REVERT: 6 5 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7786 (tp) REVERT: p 5 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (tt) REVERT: q 5 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8296 (mp) outliers start: 73 outliers final: 50 residues processed: 74 average time/residue: 0.0311 time to fit residues: 3.4878 Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain q residue 5 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.072860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065494 restraints weight = 24483.154| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 5.29 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.105 4080 Z= 1.050 Angle : 3.337 27.827 5520 Z= 1.245 Chirality : 0.123 0.406 540 Planarity : 0.009 0.022 480 Dihedral : 34.645 89.508 1200 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 31.67 % Allowed : 16.67 % Favored : 51.67 % Cbeta Deviations : 2.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.89 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.78 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02459 ( 4020) covalent geometry : angle 3.33693 ( 5520) Misc. bond : bond 0.00204 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 2 time to evaluate : 0.121 Fit side-chains REVERT: F 5 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8121 (tt) REVERT: Q 5 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7969 (tp) REVERT: 5 5 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8528 (tt) REVERT: a 5 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8230 (tt) REVERT: p 5 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8733 (tt) REVERT: r 3 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8698 (mp) outliers start: 76 outliers final: 54 residues processed: 77 average time/residue: 0.0326 time to fit residues: 3.8119 Evaluate side-chains 62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 2 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.072431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.065232 restraints weight = 24856.948| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 5.18 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.100 4080 Z= 1.052 Angle : 3.372 27.353 5520 Z= 1.259 Chirality : 0.122 0.453 540 Planarity : 0.009 0.023 480 Dihedral : 34.138 89.952 1200 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 31.67 % Allowed : 18.33 % Favored : 50.00 % Cbeta Deviations : 2.33 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.94 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.81 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02465 ( 4020) covalent geometry : angle 3.37220 ( 5520) Misc. bond : bond 0.00202 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 2 time to evaluate : 0.114 Fit side-chains REVERT: E 5 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8128 (mp) REVERT: F 5 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8141 (tt) REVERT: Q 5 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7945 (tt) REVERT: 5 5 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (tt) REVERT: p 5 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8761 (tt) REVERT: r 3 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8705 (mp) outliers start: 76 outliers final: 60 residues processed: 77 average time/residue: 0.0320 time to fit residues: 3.7656 Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 3 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 3 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.072294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.065138 restraints weight = 24900.838| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 5.22 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.100 4080 Z= 1.049 Angle : 3.350 26.694 5520 Z= 1.250 Chirality : 0.121 0.444 540 Planarity : 0.009 0.022 480 Dihedral : 34.347 89.796 1200 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 34.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 29.58 % Allowed : 22.92 % Favored : 47.50 % Cbeta Deviations : 2.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.94 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.81 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02460 ( 4020) covalent geometry : angle 3.34960 ( 5520) Misc. bond : bond 0.00193 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 3 time to evaluate : 0.111 Fit side-chains REVERT: E 5 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8113 (mp) REVERT: F 5 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8119 (tt) REVERT: Q 5 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7941 (tt) REVERT: 5 5 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (tt) REVERT: a 5 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8263 (tt) REVERT: p 5 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8704 (tt) REVERT: r 3 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8700 (mp) outliers start: 71 outliers final: 60 residues processed: 73 average time/residue: 0.0339 time to fit residues: 3.7122 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 3 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 3 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain q residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.072260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.065124 restraints weight = 24598.342| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.19 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.100 4080 Z= 1.048 Angle : 3.353 26.568 5520 Z= 1.252 Chirality : 0.121 0.444 540 Planarity : 0.009 0.022 480 Dihedral : 34.323 89.343 1200 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 33.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.83 % Favored : 84.17 % Rotamer: Outliers : 30.42 % Allowed : 23.33 % Favored : 46.25 % Cbeta Deviations : 2.33 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.96 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.83 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02457 ( 4020) covalent geometry : angle 3.35336 ( 5520) Misc. bond : bond 0.00193 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 3 time to evaluate : 0.114 Fit side-chains REVERT: E 5 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8146 (mp) REVERT: F 5 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8104 (tt) REVERT: Q 5 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7944 (tt) REVERT: 5 5 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8512 (tt) REVERT: a 5 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8245 (tt) REVERT: p 5 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8692 (tt) REVERT: r 3 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8702 (mp) outliers start: 73 outliers final: 59 residues processed: 75 average time/residue: 0.0330 time to fit residues: 3.7569 Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 3 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 3 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.072274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.065112 restraints weight = 24933.282| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 5.16 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.100 4080 Z= 1.051 Angle : 3.355 26.583 5520 Z= 1.253 Chirality : 0.121 0.443 540 Planarity : 0.009 0.022 480 Dihedral : 34.323 89.305 1200 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 34.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.83 % Favored : 84.17 % Rotamer: Outliers : 27.92 % Allowed : 26.25 % Favored : 45.83 % Cbeta Deviations : 2.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.95 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.82 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02469 ( 4020) covalent geometry : angle 3.35537 ( 5520) Misc. bond : bond 0.00195 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 3 time to evaluate : 0.124 Fit side-chains REVERT: E 5 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8129 (mp) REVERT: F 5 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8152 (tt) REVERT: Q 5 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7949 (tt) REVERT: 5 5 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (tt) REVERT: a 5 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8254 (tt) REVERT: p 5 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8753 (tt) REVERT: r 3 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8703 (mp) outliers start: 67 outliers final: 59 residues processed: 69 average time/residue: 0.0313 time to fit residues: 3.2970 Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 3 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 3 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.072287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.065121 restraints weight = 24566.197| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 5.17 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.100 4080 Z= 1.049 Angle : 3.352 26.543 5520 Z= 1.251 Chirality : 0.121 0.443 540 Planarity : 0.009 0.022 480 Dihedral : 34.331 89.291 1200 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 34.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 27.50 % Allowed : 26.25 % Favored : 46.25 % Cbeta Deviations : 2.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.95 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.82 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02462 ( 4020) covalent geometry : angle 3.35211 ( 5520) Misc. bond : bond 0.00196 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 3 time to evaluate : 0.123 Fit side-chains REVERT: E 5 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8118 (mp) REVERT: F 5 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8101 (tt) REVERT: Q 5 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7929 (tt) REVERT: 5 5 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8517 (tt) REVERT: a 5 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8229 (tt) REVERT: p 5 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8677 (tt) REVERT: r 3 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8707 (mp) outliers start: 66 outliers final: 59 residues processed: 68 average time/residue: 0.0357 time to fit residues: 3.6538 Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 3 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 3 LEU Chi-restraints excluded: chain p residue 4 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain r residue 3 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain s residue 4 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 5 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain x residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.072284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.065109 restraints weight = 24749.500| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 5.19 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.100 4080 Z= 1.050 Angle : 3.350 26.552 5520 Z= 1.250 Chirality : 0.120 0.443 540 Planarity : 0.009 0.022 480 Dihedral : 34.327 89.282 1200 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 34.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.83 % Favored : 84.17 % Rotamer: Outliers : 29.58 % Allowed : 24.58 % Favored : 45.83 % Cbeta Deviations : 2.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -8.95 (0.25), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.81 (0.19), residues: 120 Details of bonding type rmsd covalent geometry : bond 0.02465 ( 4020) covalent geometry : angle 3.35034 ( 5520) Misc. bond : bond 0.00194 ( 60) =============================================================================== Job complete usr+sys time: 544.06 seconds wall clock time: 10 minutes 3.68 seconds (603.68 seconds total)