Starting phenix.real_space_refine on Thu Oct 22 18:57:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nef_49307/10_2026/9nef_49307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nef_49307/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nef_49307/10_2026/9nef_49307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nef_49307/10_2026/9nef_49307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nef_49307/10_2026/9nef_49307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nef_49307/10_2026/9nef_49307.map" } 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-2.3rc1-6221/lib/python3.11/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: 1.15, per 1000 atoms: 0.29 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: 0.48 Conformation dependent library (CDL) restraints added in 34.7 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: 0.29 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: 0.54 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: 3.110 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.450 Find NCS groups from input model: 0.340 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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/Z covalent geometry : bond 0.04358 / 2.16 ( 4020) covalent geometry : angle 3.33735 / 1.23 ( 5520) Misc. bond : bond 0.10591 / 5.79 ( 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 : 0.120 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: 0.0351 time to fit residues: 3.1903 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 : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.085699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.076919 restraints weight = 20364.475| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 5.72 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4080 Z= 0.161 Angle : 1.205 9.411 5520 Z= 0.447 Chirality : 0.047 0.106 540 Planarity : 0.002 0.005 480 Dihedral : 32.884 89.969 1200 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 26.25 % Favored : 70.42 % 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: -6.29 (0.41), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.31), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 4020) covalent geometry : angle 1.20455 / 0.45 ( 5520) Misc. bond : bond 0.00065 / 0.03 ( 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 91 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.125 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.0310 time to fit residues: 4.1871 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain v residue 4 LEU Chi-restraints excluded: chain w residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.081893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.074004 restraints weight = 20589.537| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 5.29 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.039 4080 Z= 0.443 Angle : 1.780 10.339 5520 Z= 0.656 Chirality : 0.066 0.215 540 Planarity : 0.004 0.012 480 Dihedral : 31.719 89.881 1200 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 20.83 % Allowed : 33.75 % Favored : 45.42 % 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: -7.35 (0.31), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.59 (0.24), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01023 / 0.45 ( 4020) covalent geometry : angle 1.78016 / 0.66 ( 5520) Misc. bond : bond 0.00159 / 0.09 ( 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 80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 30 time to evaluate : 0.123 Fit side-chains REVERT: L 5 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8612 (tt) REVERT: 1 5 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8519 (tp) REVERT: a 5 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7491 (tp) REVERT: p 5 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8731 (tt) outliers start: 50 outliers final: 16 residues processed: 79 average time/residue: 0.0329 time to fit residues: 3.8900 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 24 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain 1 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 7 residue 4 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.082379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.074523 restraints weight = 20316.158| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 5.31 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4080 Z= 0.231 Angle : 1.268 8.130 5520 Z= 0.473 Chirality : 0.049 0.140 540 Planarity : 0.002 0.007 480 Dihedral : 29.394 89.765 1200 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 20.42 % Allowed : 24.17 % Favored : 55.42 % 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: -7.15 (0.33), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.45 (0.26), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 4020) covalent geometry : angle 1.26808 / 0.47 ( 5520) Misc. bond : bond 0.00079 / 0.05 ( 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 101 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 52 time to evaluate : 0.107 Fit side-chains REVERT: L 5 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8592 (tt) REVERT: Q 5 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7669 (tp) outliers start: 49 outliers final: 23 residues processed: 97 average time/residue: 0.0331 time to fit residues: 4.7394 Evaluate side-chains 65 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 I residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 5 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 V residue 4 LEU Chi-restraints excluded: chain X residue 4 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 j residue 4 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain t residue 4 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.080640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.072895 restraints weight = 21052.397| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 5.31 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 4080 Z= 0.446 Angle : 1.794 14.706 5520 Z= 0.664 Chirality : 0.063 0.211 540 Planarity : 0.004 0.014 480 Dihedral : 29.714 89.830 1200 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 25.00 % Allowed : 23.75 % Favored : 51.25 % 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: -7.51 (0.34), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.72 (0.26), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01037 / 0.45 ( 4020) covalent geometry : angle 1.79433 / 0.66 ( 5520) Misc. bond : bond 0.00128 / 0.07 ( 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 81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 21 time to evaluate : 0.103 Fit side-chains REVERT: L 5 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8476 (tt) REVERT: a 5 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7587 (tp) outliers start: 60 outliers final: 31 residues processed: 80 average time/residue: 0.0300 time to fit residues: 3.6390 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 19 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L 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 V residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 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 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 j residue 4 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.081441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.073399 restraints weight = 21204.101| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 5.56 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4080 Z= 0.230 Angle : 1.285 8.462 5520 Z= 0.475 Chirality : 0.047 0.133 540 Planarity : 0.002 0.006 480 Dihedral : 27.333 89.199 1200 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 20.00 % Allowed : 27.92 % Favored : 52.08 % 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: -7.34 (0.36), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.59 (0.27), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 4020) covalent geometry : angle 1.28546 / 0.48 ( 5520) Misc. bond : bond 0.00092 / 0.05 ( 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 84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 36 time to evaluate : 0.123 Fit side-chains REVERT: L 5 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8644 (tt) outliers start: 48 outliers final: 34 residues processed: 80 average time/residue: 0.0334 time to fit residues: 3.9724 Evaluate side-chains 64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 29 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L 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 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 Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 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 j residue 4 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain o residue 5 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 v residue 4 LEU Chi-restraints excluded: chain w residue 5 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: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.078413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.070857 restraints weight = 22469.886| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 5.47 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4080 Z= 0.436 Angle : 1.902 16.011 5520 Z= 0.702 Chirality : 0.066 0.247 540 Planarity : 0.004 0.014 480 Dihedral : 29.459 89.566 1200 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 22.50 % Allowed : 25.00 % Favored : 52.50 % 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: -7.61 (0.35), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.27), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01021 / 0.44 ( 4020) covalent geometry : angle 1.90154 / 0.70 ( 5520) Misc. bond : bond 0.00133 / 0.07 ( 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 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 18 time to evaluate : 0.123 Fit side-chains REVERT: L 5 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (tt) REVERT: a 5 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7502 (tp) outliers start: 54 outliers final: 40 residues processed: 71 average time/residue: 0.0290 time to fit residues: 3.1456 Evaluate side-chains 59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 17 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L 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 S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 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 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 3 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 o residue 5 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 v residue 4 LEU Chi-restraints excluded: chain w residue 5 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: [0] chunk 0 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.079095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.071439 restraints weight = 21656.826| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 5.45 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4080 Z= 0.228 Angle : 1.282 12.302 5520 Z= 0.475 Chirality : 0.048 0.179 540 Planarity : 0.002 0.007 480 Dihedral : 26.827 89.869 1200 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 17.92 % Allowed : 27.08 % Favored : 55.00 % 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: -7.38 (0.37), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.62 (0.28), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 ( 4020) covalent geometry : angle 1.28174 / 0.47 ( 5520) Misc. bond : bond 0.00125 / 0.07 ( 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 77 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 34 time to evaluate : 0.071 Fit side-chains REVERT: L 5 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (tt) outliers start: 43 outliers final: 37 residues processed: 73 average time/residue: 0.0303 time to fit residues: 3.2931 Evaluate side-chains 67 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 29 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F 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 L residue 5 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 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 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 j residue 3 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 n 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 w residue 5 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: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.068646 restraints weight = 22948.716| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 5.44 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.045 4080 Z= 0.435 Angle : 1.855 13.069 5520 Z= 0.686 Chirality : 0.064 0.222 540 Planarity : 0.004 0.013 480 Dihedral : 29.865 89.822 1200 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 21.25 % Allowed : 25.00 % Favored : 53.75 % 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: -7.69 (0.35), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.86 (0.27), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01022 / 0.44 ( 4020) covalent geometry : angle 1.85490 / 0.69 ( 5520) Misc. bond : bond 0.00142 / 0.08 ( 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 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 21 time to evaluate : 0.115 Fit side-chains REVERT: L 5 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8310 (tt) REVERT: a 5 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7451 (tp) outliers start: 51 outliers final: 38 residues processed: 71 average time/residue: 0.0314 time to fit residues: 3.3482 Evaluate side-chains 60 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 20 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 C residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain F residue 4 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 L residue 5 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 5 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 U residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 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 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 3 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 r residue 4 LEU Chi-restraints excluded: chain t residue 4 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.075573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.067917 restraints weight = 21856.334| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 5.09 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.050 4080 Z= 0.435 Angle : 1.765 14.010 5520 Z= 0.656 Chirality : 0.061 0.222 540 Planarity : 0.004 0.012 480 Dihedral : 29.780 89.686 1200 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 17.92 % Allowed : 27.92 % Favored : 54.17 % 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: -7.84 (0.34), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.26), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01024 / 0.44 ( 4020) covalent geometry : angle 1.76546 / 0.66 ( 5520) Misc. bond : bond 0.00118 / 0.07 ( 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 66 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 23 time to evaluate : 0.124 Fit side-chains REVERT: G 5 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8449 (tp) REVERT: a 5 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7493 (tp) outliers start: 43 outliers final: 37 residues processed: 64 average time/residue: 0.0265 time to fit residues: 2.5933 Evaluate side-chains 60 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 21 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 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 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 U residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 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 j residue 3 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 r 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.075377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067865 restraints weight = 22943.036| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 5.29 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 4080 Z= 0.436 Angle : 1.842 13.013 5520 Z= 0.683 Chirality : 0.063 0.254 540 Planarity : 0.004 0.012 480 Dihedral : 30.411 89.919 1200 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 17.50 % Allowed : 29.58 % Favored : 52.92 % 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: -7.89 (0.35), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.01 (0.26), residues: 120 Details of bonding type rmsd/Z covalent geometry : bond 0.01031 / 0.44 ( 4020) covalent geometry : angle 1.84160 / 0.68 ( 5520) Misc. bond : bond 0.00118 / 0.07 ( 60) =============================================================================== Job complete usr+sys time: 556.33 seconds wall clock time: 10 minutes 15.97 seconds (615.97 seconds total)