Starting phenix.real_space_refine on Thu Oct 22 20:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqf_23484/10_2026/7lqf_23484.cif" } resolution = 3.8 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= 0.002 sd= 0.026 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: 3 Type Number sf(0) Gaussians C 3840 2.51 5 N 704 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s 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: 5376 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.46, per 1000 atoms: 0.27 Number of scatterers: 5376 At special positions: 0 Unit cell: (70.2, 87.48, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 832 8.00 N 704 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 115.1 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.813A pdb=" N LYS A 6 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 6 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 6 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 305 through 306 removed outlier: 6.248A pdb=" N PHE j 205 " --> pdb=" O LYS k 306 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE W 305 " --> pdb=" O LYS j 206 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE V 205 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE Q 305 " --> pdb=" O LYS V 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE P 205 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE K 305 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 205 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE M 205 " --> pdb=" O LYS N 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE S 205 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE Y 205 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE m 205 " --> pdb=" O LYS n 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'a' and resid 4 through 6 removed outlier: 3.879A pdb=" N GLU a 4 " --> pdb=" O LYS r 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS r 106 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU r 104 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 104 through 106 removed outlier: 3.582A pdb=" N GLU o 104 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS o 106 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU c 4 " --> pdb=" O LYS o 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'y' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHE z 305 " --> pdb=" O PHE y 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE y 205 " --> pdb=" O PHE z 303 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU s 204 " --> pdb=" O LYS z 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GMA z 308 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS s 202 " --> pdb=" O GMA z 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE t 305 " --> pdb=" O PHE s 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE s 205 " --> pdb=" O PHE t 303 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS p 206 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU p 204 " --> pdb=" O LYS t 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE q 305 " --> pdb=" O PHE p 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE p 205 " --> pdb=" O PHE q 303 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU v 204 " --> pdb=" O LYS q 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GMA q 308 " --> pdb=" O LYS v 202 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS v 202 " --> pdb=" O GMA q 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE w 305 " --> pdb=" O PHE v 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE v 205 " --> pdb=" O PHE w 303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 1 206 " --> pdb=" O GLU w 304 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 1 204 " --> pdb=" O LYS w 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GMA w 308 " --> pdb=" O LYS 1 202 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS 1 202 " --> pdb=" O GMA w 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE 2 305 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE 1 205 " --> pdb=" O PHE 2 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS 7 206 " --> pdb=" O GLU 2 304 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU 7 204 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GMA 2 308 " --> pdb=" O LYS 7 202 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 7 202 " --> pdb=" O GMA 2 308 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 8 305 " --> pdb=" O PHE 7 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 7 205 " --> pdb=" O PHE 8 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 4 through 6 removed outlier: 3.815A pdb=" N GLU b 4 " --> pdb=" O LYS x 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'u' and resid 104 through 106 removed outlier: 3.578A pdb=" N GLU u 104 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS u 106 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 4 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.865A pdb=" N GLU d 4 " --> pdb=" O LYS 3 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 3 106 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 3 104 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 104 through 106 removed outlier: 3.619A pdb=" N GLU 0 104 " --> pdb=" O LYS g 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS 0 106 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU g 4 " --> pdb=" O LYS 0 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.795A pdb=" N GLU f 4 " --> pdb=" O LYS 9 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU 9 104 " --> pdb=" O LYS f 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 202 through 205 removed outlier: 3.693A pdb=" N PHE 5 305 " --> pdb=" O PHE 4 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 4 205 " --> pdb=" O PHE 5 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AA' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHEBA 305 " --> pdb=" O PHEAA 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHEAA 205 " --> pdb=" O PHEBA 303 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 649 1.25 - 1.33: 411 1.33 - 1.40: 1820 1.40 - 1.47: 576 1.47 - 1.54: 2112 Bond restraints: 5568 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6235 1.90 - 3.80: 717 3.80 - 5.70: 192 5.70 - 7.60: 80 7.60 - 9.50: 8 Bond angle restraints: 7232 Sorted by residual: angle pdb=" C 5CR q 301 " pdb=" CA 5CR q 301 " pdb=" CB 5CR q 301 " ideal model delta sigma weight residual 110.10 116.12 -6.02 1.90e+00 2.77e-01 1.00e+01 angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.41 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C 5CR t 301 " pdb=" CA 5CR t 301 " pdb=" CB 5CR t 301 " ideal model delta sigma weight residual 110.10 116.11 -6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C 5CR 5 301 " pdb=" CA 5CR 5 301 " pdb=" CB 5CR 5 301 " ideal model delta sigma weight residual 110.10 116.10 -6.00 1.90e+00 2.77e-01 9.99e+00 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.39 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 7227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.80: 1977 10.80 - 21.61: 416 21.61 - 32.41: 159 32.41 - 43.21: 144 43.21 - 54.01: 56 Dihedral angle restraints: 2752 sinusoidal: 1280 harmonic: 1472 Sorted by residual: dihedral pdb=" CA LYS r 106 " pdb=" CB LYS r 106 " pdb=" CG LYS r 106 " pdb=" CD LYS r 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS 9 106 " pdb=" CB LYS 9 106 " pdb=" CG LYS 9 106 " pdb=" CD LYS 9 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS u 106 " pdb=" CB LYS u 106 " pdb=" CG LYS u 106 " pdb=" CD LYS u 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.017: 172 0.017 - 0.034: 140 0.034 - 0.051: 124 0.051 - 0.067: 60 0.067 - 0.084: 16 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PHE j 203 " pdb=" N PHE j 203 " pdb=" C PHE j 203 " pdb=" CB PHE j 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PHE Y 203 " pdb=" N PHE Y 203 " pdb=" C PHE Y 203 " pdb=" CB PHE Y 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.73e-01 chirality pdb=" CA PHE m 203 " pdb=" N PHE m 203 " pdb=" C PHE m 203 " pdb=" CB PHE m 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.71e-01 ... (remaining 509 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE p 203 " 0.009 2.00e-02 2.50e+03 6.10e-03 6.51e-01 pdb=" CG PHE p 203 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE p 203 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE p 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE p 203 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE p 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE p 203 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEBA 303 " 0.005 2.00e-02 2.50e+03 5.92e-03 6.14e-01 pdb=" CG PHEBA 303 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHEBA 303 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEBA 303 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEBA 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEBA 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHEBA 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 203 " -0.009 2.00e-02 2.50e+03 5.91e-03 6.11e-01 pdb=" CG PHE 4 203 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 203 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 203 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 203 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 4 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1729 2.79 - 3.31: 4534 3.31 - 3.84: 8714 3.84 - 4.37: 11165 4.37 - 4.90: 19430 Nonbonded interactions: 45572 Sorted by model distance: nonbonded pdb=" O GMA I 108 " pdb=" N 5CR J 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA i 108 " pdb=" N 5CR j 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA X 108 " pdb=" N 5CR Y 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA l 108 " pdb=" N 5CR m 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA R 108 " pdb=" N 5CR S 201 " model vdw 2.258 3.120 ... (remaining 45567 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 'AA' selection = chain 'B' selection = chain 'BA' 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' selection = chain 'y' selection = chain 'z' } 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 group one per residue 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: 3.450 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: 0.020 Set scattering table: 0.010 Process input model: 6.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.016 0.116 5568 Z= 0.776 Angle : 1.461 9.501 7232 Z= 0.602 Chirality : 0.035 0.084 512 Planarity : 0.002 0.007 960 Dihedral : 18.365 54.014 1728 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % 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: -4.77 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE 5 303 Details of bonding type rmsd/Z covalent geometry : bond 0.01575 / 0.78 ( 5568) covalent geometry : angle 1.46064 / 0.60 ( 7232) hydrogen bonds : bond 0.29011 / 18.10 ( 52) hydrogen bonds : angle 10.62446 / 5.91 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8811 (tptm) REVERT: A 7 PHE cc_start: 0.8216 (m-10) cc_final: 0.7886 (m-10) REVERT: J 202 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7898 (ttmm) REVERT: K 306 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7586 (mmmm) REVERT: B 2 LYS cc_start: 0.9157 (tttt) cc_final: 0.8892 (tptm) REVERT: B 6 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7432 (mmmm) REVERT: L 102 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8600 (mmtt) REVERT: M 204 GLU cc_start: 0.8113 (pt0) cc_final: 0.7204 (pm20) REVERT: N 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Q 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7608 (mmmm) REVERT: D 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8722 (tptm) REVERT: D 3 PHE cc_start: 0.8401 (m-80) cc_final: 0.8172 (m-80) REVERT: D 6 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7546 (mmmm) REVERT: R 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6923 (tm-30) REVERT: S 204 GLU cc_start: 0.8108 (pt0) cc_final: 0.7535 (pm20) REVERT: T 305 PHE cc_start: 0.8456 (m-80) cc_final: 0.8254 (m-10) REVERT: T 306 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7671 (mmmm) REVERT: E 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8716 (tptm) REVERT: U 104 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7072 (tm-30) REVERT: V 204 GLU cc_start: 0.8325 (pt0) cc_final: 0.7745 (pm20) REVERT: W 302 LYS cc_start: 0.8301 (tppp) cc_final: 0.7719 (tppp) REVERT: W 306 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7862 (mmmm) REVERT: F 2 LYS cc_start: 0.9090 (tttt) cc_final: 0.8422 (tmtt) REVERT: X 104 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7017 (tm-30) REVERT: X 106 LYS cc_start: 0.7894 (tppt) cc_final: 0.7561 (tppt) REVERT: Y 204 GLU cc_start: 0.8371 (pt0) cc_final: 0.7350 (pp20) REVERT: Z 306 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7335 (mmmm) REVERT: G 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7869 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8356 (mmtt) REVERT: i 104 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7020 (tm-30) REVERT: i 106 LYS cc_start: 0.7678 (tppt) cc_final: 0.7407 (tppt) REVERT: j 204 GLU cc_start: 0.8071 (pt0) cc_final: 0.7744 (pm20) REVERT: k 304 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6755 (tm-30) REVERT: H 3 PHE cc_start: 0.8404 (m-80) cc_final: 0.8026 (m-80) REVERT: l 102 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8558 (mmtt) REVERT: m 204 GLU cc_start: 0.7904 (pt0) cc_final: 0.7370 (pm20) REVERT: m 205 PHE cc_start: 0.8286 (m-80) cc_final: 0.8052 (m-80) REVERT: n 306 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7577 (mmmm) REVERT: p 203 PHE cc_start: 0.7511 (t80) cc_final: 0.7308 (t80) REVERT: q 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7808 (t80) REVERT: q 307 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80) REVERT: r 105 PHE cc_start: 0.9015 (p90) cc_final: 0.8791 (p90) REVERT: t 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7770 (t80) REVERT: t 305 PHE cc_start: 0.7586 (t80) cc_final: 0.7183 (t80) REVERT: v 204 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7051 (tm-30) REVERT: w 302 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8490 (tmtt) REVERT: x 105 PHE cc_start: 0.8978 (p90) cc_final: 0.8358 (p90) REVERT: x 107 PHE cc_start: 0.8027 (t80) cc_final: 0.7191 (t80) REVERT: z 305 PHE cc_start: 0.7904 (t80) cc_final: 0.7476 (t80) REVERT: e 6 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8167 (ttmm) REVERT: e 7 PHE cc_start: 0.9053 (t80) cc_final: 0.8752 (t80) REVERT: 1 202 LYS cc_start: 0.8057 (tptp) cc_final: 0.7783 (tptp) REVERT: 2 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7673 (t80) REVERT: f 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8383 (t80) REVERT: 3 105 PHE cc_start: 0.8867 (p90) cc_final: 0.8660 (p90) REVERT: 3 106 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8356 (ttpp) REVERT: 4 204 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 5 303 PHE cc_start: 0.8146 (t80) cc_final: 0.7910 (t80) REVERT: g 2 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8492 (mmtt) REVERT: 6 106 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8435 (ttpp) REVERT: 7 204 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 8 302 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8593 (tmtt) REVERT: 8 307 PHE cc_start: 0.7753 (t80) cc_final: 0.7394 (t80) REVERT: 9 107 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) outliers start: 8 outliers final: 0 residues processed: 164 average time/residue: 0.1501 time to fit residues: 28.2359 Evaluate side-chains 161 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain G residue 6 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081530 restraints weight = 12847.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084364 restraints weight = 5607.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086163 restraints weight = 3061.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087360 restraints weight = 1882.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.088240 restraints weight = 1266.091| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5568 Z= 0.121 Angle : 0.709 8.794 7232 Z= 0.315 Chirality : 0.029 0.089 512 Planarity : 0.002 0.013 960 Dihedral : 13.302 59.372 652 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 17.19 % Favored : 81.77 % 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: -4.56 (0.29), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.22), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHE z 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5568) covalent geometry : angle 0.70873 / 0.31 ( 7232) hydrogen bonds : bond 0.03638 / 2.16 ( 52) hydrogen bonds : angle 6.90684 / 3.91 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8952 (tttt) cc_final: 0.8606 (tptm) REVERT: I 104 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6594 (tm-30) REVERT: J 203 PHE cc_start: 0.8303 (m-80) cc_final: 0.8090 (m-80) REVERT: J 206 LYS cc_start: 0.8084 (tttm) cc_final: 0.7513 (tttm) REVERT: K 304 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6624 (tm-30) REVERT: K 306 LYS cc_start: 0.8159 (mmmm) cc_final: 0.6574 (mmmm) REVERT: B 3 PHE cc_start: 0.8402 (m-80) cc_final: 0.8122 (m-80) REVERT: B 6 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7329 (mmmm) REVERT: L 102 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8516 (mmtt) REVERT: M 203 PHE cc_start: 0.8253 (m-80) cc_final: 0.7980 (m-80) REVERT: M 204 GLU cc_start: 0.7937 (pt0) cc_final: 0.7167 (pm20) REVERT: N 306 LYS cc_start: 0.8321 (mmmm) cc_final: 0.7513 (mmmm) REVERT: C 2 LYS cc_start: 0.8898 (tttt) cc_final: 0.8383 (tttm) REVERT: C 3 PHE cc_start: 0.8323 (m-80) cc_final: 0.7991 (m-80) REVERT: O 106 LYS cc_start: 0.8235 (tppt) cc_final: 0.7888 (tppt) REVERT: P 206 LYS cc_start: 0.8304 (tttm) cc_final: 0.7471 (tttm) REVERT: Q 304 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6517 (tm-30) REVERT: Q 306 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7354 (mmmm) REVERT: D 2 LYS cc_start: 0.9009 (tttt) cc_final: 0.8755 (tttm) REVERT: R 104 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6662 (tm-30) REVERT: R 106 LYS cc_start: 0.8034 (tppt) cc_final: 0.7429 (tppt) REVERT: S 202 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8093 (ttmm) REVERT: T 306 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7581 (mmmm) REVERT: E 2 LYS cc_start: 0.8886 (tttt) cc_final: 0.8544 (tptm) REVERT: U 102 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8566 (mmtt) REVERT: U 104 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6624 (tm-30) REVERT: V 202 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8193 (ttmm) REVERT: W 306 LYS cc_start: 0.8349 (mmmm) cc_final: 0.7788 (mmmm) REVERT: X 104 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6730 (tm-30) REVERT: X 106 LYS cc_start: 0.8200 (tppt) cc_final: 0.7638 (tppt) REVERT: Y 204 GLU cc_start: 0.8187 (pt0) cc_final: 0.7617 (pm20) REVERT: Y 206 LYS cc_start: 0.8070 (tttm) cc_final: 0.7524 (tttm) REVERT: Z 306 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7286 (mmmm) REVERT: G 6 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7680 (mtpp) REVERT: i 102 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8410 (mmtt) REVERT: i 104 GLU cc_start: 0.7739 (tm-30) cc_final: 0.6940 (tm-30) REVERT: i 106 LYS cc_start: 0.7639 (tppt) cc_final: 0.7332 (tppt) REVERT: j 204 GLU cc_start: 0.8226 (pt0) cc_final: 0.7668 (pm20) REVERT: k 304 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6563 (tm-30) REVERT: H 3 PHE cc_start: 0.8413 (m-80) cc_final: 0.8068 (m-80) REVERT: l 102 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8763 (mmtt) REVERT: m 204 GLU cc_start: 0.8163 (pt0) cc_final: 0.7409 (pm20) REVERT: n 304 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6772 (tp30) REVERT: n 306 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7102 (mmmm) REVERT: p 204 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7304 (tm-30) REVERT: q 303 PHE cc_start: 0.7908 (t80) cc_final: 0.7603 (t80) REVERT: t 303 PHE cc_start: 0.7919 (t80) cc_final: 0.7630 (t80) REVERT: t 305 PHE cc_start: 0.7504 (t80) cc_final: 0.7211 (t80) REVERT: c 7 PHE cc_start: 0.8925 (t80) cc_final: 0.8619 (t80) REVERT: v 204 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6532 (tm-30) REVERT: w 302 LYS cc_start: 0.8725 (tmtt) cc_final: 0.8170 (tmtt) REVERT: w 303 PHE cc_start: 0.8016 (t80) cc_final: 0.7755 (t80) REVERT: x 104 GLU cc_start: 0.8436 (pp20) cc_final: 0.8227 (tm-30) REVERT: x 105 PHE cc_start: 0.8809 (p90) cc_final: 0.8372 (p90) REVERT: x 107 PHE cc_start: 0.7966 (t80) cc_final: 0.7243 (t80) REVERT: z 305 PHE cc_start: 0.7790 (t80) cc_final: 0.7346 (t80) REVERT: e 7 PHE cc_start: 0.8977 (t80) cc_final: 0.8727 (t80) REVERT: 0 104 GLU cc_start: 0.8190 (pp20) cc_final: 0.7773 (tm-30) REVERT: 1 202 LYS cc_start: 0.7820 (tptp) cc_final: 0.7571 (tptp) REVERT: 2 302 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8201 (tptp) REVERT: f 7 PHE cc_start: 0.8881 (t80) cc_final: 0.8537 (t80) REVERT: 3 105 PHE cc_start: 0.8871 (p90) cc_final: 0.8607 (p90) REVERT: 4 204 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7005 (tm-30) REVERT: 5 303 PHE cc_start: 0.7959 (t80) cc_final: 0.7433 (t80) REVERT: g 2 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8447 (mmtt) REVERT: 6 106 LYS cc_start: 0.8609 (tmtt) cc_final: 0.8183 (ttpp) REVERT: 7 202 LYS cc_start: 0.7843 (tptp) cc_final: 0.7540 (tptp) REVERT: 7 204 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6876 (tm-30) outliers start: 4 outliers final: 2 residues processed: 162 average time/residue: 0.1442 time to fit residues: 27.0923 Evaluate side-chains 158 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain h residue 7 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.088627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.079622 restraints weight = 13382.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082316 restraints weight = 5798.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083993 restraints weight = 3134.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085143 restraints weight = 1884.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085943 restraints weight = 1226.650| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.058 5568 Z= 0.678 Angle : 1.093 12.126 7232 Z= 0.507 Chirality : 0.049 0.163 512 Planarity : 0.005 0.018 960 Dihedral : 15.202 58.785 640 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.86 % Allowed : 22.66 % Favored : 74.48 % 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: -5.01 (0.28), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.22), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.005 PHE P 205 Details of bonding type rmsd/Z covalent geometry : bond 0.01501 / 0.68 ( 5568) covalent geometry : angle 1.09253 / 0.51 ( 7232) hydrogen bonds : bond 0.05773 / 3.45 ( 52) hydrogen bonds : angle 7.57678 / 3.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9212 (tttt) cc_final: 0.8991 (ttmt) REVERT: A 4 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 7 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: K 302 LYS cc_start: 0.8646 (tppp) cc_final: 0.8155 (tppp) REVERT: K 304 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6772 (tm-30) REVERT: K 306 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7553 (mmmm) REVERT: B 2 LYS cc_start: 0.9207 (tttt) cc_final: 0.8933 (tptm) REVERT: B 6 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7500 (mtpp) REVERT: M 202 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8301 (ttmm) REVERT: N 302 LYS cc_start: 0.8396 (tppp) cc_final: 0.8049 (tppp) REVERT: N 306 LYS cc_start: 0.8507 (mmmm) cc_final: 0.7854 (mmmm) REVERT: Q 302 LYS cc_start: 0.8199 (tppp) cc_final: 0.7566 (tppp) REVERT: Q 304 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6997 (tm-30) REVERT: Q 306 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7372 (mmmm) REVERT: D 6 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7718 (mtpp) REVERT: R 104 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7498 (tm-30) REVERT: R 106 LYS cc_start: 0.8108 (tppt) cc_final: 0.7476 (tppt) REVERT: S 206 LYS cc_start: 0.8462 (tttm) cc_final: 0.7738 (tttm) REVERT: T 306 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7477 (mmmm) REVERT: E 2 LYS cc_start: 0.9139 (tttt) cc_final: 0.8847 (tptm) REVERT: U 104 GLU cc_start: 0.7766 (tm-30) cc_final: 0.6897 (tm-30) REVERT: W 302 LYS cc_start: 0.8540 (tppp) cc_final: 0.8143 (tppp) REVERT: W 306 LYS cc_start: 0.8473 (mmmm) cc_final: 0.7928 (mmmm) REVERT: F 6 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7402 (mmmm) REVERT: X 104 GLU cc_start: 0.8072 (tm-30) cc_final: 0.6936 (tm-30) REVERT: Y 202 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8410 (ttmm) REVERT: Y 204 GLU cc_start: 0.8509 (pt0) cc_final: 0.7781 (pm20) REVERT: Y 206 LYS cc_start: 0.8148 (tttm) cc_final: 0.7592 (tttm) REVERT: Z 304 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7150 (tm-30) REVERT: G 2 LYS cc_start: 0.9113 (tttt) cc_final: 0.8774 (ttmm) REVERT: i 102 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8744 (mmtt) REVERT: i 106 LYS cc_start: 0.7292 (tppt) cc_final: 0.6891 (tppt) REVERT: i 107 PHE cc_start: 0.8783 (m-80) cc_final: 0.5395 (p90) REVERT: l 102 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8668 (mmtt) REVERT: l 106 LYS cc_start: 0.8332 (tppt) cc_final: 0.7868 (tppt) REVERT: m 204 GLU cc_start: 0.8492 (pt0) cc_final: 0.7726 (pm20) REVERT: n 302 LYS cc_start: 0.8423 (tppp) cc_final: 0.8146 (tppp) REVERT: n 304 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6809 (tp30) REVERT: n 306 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7113 (mmmm) REVERT: o 102 LYS cc_start: 0.8534 (tptp) cc_final: 0.8241 (tptp) REVERT: o 106 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8327 (ttmm) REVERT: s 202 LYS cc_start: 0.8127 (tptp) cc_final: 0.7831 (tptt) REVERT: s 206 LYS cc_start: 0.8283 (tptp) cc_final: 0.7783 (tptp) REVERT: t 302 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8187 (tmtt) REVERT: t 305 PHE cc_start: 0.7756 (t80) cc_final: 0.7357 (t80) REVERT: c 7 PHE cc_start: 0.9021 (t80) cc_final: 0.8766 (t80) REVERT: u 102 LYS cc_start: 0.8438 (tptp) cc_final: 0.8214 (tptp) REVERT: v 202 LYS cc_start: 0.7927 (tptp) cc_final: 0.7578 (tptp) REVERT: v 204 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6597 (tm-30) REVERT: x 105 PHE cc_start: 0.8917 (p90) cc_final: 0.8101 (p90) REVERT: y 202 LYS cc_start: 0.7979 (tptp) cc_final: 0.7655 (tptp) REVERT: y 203 PHE cc_start: 0.7899 (t80) cc_final: 0.7572 (t80) REVERT: y 204 GLU cc_start: 0.7725 (tm-30) cc_final: 0.6989 (tm-30) REVERT: z 302 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8149 (tmtt) REVERT: 1 202 LYS cc_start: 0.8219 (tptp) cc_final: 0.7851 (tptp) REVERT: 2 305 PHE cc_start: 0.8029 (t80) cc_final: 0.7548 (t80) REVERT: f 2 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8525 (mmtt) REVERT: f 7 PHE cc_start: 0.9036 (t80) cc_final: 0.8812 (t80) REVERT: 3 106 LYS cc_start: 0.8824 (tmtt) cc_final: 0.8362 (ttmm) REVERT: 4 204 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7240 (tm-30) REVERT: 5 302 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8287 (tmtt) REVERT: 5 303 PHE cc_start: 0.8109 (t80) cc_final: 0.7636 (t80) REVERT: g 2 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8509 (mmtt) REVERT: g 7 PHE cc_start: 0.8950 (t80) cc_final: 0.8632 (t80) REVERT: 6 106 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8402 (ttpp) REVERT: 7 202 LYS cc_start: 0.8005 (tptp) cc_final: 0.7582 (tptp) REVERT: 7 204 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7194 (tm-30) REVERT: 8 302 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8408 (tmtt) REVERT: 8 307 PHE cc_start: 0.7833 (t80) cc_final: 0.7317 (t80) REVERT: h 2 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8465 (mmtt) REVERT: 9 103 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7854 (t80) REVERT: 9 107 PHE cc_start: 0.8229 (t80) cc_final: 0.7104 (t80) REVERT: BA 302 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8275 (tmtt) outliers start: 11 outliers final: 4 residues processed: 189 average time/residue: 0.1451 time to fit residues: 31.6551 Evaluate side-chains 189 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain P residue 204 GLU Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain u residue 103 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain 9 residue 103 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.092389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082657 restraints weight = 12807.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.085325 restraints weight = 5430.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.087094 restraints weight = 2967.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088191 restraints weight = 1811.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089035 restraints weight = 1233.223| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5568 Z= 0.123 Angle : 0.700 8.211 7232 Z= 0.320 Chirality : 0.031 0.103 512 Planarity : 0.002 0.013 960 Dihedral : 12.479 58.488 640 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.78 % Allowed : 25.52 % Favored : 73.70 % 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: -4.58 (0.30), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.23), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE w 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 5568) covalent geometry : angle 0.69976 / 0.32 ( 7232) hydrogen bonds : bond 0.03063 / 1.77 ( 52) hydrogen bonds : angle 6.32625 / 3.35 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8600 (tptm) REVERT: A 4 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7054 (mm-30) REVERT: I 104 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7441 (tm-30) REVERT: J 203 PHE cc_start: 0.8609 (m-80) cc_final: 0.8406 (m-80) REVERT: J 204 GLU cc_start: 0.8133 (pt0) cc_final: 0.7857 (pt0) REVERT: K 304 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6682 (tm-30) REVERT: K 306 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7341 (mmmm) REVERT: B 2 LYS cc_start: 0.8917 (tttt) cc_final: 0.8487 (tttp) REVERT: B 3 PHE cc_start: 0.8305 (m-80) cc_final: 0.8084 (m-80) REVERT: L 102 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8398 (mmtt) REVERT: M 202 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8218 (ttmm) REVERT: N 306 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7845 (mmmm) REVERT: C 2 LYS cc_start: 0.8762 (tttt) cc_final: 0.8310 (tttm) REVERT: C 4 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7494 (mm-30) REVERT: O 102 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8727 (mmtt) REVERT: P 202 LYS cc_start: 0.8682 (ttmm) cc_final: 0.7753 (tppt) REVERT: Q 304 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6728 (tm-30) REVERT: Q 306 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7327 (mmmm) REVERT: D 6 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7097 (mtpp) REVERT: R 104 GLU cc_start: 0.7778 (tm-30) cc_final: 0.6735 (tm-30) REVERT: S 206 LYS cc_start: 0.8353 (tttm) cc_final: 0.7521 (tttm) REVERT: T 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7537 (mmmm) REVERT: E 2 LYS cc_start: 0.8882 (tttt) cc_final: 0.8552 (tptm) REVERT: U 104 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6384 (tm-30) REVERT: V 202 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8100 (ttmm) REVERT: W 306 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7764 (mmmm) REVERT: X 104 GLU cc_start: 0.7917 (tm-30) cc_final: 0.6757 (tm-30) REVERT: X 106 LYS cc_start: 0.8270 (tppt) cc_final: 0.7672 (tppt) REVERT: Y 206 LYS cc_start: 0.7994 (tttm) cc_final: 0.7395 (tttm) REVERT: Z 306 LYS cc_start: 0.7969 (mmmm) cc_final: 0.6719 (mmmm) REVERT: G 2 LYS cc_start: 0.8682 (tttt) cc_final: 0.8244 (ttmm) REVERT: G 6 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7766 (ttmm) REVERT: i 102 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8616 (mmtt) REVERT: i 106 LYS cc_start: 0.7323 (tppt) cc_final: 0.6623 (tppt) REVERT: i 107 PHE cc_start: 0.8836 (m-80) cc_final: 0.5146 (p90) REVERT: k 302 LYS cc_start: 0.3679 (tppt) cc_final: 0.3358 (tppt) REVERT: l 102 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8568 (mmtt) REVERT: l 104 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6995 (tm-30) REVERT: l 106 LYS cc_start: 0.8309 (tppt) cc_final: 0.7614 (tppt) REVERT: m 204 GLU cc_start: 0.8353 (pt0) cc_final: 0.7509 (pm20) REVERT: n 302 LYS cc_start: 0.7928 (tppp) cc_final: 0.7686 (tppp) REVERT: n 304 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6195 (tm-30) REVERT: n 306 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7079 (mmmm) REVERT: o 104 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7816 (tm-30) REVERT: p 204 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6614 (tm-30) REVERT: s 202 LYS cc_start: 0.8008 (tptp) cc_final: 0.7493 (tptt) REVERT: s 203 PHE cc_start: 0.7676 (t80) cc_final: 0.7252 (t80) REVERT: s 204 GLU cc_start: 0.7516 (tp30) cc_final: 0.7177 (tp30) REVERT: t 303 PHE cc_start: 0.7854 (t80) cc_final: 0.7589 (t80) REVERT: t 305 PHE cc_start: 0.7735 (t80) cc_final: 0.7388 (t80) REVERT: c 7 PHE cc_start: 0.8830 (t80) cc_final: 0.8616 (t80) REVERT: v 202 LYS cc_start: 0.7787 (tptp) cc_final: 0.7473 (tptp) REVERT: v 203 PHE cc_start: 0.7637 (t80) cc_final: 0.7216 (t80) REVERT: x 104 GLU cc_start: 0.8631 (pp20) cc_final: 0.8269 (tm-30) REVERT: x 105 PHE cc_start: 0.8905 (p90) cc_final: 0.8473 (p90) REVERT: y 204 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6690 (tm-30) REVERT: z 302 LYS cc_start: 0.8644 (tmtt) cc_final: 0.7965 (tmtt) REVERT: 1 202 LYS cc_start: 0.7971 (tptp) cc_final: 0.7642 (tptp) REVERT: 1 203 PHE cc_start: 0.7671 (t80) cc_final: 0.7403 (t80) REVERT: 2 302 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8369 (tmtt) REVERT: 2 305 PHE cc_start: 0.7981 (t80) cc_final: 0.7513 (t80) REVERT: f 7 PHE cc_start: 0.8893 (t80) cc_final: 0.8576 (t80) REVERT: 3 104 GLU cc_start: 0.8357 (pp20) cc_final: 0.7885 (tm-30) REVERT: 3 105 PHE cc_start: 0.8893 (p90) cc_final: 0.8543 (p90) REVERT: 3 106 LYS cc_start: 0.8676 (tmtt) cc_final: 0.8076 (ttmm) REVERT: 4 202 LYS cc_start: 0.7762 (tptp) cc_final: 0.7376 (tptp) REVERT: 4 204 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6805 (tm-30) REVERT: 5 303 PHE cc_start: 0.7941 (t80) cc_final: 0.7368 (t80) REVERT: g 2 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8317 (mmtt) REVERT: g 7 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8417 (t80) REVERT: 6 105 PHE cc_start: 0.8881 (p90) cc_final: 0.8205 (p90) REVERT: 6 106 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8069 (tmtt) REVERT: 7 202 LYS cc_start: 0.7934 (tptp) cc_final: 0.7605 (tptp) REVERT: 7 204 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6805 (tm-30) REVERT: 8 302 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8348 (tmtt) REVERT: h 2 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8545 (mmtt) REVERT: AA 204 GLU cc_start: 0.5477 (pm20) cc_final: 0.5261 (pm20) REVERT: BA 302 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8174 (tmtt) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.1282 time to fit residues: 24.9296 Evaluate side-chains 169 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 7 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.090382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081117 restraints weight = 13501.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.083970 restraints weight = 6097.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085709 restraints weight = 3358.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.086928 restraints weight = 2057.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087692 restraints weight = 1343.022| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.082 5568 Z= 0.682 Angle : 1.084 11.219 7232 Z= 0.511 Chirality : 0.051 0.146 512 Planarity : 0.005 0.018 960 Dihedral : 14.245 69.838 640 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.12 % Allowed : 27.34 % Favored : 69.53 % 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: -5.25 (0.29), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.22), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.005 PHE P 205 Details of bonding type rmsd/Z covalent geometry : bond 0.01516 / 0.68 ( 5568) covalent geometry : angle 1.08352 / 0.51 ( 7232) hydrogen bonds : bond 0.05624 / 3.28 ( 52) hydrogen bonds : angle 7.58646 / 3.89 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9204 (tttt) cc_final: 0.8987 (ttmt) REVERT: A 4 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7115 (mm-30) REVERT: K 302 LYS cc_start: 0.8686 (tppp) cc_final: 0.8172 (tppp) REVERT: K 304 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6784 (tm-30) REVERT: K 306 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7564 (mmmm) REVERT: B 2 LYS cc_start: 0.9147 (tttt) cc_final: 0.8870 (tptm) REVERT: M 202 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8328 (ttmm) REVERT: N 302 LYS cc_start: 0.8384 (tppp) cc_final: 0.7897 (tppp) REVERT: N 306 LYS cc_start: 0.8542 (mmmm) cc_final: 0.7877 (mmmm) REVERT: C 2 LYS cc_start: 0.8930 (tttt) cc_final: 0.7936 (tmtt) REVERT: C 4 GLU cc_start: 0.7843 (mm-30) cc_final: 0.6135 (mm-30) REVERT: O 102 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8816 (mmtt) REVERT: P 202 LYS cc_start: 0.8754 (ttmm) cc_final: 0.7626 (tppt) REVERT: Q 302 LYS cc_start: 0.8182 (tppp) cc_final: 0.7532 (tppp) REVERT: Q 304 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6963 (tm-30) REVERT: Q 306 LYS cc_start: 0.8136 (mmmm) cc_final: 0.6984 (mmmm) REVERT: D 4 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 6 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7769 (mtpp) REVERT: R 104 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7655 (tm-30) REVERT: R 106 LYS cc_start: 0.8159 (tppt) cc_final: 0.7443 (tppt) REVERT: S 206 LYS cc_start: 0.8417 (tttm) cc_final: 0.7663 (tttm) REVERT: T 306 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7496 (mmmm) REVERT: E 2 LYS cc_start: 0.9111 (tttt) cc_final: 0.8819 (tptm) REVERT: U 104 GLU cc_start: 0.7754 (tm-30) cc_final: 0.6917 (tm-30) REVERT: V 204 GLU cc_start: 0.8349 (pt0) cc_final: 0.8093 (pt0) REVERT: V 206 LYS cc_start: 0.8369 (tttm) cc_final: 0.7404 (tttm) REVERT: W 302 LYS cc_start: 0.8640 (tppp) cc_final: 0.8226 (tppp) REVERT: W 306 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7829 (mmmm) REVERT: Y 206 LYS cc_start: 0.8183 (tttm) cc_final: 0.7607 (tttm) REVERT: Z 304 GLU cc_start: 0.7260 (tm-30) cc_final: 0.5955 (tm-30) REVERT: Z 306 LYS cc_start: 0.8044 (mmmm) cc_final: 0.6764 (mmmm) REVERT: i 102 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8603 (mmmt) REVERT: i 106 LYS cc_start: 0.5376 (tppt) cc_final: 0.4886 (tppt) REVERT: i 107 PHE cc_start: 0.8762 (m-80) cc_final: 0.5468 (p90) REVERT: l 102 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8601 (mmtt) REVERT: l 106 LYS cc_start: 0.8309 (tppt) cc_final: 0.7725 (tppt) REVERT: m 204 GLU cc_start: 0.8496 (pt0) cc_final: 0.7618 (pm20) REVERT: n 302 LYS cc_start: 0.8582 (tppp) cc_final: 0.8278 (tppp) REVERT: n 304 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6183 (tm-30) REVERT: n 306 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7222 (mmmm) REVERT: o 102 LYS cc_start: 0.8632 (tptp) cc_final: 0.8397 (tptp) REVERT: o 106 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8343 (ttmm) REVERT: s 202 LYS cc_start: 0.8089 (tptp) cc_final: 0.7867 (tptp) REVERT: s 206 LYS cc_start: 0.8324 (tptp) cc_final: 0.7882 (tptp) REVERT: t 305 PHE cc_start: 0.7866 (t80) cc_final: 0.7555 (t80) REVERT: c 2 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8240 (mmtt) REVERT: c 7 PHE cc_start: 0.9021 (t80) cc_final: 0.8788 (t80) REVERT: v 202 LYS cc_start: 0.7915 (tptp) cc_final: 0.7544 (tptp) REVERT: v 203 PHE cc_start: 0.7828 (t80) cc_final: 0.7215 (t80) REVERT: x 105 PHE cc_start: 0.8874 (p90) cc_final: 0.8128 (p90) REVERT: y 202 LYS cc_start: 0.7976 (tptp) cc_final: 0.7595 (tptp) REVERT: y 204 GLU cc_start: 0.7761 (tm-30) cc_final: 0.6865 (tm-30) REVERT: 1 202 LYS cc_start: 0.8174 (tptp) cc_final: 0.7797 (tptp) REVERT: 1 203 PHE cc_start: 0.7890 (t80) cc_final: 0.7375 (t80) REVERT: 2 305 PHE cc_start: 0.8022 (t80) cc_final: 0.7600 (t80) REVERT: f 7 PHE cc_start: 0.9027 (t80) cc_final: 0.8667 (t80) REVERT: 3 106 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8040 (tmtt) REVERT: 4 202 LYS cc_start: 0.7815 (tptp) cc_final: 0.7544 (tptt) REVERT: 4 204 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6897 (tm-30) REVERT: 5 303 PHE cc_start: 0.8118 (t80) cc_final: 0.7826 (t80) REVERT: g 2 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8415 (mmtt) REVERT: g 7 PHE cc_start: 0.8937 (t80) cc_final: 0.8591 (t80) REVERT: 7 202 LYS cc_start: 0.8089 (tptp) cc_final: 0.7640 (tptp) REVERT: 7 204 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7258 (tm-30) REVERT: 8 302 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8480 (tmtt) REVERT: 8 303 PHE cc_start: 0.7382 (t80) cc_final: 0.7120 (t80) REVERT: 8 307 PHE cc_start: 0.7803 (t80) cc_final: 0.7370 (t80) REVERT: 9 107 PHE cc_start: 0.8200 (t80) cc_final: 0.7801 (t80) REVERT: BA 302 LYS cc_start: 0.8852 (tmtt) cc_final: 0.8233 (tmtt) REVERT: BA 306 LYS cc_start: 0.8604 (tptm) cc_final: 0.8332 (tptm) outliers start: 12 outliers final: 9 residues processed: 182 average time/residue: 0.1474 time to fit residues: 30.9700 Evaluate side-chains 187 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 204 GLU Chi-restraints excluded: chain P residue 204 GLU Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain u residue 103 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain z residue 305 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.094428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084936 restraints weight = 12921.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.087739 restraints weight = 5572.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089468 restraints weight = 2978.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.090635 restraints weight = 1799.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091305 restraints weight = 1182.244| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5568 Z= 0.126 Angle : 0.725 8.270 7232 Z= 0.336 Chirality : 0.032 0.114 512 Planarity : 0.002 0.012 960 Dihedral : 12.248 67.181 640 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.78 % Allowed : 31.51 % Favored : 67.71 % 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: -4.72 (0.30), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.23), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE 9 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5568) covalent geometry : angle 0.72520 / 0.34 ( 7232) hydrogen bonds : bond 0.03203 / 1.77 ( 52) hydrogen bonds : angle 6.15295 / 3.21 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8977 (tttt) cc_final: 0.8593 (tptm) REVERT: A 4 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6878 (mm-30) REVERT: K 304 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6579 (tm-30) REVERT: K 306 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7552 (mmmm) REVERT: B 2 LYS cc_start: 0.8928 (tttt) cc_final: 0.8414 (tttp) REVERT: B 6 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7737 (mmmm) REVERT: L 102 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8439 (mmtt) REVERT: M 206 LYS cc_start: 0.8365 (tttm) cc_final: 0.7339 (tttm) REVERT: N 306 LYS cc_start: 0.8450 (mmmm) cc_final: 0.7998 (mmmm) REVERT: C 4 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7464 (mm-30) REVERT: O 102 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8698 (mmtt) REVERT: P 202 LYS cc_start: 0.8614 (ttmm) cc_final: 0.7786 (tppt) REVERT: Q 304 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6560 (tm-30) REVERT: Q 306 LYS cc_start: 0.8155 (mmmm) cc_final: 0.6968 (mmmm) REVERT: D 2 LYS cc_start: 0.8742 (tttt) cc_final: 0.8269 (tttm) REVERT: D 6 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7583 (mtpp) REVERT: R 104 GLU cc_start: 0.7824 (tm-30) cc_final: 0.6752 (tm-30) REVERT: S 204 GLU cc_start: 0.8121 (pt0) cc_final: 0.7800 (pt0) REVERT: S 206 LYS cc_start: 0.8393 (tttm) cc_final: 0.7567 (tttm) REVERT: T 306 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7220 (mmmm) REVERT: E 2 LYS cc_start: 0.8867 (tttt) cc_final: 0.8529 (tptm) REVERT: U 103 PHE cc_start: 0.8269 (m-80) cc_final: 0.8069 (m-80) REVERT: U 104 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6445 (tm-30) REVERT: V 204 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: V 206 LYS cc_start: 0.8331 (tttm) cc_final: 0.7311 (tttm) REVERT: W 302 LYS cc_start: 0.8433 (tppp) cc_final: 0.7945 (tppp) REVERT: W 304 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6711 (tm-30) REVERT: W 306 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7484 (mmmm) REVERT: X 104 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7473 (tm-30) REVERT: Y 202 LYS cc_start: 0.8534 (ttmm) cc_final: 0.7805 (tppt) REVERT: Y 206 LYS cc_start: 0.8094 (tttm) cc_final: 0.7519 (tttm) REVERT: Z 304 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6788 (tm-30) REVERT: Z 306 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7194 (mmmm) REVERT: G 6 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7857 (ttmm) REVERT: i 102 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8568 (mmtt) REVERT: i 107 PHE cc_start: 0.8829 (m-80) cc_final: 0.5257 (p90) REVERT: l 102 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8580 (mmtt) REVERT: l 106 LYS cc_start: 0.8260 (tppt) cc_final: 0.7612 (tppt) REVERT: m 204 GLU cc_start: 0.8379 (pt0) cc_final: 0.7700 (pm20) REVERT: n 302 LYS cc_start: 0.8053 (tppp) cc_final: 0.7842 (tppp) REVERT: n 304 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6983 (tm-30) REVERT: o 104 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7847 (tm-30) REVERT: p 204 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7392 (tm-30) REVERT: q 306 LYS cc_start: 0.8551 (tptp) cc_final: 0.8207 (tptp) REVERT: s 202 LYS cc_start: 0.7900 (tptp) cc_final: 0.7387 (tptt) REVERT: s 203 PHE cc_start: 0.7733 (t80) cc_final: 0.7316 (t80) REVERT: s 204 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7207 (tm-30) REVERT: s 206 LYS cc_start: 0.8142 (tptp) cc_final: 0.7422 (tptp) REVERT: t 305 PHE cc_start: 0.7778 (t80) cc_final: 0.7467 (t80) REVERT: c 7 PHE cc_start: 0.8852 (t80) cc_final: 0.8506 (t80) REVERT: v 202 LYS cc_start: 0.7742 (tptp) cc_final: 0.7345 (tptp) REVERT: v 203 PHE cc_start: 0.7841 (t80) cc_final: 0.7248 (t80) REVERT: x 104 GLU cc_start: 0.8578 (pp20) cc_final: 0.8277 (tm-30) REVERT: x 105 PHE cc_start: 0.8904 (p90) cc_final: 0.8501 (p90) REVERT: y 202 LYS cc_start: 0.7904 (tptp) cc_final: 0.7578 (tptp) REVERT: y 203 PHE cc_start: 0.7774 (t80) cc_final: 0.7544 (t80) REVERT: y 204 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6936 (tm-30) REVERT: z 302 LYS cc_start: 0.8635 (tmtt) cc_final: 0.8006 (tmtt) REVERT: 1 202 LYS cc_start: 0.8003 (tptp) cc_final: 0.7660 (tptp) REVERT: 1 203 PHE cc_start: 0.7787 (t80) cc_final: 0.7528 (t80) REVERT: 2 303 PHE cc_start: 0.7861 (t80) cc_final: 0.7525 (t80) REVERT: 2 305 PHE cc_start: 0.8070 (t80) cc_final: 0.7686 (t80) REVERT: 3 106 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8247 (ttmm) REVERT: 4 204 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6845 (tm-30) REVERT: 5 303 PHE cc_start: 0.7918 (t80) cc_final: 0.7513 (t80) REVERT: g 2 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8400 (mmtt) REVERT: g 7 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (t80) REVERT: 6 105 PHE cc_start: 0.8768 (p90) cc_final: 0.8521 (p90) REVERT: 7 202 LYS cc_start: 0.7903 (tptp) cc_final: 0.7550 (tptp) REVERT: 7 204 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7164 (tm-30) REVERT: 8 302 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8494 (tmtt) REVERT: h 2 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8482 (mmtt) REVERT: 9 107 PHE cc_start: 0.8165 (t80) cc_final: 0.7754 (t80) REVERT: BA 302 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8228 (tmtt) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.1459 time to fit residues: 28.1325 Evaluate side-chains 167 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain g residue 7 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.087667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077925 restraints weight = 13450.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080794 restraints weight = 6530.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082663 restraints weight = 3820.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083946 restraints weight = 2404.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084806 restraints weight = 1604.705| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.066 5568 Z= 0.683 Angle : 1.091 11.051 7232 Z= 0.515 Chirality : 0.052 0.145 512 Planarity : 0.005 0.020 960 Dihedral : 14.399 86.944 640 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 32.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 3.91 % Allowed : 28.91 % Favored : 67.19 % 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: -5.39 (0.30), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.23), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.045 0.005 PHE 2 307 Details of bonding type rmsd/Z covalent geometry : bond 0.01519 / 0.68 ( 5568) covalent geometry : angle 1.09107 / 0.52 ( 7232) hydrogen bonds : bond 0.05736 / 3.30 ( 52) hydrogen bonds : angle 7.53039 / 3.83 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9204 (tttt) cc_final: 0.8994 (ttmt) REVERT: A 4 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7147 (mm-30) REVERT: K 302 LYS cc_start: 0.8664 (tppp) cc_final: 0.8115 (tppp) REVERT: K 304 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6734 (tm-30) REVERT: K 305 PHE cc_start: 0.8408 (m-80) cc_final: 0.8116 (m-80) REVERT: K 306 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7612 (mmmm) REVERT: B 2 LYS cc_start: 0.9108 (tttt) cc_final: 0.8818 (tptm) REVERT: M 202 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8388 (ttmm) REVERT: M 206 LYS cc_start: 0.8543 (tttm) cc_final: 0.7455 (tttm) REVERT: N 302 LYS cc_start: 0.8452 (tppp) cc_final: 0.7959 (tppp) REVERT: N 306 LYS cc_start: 0.8565 (mmmm) cc_final: 0.7897 (mmmm) REVERT: O 102 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8847 (mmtt) REVERT: P 202 LYS cc_start: 0.8731 (ttmm) cc_final: 0.7944 (ttmm) REVERT: Q 302 LYS cc_start: 0.8272 (tppp) cc_final: 0.7705 (tppp) REVERT: Q 304 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6910 (tm-30) REVERT: Q 306 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7036 (mmmm) REVERT: D 6 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7852 (mtpp) REVERT: R 104 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7488 (tm-30) REVERT: S 206 LYS cc_start: 0.8481 (tttm) cc_final: 0.7815 (tttm) REVERT: T 306 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7151 (mmmm) REVERT: E 2 LYS cc_start: 0.9110 (tttt) cc_final: 0.8830 (tptm) REVERT: U 104 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7360 (tm-30) REVERT: V 204 GLU cc_start: 0.8257 (pt0) cc_final: 0.7992 (pt0) REVERT: V 206 LYS cc_start: 0.8423 (tttm) cc_final: 0.7573 (tttm) REVERT: W 302 LYS cc_start: 0.8758 (tppp) cc_final: 0.8360 (tppp) REVERT: W 304 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6594 (tm-30) REVERT: W 306 LYS cc_start: 0.8544 (mmmm) cc_final: 0.7672 (mmmm) REVERT: Y 206 LYS cc_start: 0.8236 (tttm) cc_final: 0.7729 (tttm) REVERT: Z 304 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6699 (tm-30) REVERT: G 6 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8074 (ttmm) REVERT: i 102 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8573 (mmmt) REVERT: i 107 PHE cc_start: 0.8622 (m-80) cc_final: 0.5264 (p90) REVERT: l 102 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8692 (mmtt) REVERT: l 106 LYS cc_start: 0.8351 (tppt) cc_final: 0.7781 (tppt) REVERT: m 204 GLU cc_start: 0.8463 (pt0) cc_final: 0.7651 (pm20) REVERT: n 302 LYS cc_start: 0.8640 (tppp) cc_final: 0.8314 (tppp) REVERT: n 304 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6084 (tm-30) REVERT: n 306 LYS cc_start: 0.8404 (mmmm) cc_final: 0.7287 (mmmm) REVERT: o 104 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7877 (tm-30) REVERT: o 106 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8348 (ttmm) REVERT: s 202 LYS cc_start: 0.8115 (tptp) cc_final: 0.7880 (tptp) REVERT: s 206 LYS cc_start: 0.8328 (tptp) cc_final: 0.7960 (tptp) REVERT: t 305 PHE cc_start: 0.7942 (t80) cc_final: 0.7607 (t80) REVERT: t 306 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8244 (tptp) REVERT: c 2 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8264 (mmtt) REVERT: c 7 PHE cc_start: 0.9020 (t80) cc_final: 0.8797 (t80) REVERT: x 105 PHE cc_start: 0.8914 (p90) cc_final: 0.8181 (p90) REVERT: y 202 LYS cc_start: 0.7957 (tptp) cc_final: 0.7583 (tptp) REVERT: y 204 GLU cc_start: 0.7850 (tm-30) cc_final: 0.6961 (tm-30) REVERT: 1 202 LYS cc_start: 0.8106 (tptp) cc_final: 0.7735 (tptp) REVERT: 2 305 PHE cc_start: 0.8088 (t80) cc_final: 0.7652 (t80) REVERT: 3 106 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8050 (tmtt) REVERT: 4 202 LYS cc_start: 0.7808 (tptp) cc_final: 0.7532 (tptt) REVERT: 4 204 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6980 (tm-30) REVERT: 5 303 PHE cc_start: 0.8176 (t80) cc_final: 0.7806 (t80) REVERT: g 7 PHE cc_start: 0.8920 (t80) cc_final: 0.8552 (t80) REVERT: 7 202 LYS cc_start: 0.8026 (tptp) cc_final: 0.7550 (tptp) REVERT: 7 204 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7299 (tm-30) REVERT: 8 302 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8515 (tmtt) REVERT: 8 307 PHE cc_start: 0.7797 (t80) cc_final: 0.7431 (t80) REVERT: 9 103 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7636 (t80) REVERT: BA 302 LYS cc_start: 0.8865 (tmtt) cc_final: 0.8279 (tmtt) outliers start: 15 outliers final: 10 residues processed: 187 average time/residue: 0.1399 time to fit residues: 30.0481 Evaluate side-chains 193 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 204 GLU Chi-restraints excluded: chain P residue 204 GLU Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain u residue 103 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain z residue 305 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 9 residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.095809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086120 restraints weight = 12717.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089018 restraints weight = 5555.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.090817 restraints weight = 3007.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092036 restraints weight = 1825.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092803 restraints weight = 1197.426| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5568 Z= 0.133 Angle : 0.730 8.406 7232 Z= 0.341 Chirality : 0.033 0.134 512 Planarity : 0.002 0.014 960 Dihedral : 12.667 73.618 640 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.04 % Allowed : 33.07 % Favored : 65.89 % 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: -4.73 (0.31), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.23), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE 3 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5568) covalent geometry : angle 0.72965 / 0.34 ( 7232) hydrogen bonds : bond 0.03286 / 1.79 ( 52) hydrogen bonds : angle 6.10482 / 3.16 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8940 (tttt) cc_final: 0.8545 (tptm) REVERT: A 4 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6882 (mm-30) REVERT: J 204 GLU cc_start: 0.8129 (pt0) cc_final: 0.7393 (pm20) REVERT: K 304 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6521 (tm-30) REVERT: K 306 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7324 (mmmm) REVERT: B 2 LYS cc_start: 0.8873 (tttt) cc_final: 0.8369 (tttp) REVERT: B 6 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7794 (mmmm) REVERT: L 102 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8427 (mmtt) REVERT: M 202 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8357 (ttmm) REVERT: M 203 PHE cc_start: 0.8178 (m-80) cc_final: 0.7767 (m-80) REVERT: N 302 LYS cc_start: 0.8154 (tppp) cc_final: 0.7794 (tppp) REVERT: N 306 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7953 (mmmm) REVERT: O 106 LYS cc_start: 0.8248 (tppt) cc_final: 0.7717 (tppt) REVERT: P 202 LYS cc_start: 0.8484 (ttmm) cc_final: 0.7764 (ttmm) REVERT: Q 304 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6516 (tm-30) REVERT: Q 306 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7036 (mmmm) REVERT: D 2 LYS cc_start: 0.8671 (tttt) cc_final: 0.8205 (tttp) REVERT: D 6 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7573 (mtpp) REVERT: R 104 GLU cc_start: 0.7746 (tm-30) cc_final: 0.6680 (tm-30) REVERT: S 202 LYS cc_start: 0.8643 (ttmm) cc_final: 0.7445 (ttmm) REVERT: S 206 LYS cc_start: 0.8405 (tttm) cc_final: 0.7586 (tttm) REVERT: T 306 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7571 (mmmm) REVERT: E 2 LYS cc_start: 0.8753 (tttt) cc_final: 0.8423 (tptm) REVERT: E 6 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7294 (mmmm) REVERT: U 103 PHE cc_start: 0.8161 (m-80) cc_final: 0.7870 (m-80) REVERT: U 104 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6377 (tm-30) REVERT: V 204 GLU cc_start: 0.8120 (pt0) cc_final: 0.7813 (pt0) REVERT: V 206 LYS cc_start: 0.8334 (tttm) cc_final: 0.7372 (tttm) REVERT: W 302 LYS cc_start: 0.8514 (tppp) cc_final: 0.8082 (tppp) REVERT: W 304 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6520 (tm-30) REVERT: W 306 LYS cc_start: 0.8376 (mmmm) cc_final: 0.7497 (mmmm) REVERT: F 2 LYS cc_start: 0.8739 (tttp) cc_final: 0.8310 (tttp) REVERT: X 104 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7306 (tm-30) REVERT: Y 206 LYS cc_start: 0.8089 (tttm) cc_final: 0.7552 (tttm) REVERT: Z 306 LYS cc_start: 0.8045 (mmmm) cc_final: 0.6754 (mmmm) REVERT: i 102 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8556 (mmtt) REVERT: i 104 GLU cc_start: 0.7569 (tm-30) cc_final: 0.6728 (tm-30) REVERT: i 107 PHE cc_start: 0.8730 (m-80) cc_final: 0.5224 (p90) REVERT: l 106 LYS cc_start: 0.8236 (tppt) cc_final: 0.7576 (tppt) REVERT: m 204 GLU cc_start: 0.8391 (pt0) cc_final: 0.7786 (pm20) REVERT: n 302 LYS cc_start: 0.8071 (tppp) cc_final: 0.7788 (tppp) REVERT: n 306 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7360 (mmmm) REVERT: o 104 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7871 (tm-30) REVERT: p 204 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7392 (tm-30) REVERT: q 306 LYS cc_start: 0.8512 (tptm) cc_final: 0.8137 (tptp) REVERT: s 202 LYS cc_start: 0.7919 (tptp) cc_final: 0.7403 (tptt) REVERT: s 203 PHE cc_start: 0.7752 (t80) cc_final: 0.7387 (t80) REVERT: t 305 PHE cc_start: 0.7815 (t80) cc_final: 0.7510 (t80) REVERT: c 7 PHE cc_start: 0.8910 (t80) cc_final: 0.8614 (t80) REVERT: v 202 LYS cc_start: 0.7737 (tptp) cc_final: 0.7318 (tptp) REVERT: x 104 GLU cc_start: 0.8571 (pp20) cc_final: 0.8240 (tm-30) REVERT: x 105 PHE cc_start: 0.8903 (p90) cc_final: 0.8403 (p90) REVERT: y 202 LYS cc_start: 0.7855 (tptp) cc_final: 0.7460 (tptp) REVERT: y 204 GLU cc_start: 0.7654 (tm-30) cc_final: 0.6770 (tm-30) REVERT: z 302 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8063 (tmtt) REVERT: 1 202 LYS cc_start: 0.7987 (tptp) cc_final: 0.7610 (tptp) REVERT: 1 203 PHE cc_start: 0.7816 (t80) cc_final: 0.7484 (t80) REVERT: 2 303 PHE cc_start: 0.7752 (t80) cc_final: 0.7431 (t80) REVERT: 2 305 PHE cc_start: 0.8108 (t80) cc_final: 0.7576 (t80) REVERT: 3 106 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8131 (ttmm) REVERT: 4 204 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6908 (tm-30) REVERT: 5 303 PHE cc_start: 0.7791 (t80) cc_final: 0.7544 (t80) REVERT: g 2 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8363 (mmtt) REVERT: g 7 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8267 (t80) REVERT: 6 105 PHE cc_start: 0.8724 (p90) cc_final: 0.8454 (p90) REVERT: 7 202 LYS cc_start: 0.7913 (tptp) cc_final: 0.7566 (tptp) REVERT: h 2 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8240 (mmtt) REVERT: h 5 PHE cc_start: 0.8221 (t80) cc_final: 0.7995 (t80) REVERT: 9 106 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7533 (tptp) REVERT: BA 302 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8137 (tmtt) REVERT: BA 306 LYS cc_start: 0.8534 (tptm) cc_final: 0.8070 (tptp) outliers start: 4 outliers final: 1 residues processed: 166 average time/residue: 0.1468 time to fit residues: 28.1270 Evaluate side-chains 167 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 204 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain g residue 7 PHE Chi-restraints excluded: chain 9 residue 106 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.087882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078163 restraints weight = 13304.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081023 restraints weight = 6418.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.082907 restraints weight = 3748.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.084099 restraints weight = 2349.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084998 restraints weight = 1589.542| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.068 5568 Z= 0.681 Angle : 1.088 10.621 7232 Z= 0.513 Chirality : 0.052 0.149 512 Planarity : 0.004 0.022 960 Dihedral : 14.273 73.613 640 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 32.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 2.60 % Allowed : 32.29 % Favored : 65.10 % 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: -5.23 (0.33), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.051 0.005 PHE i 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01516 / 0.68 ( 5568) covalent geometry : angle 1.08773 / 0.51 ( 7232) hydrogen bonds : bond 0.05705 / 3.26 ( 52) hydrogen bonds : angle 7.53580 / 3.81 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9192 (tttt) cc_final: 0.8972 (ttmt) REVERT: A 4 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7076 (mm-30) REVERT: J 204 GLU cc_start: 0.8229 (pt0) cc_final: 0.7871 (pm20) REVERT: K 302 LYS cc_start: 0.8763 (tppp) cc_final: 0.8174 (tppp) REVERT: K 304 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6690 (tm-30) REVERT: K 305 PHE cc_start: 0.8400 (m-80) cc_final: 0.8123 (m-80) REVERT: K 306 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7629 (mmmm) REVERT: B 2 LYS cc_start: 0.9081 (tttt) cc_final: 0.8788 (tptm) REVERT: N 302 LYS cc_start: 0.8436 (tppp) cc_final: 0.8094 (tppp) REVERT: N 306 LYS cc_start: 0.8570 (mmmm) cc_final: 0.7870 (mmmm) REVERT: O 102 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8865 (mmtt) REVERT: P 202 LYS cc_start: 0.8701 (ttmm) cc_final: 0.7657 (ttmm) REVERT: Q 302 LYS cc_start: 0.8296 (tppp) cc_final: 0.7497 (tppp) REVERT: Q 304 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7032 (tm-30) REVERT: Q 305 PHE cc_start: 0.8436 (m-80) cc_final: 0.8196 (m-10) REVERT: Q 306 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7103 (mmmm) REVERT: D 6 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7913 (mtpp) REVERT: R 104 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7474 (tm-30) REVERT: S 206 LYS cc_start: 0.8501 (tttm) cc_final: 0.7872 (tttm) REVERT: T 306 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7677 (mmmm) REVERT: E 2 LYS cc_start: 0.9095 (tttt) cc_final: 0.8819 (tptm) REVERT: U 104 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7341 (tm-30) REVERT: V 204 GLU cc_start: 0.8181 (pt0) cc_final: 0.7891 (pt0) REVERT: V 206 LYS cc_start: 0.8430 (tttm) cc_final: 0.7613 (tttm) REVERT: W 302 LYS cc_start: 0.8721 (tppp) cc_final: 0.8320 (tppp) REVERT: W 304 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6619 (tm-30) REVERT: W 306 LYS cc_start: 0.8569 (mmmm) cc_final: 0.7696 (mmmm) REVERT: F 6 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7533 (mmmm) REVERT: Y 202 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8527 (tppt) REVERT: Y 206 LYS cc_start: 0.8215 (tttm) cc_final: 0.7709 (tttm) REVERT: Z 304 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6650 (tm-30) REVERT: G 6 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8017 (ttmm) REVERT: i 102 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8577 (mmmt) REVERT: i 104 GLU cc_start: 0.7684 (tm-30) cc_final: 0.6702 (tm-30) REVERT: l 102 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8693 (mmtt) REVERT: l 106 LYS cc_start: 0.8441 (tppt) cc_final: 0.7840 (tppt) REVERT: m 204 GLU cc_start: 0.8434 (pt0) cc_final: 0.7636 (pm20) REVERT: n 302 LYS cc_start: 0.8591 (tppp) cc_final: 0.8312 (tppp) REVERT: n 304 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6062 (tm-30) REVERT: n 306 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7310 (mmmm) REVERT: p 204 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7584 (tm-30) REVERT: s 202 LYS cc_start: 0.8119 (tptp) cc_final: 0.7877 (tptp) REVERT: s 206 LYS cc_start: 0.8352 (tptp) cc_final: 0.8055 (tptp) REVERT: t 305 PHE cc_start: 0.7948 (t80) cc_final: 0.7646 (t80) REVERT: t 306 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8267 (tptp) REVERT: c 2 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8231 (mmtt) REVERT: c 7 PHE cc_start: 0.9051 (t80) cc_final: 0.8798 (t80) REVERT: v 202 LYS cc_start: 0.7959 (tptp) cc_final: 0.7555 (tptp) REVERT: x 105 PHE cc_start: 0.8923 (p90) cc_final: 0.8213 (p90) REVERT: y 202 LYS cc_start: 0.7921 (tptp) cc_final: 0.7483 (tptp) REVERT: 1 202 LYS cc_start: 0.8090 (tptp) cc_final: 0.7716 (tptp) REVERT: 2 305 PHE cc_start: 0.8117 (t80) cc_final: 0.7680 (t80) REVERT: f 2 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8328 (mmtt) REVERT: 3 106 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8015 (tmtt) REVERT: 4 202 LYS cc_start: 0.7810 (tptp) cc_final: 0.7546 (tptt) REVERT: 4 204 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6974 (tm-30) REVERT: 5 303 PHE cc_start: 0.8171 (t80) cc_final: 0.7705 (t80) REVERT: g 7 PHE cc_start: 0.8904 (t80) cc_final: 0.8539 (t80) REVERT: 7 202 LYS cc_start: 0.8012 (tptp) cc_final: 0.7510 (tptp) REVERT: 7 204 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7191 (tm-30) REVERT: 8 307 PHE cc_start: 0.7789 (t80) cc_final: 0.7413 (t80) REVERT: 9 103 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7555 (t80) REVERT: 9 106 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7923 (ttmm) REVERT: BA 302 LYS cc_start: 0.8899 (tmtt) cc_final: 0.8324 (tmtt) outliers start: 10 outliers final: 4 residues processed: 183 average time/residue: 0.1454 time to fit residues: 30.6567 Evaluate side-chains 185 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 204 GLU Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 9 residue 103 PHE Chi-restraints excluded: chain 9 residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.095919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086260 restraints weight = 12841.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089207 restraints weight = 5606.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.091026 restraints weight = 3008.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092229 restraints weight = 1807.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093057 restraints weight = 1176.982| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5568 Z= 0.135 Angle : 0.755 8.315 7232 Z= 0.355 Chirality : 0.034 0.124 512 Planarity : 0.002 0.013 960 Dihedral : 12.823 79.890 640 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.78 % Allowed : 33.85 % Favored : 65.36 % 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: -4.65 (0.33), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.25), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.002 PHE 3 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5568) covalent geometry : angle 0.75477 / 0.35 ( 7232) hydrogen bonds : bond 0.03134 / 1.69 ( 52) hydrogen bonds : angle 6.27672 / 3.20 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8956 (tttt) cc_final: 0.8554 (tptm) REVERT: A 4 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6892 (mm-30) REVERT: J 204 GLU cc_start: 0.8088 (pt0) cc_final: 0.7329 (pm20) REVERT: K 302 LYS cc_start: 0.8529 (tppp) cc_final: 0.8225 (tppp) REVERT: K 304 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6348 (tm-30) REVERT: K 306 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7323 (mmmm) REVERT: B 2 LYS cc_start: 0.8890 (tttt) cc_final: 0.8506 (tptm) REVERT: B 6 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7859 (mmmm) REVERT: L 102 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8451 (mmtt) REVERT: M 202 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8383 (ttmm) REVERT: N 302 LYS cc_start: 0.8190 (tppp) cc_final: 0.7804 (tppp) REVERT: N 306 LYS cc_start: 0.8467 (mmmm) cc_final: 0.7959 (mmmm) REVERT: O 106 LYS cc_start: 0.8268 (tppt) cc_final: 0.7723 (tppt) REVERT: P 202 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7650 (ttmm) REVERT: Q 306 LYS cc_start: 0.8273 (mmmm) cc_final: 0.7182 (mmmm) REVERT: D 2 LYS cc_start: 0.8662 (tttt) cc_final: 0.8230 (tttp) REVERT: D 6 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7672 (mtpp) REVERT: R 104 GLU cc_start: 0.7717 (tm-30) cc_final: 0.6718 (tm-30) REVERT: S 206 LYS cc_start: 0.8494 (tttm) cc_final: 0.7698 (tttm) REVERT: T 306 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7601 (mmmm) REVERT: E 2 LYS cc_start: 0.8724 (tttt) cc_final: 0.8407 (tptm) REVERT: E 6 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7354 (mmmm) REVERT: U 104 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6944 (tm-30) REVERT: V 204 GLU cc_start: 0.8042 (pt0) cc_final: 0.7729 (pt0) REVERT: V 206 LYS cc_start: 0.8416 (tttm) cc_final: 0.7433 (tttm) REVERT: W 302 LYS cc_start: 0.8524 (tppp) cc_final: 0.8081 (tppp) REVERT: W 306 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7676 (mmmm) REVERT: F 6 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7413 (mmmm) REVERT: Y 202 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8179 (tppt) REVERT: Y 206 LYS cc_start: 0.8103 (tttm) cc_final: 0.7582 (tttm) REVERT: Z 306 LYS cc_start: 0.8037 (mmmm) cc_final: 0.6682 (mmmm) REVERT: G 6 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7732 (mtpp) REVERT: i 102 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8359 (mmmt) REVERT: i 104 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6567 (tm-30) REVERT: l 102 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8534 (mmtt) REVERT: l 106 LYS cc_start: 0.8274 (tppt) cc_final: 0.7665 (tppt) REVERT: m 204 GLU cc_start: 0.8437 (pt0) cc_final: 0.7769 (pm20) REVERT: n 302 LYS cc_start: 0.8246 (tppp) cc_final: 0.7979 (tppp) REVERT: n 304 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6952 (tm-30) REVERT: o 104 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7928 (tm-30) REVERT: p 204 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7385 (tm-30) REVERT: q 306 LYS cc_start: 0.8517 (tptm) cc_final: 0.8169 (tptp) REVERT: s 203 PHE cc_start: 0.7822 (t80) cc_final: 0.7448 (t80) REVERT: s 206 LYS cc_start: 0.8252 (tptp) cc_final: 0.7921 (tptp) REVERT: t 305 PHE cc_start: 0.7853 (t80) cc_final: 0.7522 (t80) REVERT: c 7 PHE cc_start: 0.8930 (t80) cc_final: 0.8596 (t80) REVERT: v 202 LYS cc_start: 0.7836 (tptp) cc_final: 0.7374 (tptp) REVERT: x 104 GLU cc_start: 0.8527 (pp20) cc_final: 0.8166 (tm-30) REVERT: x 105 PHE cc_start: 0.8904 (p90) cc_final: 0.8390 (p90) REVERT: y 202 LYS cc_start: 0.7885 (tptp) cc_final: 0.7531 (tptp) REVERT: y 203 PHE cc_start: 0.7899 (t80) cc_final: 0.7497 (t80) REVERT: 1 202 LYS cc_start: 0.7997 (tptp) cc_final: 0.7688 (tptp) REVERT: 2 303 PHE cc_start: 0.7732 (t80) cc_final: 0.7435 (t80) REVERT: f 2 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8493 (mmtt) REVERT: 3 106 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8181 (ttmm) REVERT: 4 204 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6871 (tm-30) REVERT: 5 303 PHE cc_start: 0.7824 (t80) cc_final: 0.7505 (t80) REVERT: g 2 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8352 (mmtt) REVERT: g 7 PHE cc_start: 0.8620 (t80) cc_final: 0.8280 (t80) REVERT: 7 202 LYS cc_start: 0.7904 (tptp) cc_final: 0.7571 (tptp) REVERT: 7 204 GLU cc_start: 0.7569 (tm-30) cc_final: 0.6847 (tm-30) REVERT: h 2 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8185 (mmtt) REVERT: 9 106 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7494 (tptp) REVERT: BA 302 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8146 (tmtt) outliers start: 3 outliers final: 1 residues processed: 164 average time/residue: 0.1469 time to fit residues: 27.7408 Evaluate side-chains 164 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 204 GLU Chi-restraints excluded: chain 9 residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.091048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.081993 restraints weight = 13482.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084844 restraints weight = 5947.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086589 restraints weight = 3228.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087797 restraints weight = 1935.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088608 restraints weight = 1238.897| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.062 5568 Z= 0.676 Angle : 1.075 10.189 7232 Z= 0.509 Chirality : 0.052 0.157 512 Planarity : 0.004 0.019 960 Dihedral : 14.203 73.639 640 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 2.34 % Allowed : 32.81 % Favored : 64.84 % 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: -5.35 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.044 0.005 PHE i 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01506 / 0.68 ( 5568) covalent geometry : angle 1.07483 / 0.51 ( 7232) hydrogen bonds : bond 0.05626 / 3.22 ( 52) hydrogen bonds : angle 7.42983 / 3.72 ( 126) =============================================================================== Job complete usr+sys time: 799.69 seconds wall clock time: 14 minutes 44.98 seconds (884.98 seconds total)