Starting phenix.real_space_refine on Thu Mar 6 07:45:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_23484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_23484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_23484.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_23484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqf_23484/03_2025/7lqf_23484.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.70, per 1000 atoms: 0.69 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: 1.36 Conformation dependent library (CDL) restraints added in 277.0 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: 0.86 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: 1.25 Time building geometry restraints manager: 1.54 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: 2.320 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.680 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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= 0.863 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 : 22.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (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 *********************** 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 : 0.516 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: 0.8717 (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: 0.7746 (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: 0.7868 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8357 (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: 0.7905 (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: 0.7309 (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: 0.7753 (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: 0.8382 (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: 0.3453 time to fit residues: 64.4694 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 : 0.557 ------------------------------------------------------------------------------- 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: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.046119 restraints weight = 20143.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.047974 restraints weight = 10931.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.049268 restraints weight = 6878.503| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.153 0.471 5568 Z= 8.411 Angle : 6.008 58.256 7232 Z= 2.679 Chirality : 0.409 1.111 512 Planarity : 0.029 0.097 960 Dihedral : 25.177 84.646 652 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 194.90 Ramachandran Plot: Outliers : 7.42 % Allowed : 33.59 % Favored : 58.98 % Rotamer: Outliers : 15.89 % Allowed : 27.08 % Favored : 57.03 % Cbeta Deviations : 47.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.46 (0.26), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.20), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.199 0.029 PHE 3 107 *********************** 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 230 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.9023 (m-10) REVERT: I 107 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8576 (m-10) REVERT: J 206 LYS cc_start: 0.9068 (tttm) cc_final: 0.7879 (ttpp) REVERT: K 306 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8296 (mmmm) REVERT: M 202 LYS cc_start: 0.9404 (ttmm) cc_final: 0.9155 (ttmm) REVERT: M 206 LYS cc_start: 0.8857 (tttm) cc_final: 0.8221 (tttm) REVERT: N 304 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8004 (tm-30) REVERT: N 306 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8090 (mmmm) REVERT: N 307 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8448 (t80) REVERT: Q 303 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: S 202 LYS cc_start: 0.9489 (ttmm) cc_final: 0.9170 (ttpp) REVERT: S 206 LYS cc_start: 0.9029 (tttm) cc_final: 0.7946 (ttpp) REVERT: T 306 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8074 (mmmm) REVERT: E 6 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8747 (ttmm) REVERT: U 103 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: W 304 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7341 (tm-30) REVERT: W 306 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8329 (mmmm) REVERT: Y 206 LYS cc_start: 0.8753 (tttm) cc_final: 0.8408 (tttm) REVERT: Z 304 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8261 (tm-30) REVERT: Z 306 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8059 (mmmm) REVERT: Z 307 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: G 2 LYS cc_start: 0.9435 (tptt) cc_final: 0.9147 (tptm) REVERT: G 6 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8564 (ttmm) REVERT: G 7 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: i 106 LYS cc_start: 0.5541 (tppt) cc_final: 0.4741 (tptt) REVERT: i 107 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: l 103 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: l 106 LYS cc_start: 0.9063 (tppt) cc_final: 0.8712 (tppt) REVERT: m 202 LYS cc_start: 0.9321 (ttmm) cc_final: 0.8954 (ttmm) REVERT: m 204 GLU cc_start: 0.9029 (pt0) cc_final: 0.8657 (pt0) REVERT: n 304 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7943 (tm-30) REVERT: n 306 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8390 (mmmm) REVERT: n 307 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8846 (t80) REVERT: a 2 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8543 (mmtt) REVERT: p 204 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8070 (tm-30) REVERT: r 104 GLU cc_start: 0.9127 (pp20) cc_final: 0.8872 (pp20) REVERT: s 206 LYS cc_start: 0.8808 (tptp) cc_final: 0.8438 (tptp) REVERT: t 306 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8439 (tmtt) REVERT: u 104 GLU cc_start: 0.8994 (pp20) cc_final: 0.8750 (pp20) REVERT: v 204 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7879 (tm-30) REVERT: d 7 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8971 (t80) REVERT: y 204 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7790 (tm-30) REVERT: z 306 LYS cc_start: 0.9216 (tttt) cc_final: 0.8233 (tmtt) REVERT: z 307 PHE cc_start: 0.8892 (t80) cc_final: 0.8653 (t80) REVERT: 0 106 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9023 (ttpp) REVERT: 2 302 LYS cc_start: 0.9386 (tmtt) cc_final: 0.8895 (tmtt) REVERT: 3 102 LYS cc_start: 0.9135 (tptp) cc_final: 0.8914 (tptp) REVERT: 3 103 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8279 (p90) REVERT: 3 107 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8625 (t80) REVERT: 4 204 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8054 (tm-30) REVERT: g 2 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8675 (mmtt) REVERT: 7 202 LYS cc_start: 0.9205 (tptp) cc_final: 0.8867 (tptp) REVERT: 7 204 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7878 (tm-30) REVERT: 8 306 LYS cc_start: 0.8692 (tttt) cc_final: 0.7973 (tmtt) REVERT: 8 307 PHE cc_start: 0.8699 (t80) cc_final: 0.8370 (t80) REVERT: AA 206 LYS cc_start: 0.8811 (tptp) cc_final: 0.8400 (tptp) REVERT: BA 307 PHE cc_start: 0.8814 (t80) cc_final: 0.8545 (t80) outliers start: 61 outliers final: 29 residues processed: 210 average time/residue: 0.3755 time to fit residues: 88.7602 Evaluate side-chains 206 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 107 PHE Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.054624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047240 restraints weight = 20200.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049037 restraints weight = 11148.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.050280 restraints weight = 7056.853| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.9570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.578 5568 Z= 8.461 Angle : 6.183 58.751 7232 Z= 2.746 Chirality : 0.414 1.065 512 Planarity : 0.028 0.091 960 Dihedral : 25.337 89.307 648 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 194.20 Ramachandran Plot: Outliers : 2.73 % Allowed : 54.30 % Favored : 42.97 % Rotamer: Outliers : 20.83 % Allowed : 31.25 % Favored : 47.92 % Cbeta Deviations : 46.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.07 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.91 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.186 0.027 PHE 5 303 *********************** 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 239 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9426 (tptt) cc_final: 0.9151 (tptt) REVERT: A 5 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8472 (m-10) REVERT: A 7 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8994 (m-10) REVERT: I 107 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8659 (m-10) REVERT: J 206 LYS cc_start: 0.9063 (tttm) cc_final: 0.8497 (ttpp) REVERT: K 306 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8320 (mmmm) REVERT: M 202 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9112 (ttmm) REVERT: N 302 LYS cc_start: 0.9146 (tppp) cc_final: 0.8921 (tppp) REVERT: N 304 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8089 (tm-30) REVERT: N 306 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8242 (mmmm) REVERT: N 307 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8354 (t80) REVERT: P 206 LYS cc_start: 0.8810 (tttm) cc_final: 0.8521 (tttm) REVERT: S 202 LYS cc_start: 0.9426 (ttmm) cc_final: 0.8422 (ttpp) REVERT: S 206 LYS cc_start: 0.9036 (tttm) cc_final: 0.8174 (ttpp) REVERT: T 304 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 6 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8848 (ttmm) REVERT: U 103 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: W 302 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8719 (ttpp) REVERT: W 304 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7295 (tm-30) REVERT: X 103 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8794 (m-10) REVERT: Y 206 LYS cc_start: 0.8726 (tttm) cc_final: 0.8478 (tttm) REVERT: Z 302 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8503 (tppp) REVERT: Z 304 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8393 (tm-30) REVERT: Z 306 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8160 (mmmm) REVERT: Z 307 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: G 5 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: G 6 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9060 (ttmm) REVERT: G 7 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: j 206 LYS cc_start: 0.9113 (tttm) cc_final: 0.8753 (ttpp) REVERT: k 304 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7346 (tm-30) REVERT: l 102 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9189 (mmtt) REVERT: l 103 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: m 202 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9045 (ttmm) REVERT: m 204 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8619 (pt0) REVERT: m 206 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8276 (pttm) REVERT: n 302 LYS cc_start: 0.9014 (tppp) cc_final: 0.8785 (tppp) REVERT: n 304 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8022 (tm-30) REVERT: n 306 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8533 (mmmm) REVERT: n 307 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8850 (t80) REVERT: a 2 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8552 (mmtt) REVERT: p 203 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8511 (t80) REVERT: q 306 LYS cc_start: 0.9118 (tttt) cc_final: 0.8783 (tttp) REVERT: q 307 PHE cc_start: 0.8747 (t80) cc_final: 0.8181 (t80) REVERT: s 202 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8868 (tppp) REVERT: t 303 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7434 (t80) REVERT: c 2 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8808 (mmtt) REVERT: v 204 GLU cc_start: 0.8666 (tm-30) cc_final: 0.7956 (tm-30) REVERT: v 207 PHE cc_start: 0.8852 (t80) cc_final: 0.7895 (t80) REVERT: y 202 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8672 (ttmm) REVERT: y 204 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8013 (tm-30) REVERT: z 302 LYS cc_start: 0.9153 (tmtt) cc_final: 0.8691 (tmtt) REVERT: 1 203 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8467 (t80) REVERT: 2 302 LYS cc_start: 0.9366 (tmtt) cc_final: 0.8893 (tmtt) REVERT: 3 102 LYS cc_start: 0.9198 (tptp) cc_final: 0.8947 (tptp) REVERT: 3 103 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8641 (p90) REVERT: 3 107 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8760 (t80) REVERT: 5 306 LYS cc_start: 0.8946 (tttt) cc_final: 0.8677 (tttt) REVERT: 5 307 PHE cc_start: 0.8901 (t80) cc_final: 0.8630 (t80) REVERT: g 2 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8709 (mmtt) REVERT: 7 204 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8073 (tm-30) REVERT: 8 307 PHE cc_start: 0.8595 (t80) cc_final: 0.8314 (t80) REVERT: AA 206 LYS cc_start: 0.8713 (tptp) cc_final: 0.8318 (tptp) REVERT: BA 302 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8876 (tmtt) REVERT: BA 307 PHE cc_start: 0.8758 (t80) cc_final: 0.8451 (t80) outliers start: 80 outliers final: 41 residues processed: 212 average time/residue: 0.3663 time to fit residues: 87.8813 Evaluate side-chains 220 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.047168 restraints weight = 20692.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049000 restraints weight = 11162.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.050248 restraints weight = 6992.803| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.9793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.496 5568 Z= 8.442 Angle : 6.202 59.093 7232 Z= 2.757 Chirality : 0.415 1.043 512 Planarity : 0.028 0.089 960 Dihedral : 25.201 89.273 648 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 195.42 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.47 % Favored : 42.58 % Rotamer: Outliers : 25.26 % Allowed : 33.07 % Favored : 41.67 % Cbeta Deviations : 46.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.06 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.90 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.181 0.026 PHE 5 303 *********************** 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 259 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 162 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8399 (m-10) REVERT: A 7 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.9009 (m-10) REVERT: I 107 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8669 (m-10) REVERT: J 206 LYS cc_start: 0.9007 (tttm) cc_final: 0.8587 (ttpp) REVERT: K 306 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8325 (mmmm) REVERT: L 103 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: M 202 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9094 (ttmm) REVERT: N 304 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8182 (tm-30) REVERT: N 306 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8249 (mmmm) REVERT: N 307 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8434 (t80) REVERT: P 206 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8598 (tttm) REVERT: Q 302 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8713 (mmmm) REVERT: Q 303 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: Q 306 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7931 (mmmm) REVERT: Q 307 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8204 (t80) REVERT: S 202 LYS cc_start: 0.9467 (ttmm) cc_final: 0.8422 (ttpp) REVERT: S 206 LYS cc_start: 0.9020 (tttm) cc_final: 0.8746 (ttpp) REVERT: T 304 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7501 (tm-30) REVERT: T 306 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8303 (mmtp) REVERT: E 6 LYS cc_start: 0.9293 (mmmm) cc_final: 0.8921 (ttmm) REVERT: U 103 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: U 106 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8785 (tppt) REVERT: V 206 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8279 (ttpp) REVERT: W 304 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7243 (tm-30) REVERT: Y 206 LYS cc_start: 0.8804 (tttm) cc_final: 0.8582 (tttm) REVERT: Z 302 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8480 (tppp) REVERT: Z 307 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: G 5 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: G 6 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8418 (ttmm) REVERT: G 7 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.8779 (m-80) REVERT: H 4 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5578 (pt0) REVERT: l 102 LYS cc_start: 0.9484 (mmtt) cc_final: 0.9228 (mmtm) REVERT: l 103 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: m 204 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8731 (pt0) REVERT: m 206 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8339 (pttm) REVERT: n 304 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8056 (tm-30) REVERT: n 306 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8572 (mmmm) REVERT: n 307 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8824 (t80) REVERT: a 2 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8538 (mmtt) REVERT: o 107 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8296 (t80) REVERT: p 203 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8490 (t80) REVERT: q 303 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7700 (t80) REVERT: q 306 LYS cc_start: 0.9131 (tttt) cc_final: 0.8861 (tttp) REVERT: q 307 PHE cc_start: 0.8736 (t80) cc_final: 0.8195 (t80) REVERT: t 303 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7474 (t80) REVERT: c 2 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8850 (mmtt) REVERT: v 204 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7985 (tm-30) REVERT: v 207 PHE cc_start: 0.8876 (t80) cc_final: 0.7861 (t80) REVERT: y 202 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8777 (ttmm) REVERT: y 203 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (t80) REVERT: z 302 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8669 (tmtt) REVERT: 1 203 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8405 (t80) REVERT: 2 302 LYS cc_start: 0.9380 (tmtt) cc_final: 0.8920 (tmtt) REVERT: 2 306 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8661 (tmtt) REVERT: f 2 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8625 (mmtt) REVERT: 3 102 LYS cc_start: 0.9135 (tptp) cc_final: 0.8910 (tptp) REVERT: 5 306 LYS cc_start: 0.8979 (tttp) cc_final: 0.8674 (tttt) REVERT: 5 307 PHE cc_start: 0.8910 (t80) cc_final: 0.8539 (t80) REVERT: g 2 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8687 (mmtt) REVERT: 6 102 LYS cc_start: 0.9064 (tptp) cc_final: 0.8836 (ttpt) REVERT: 8 307 PHE cc_start: 0.8615 (t80) cc_final: 0.8361 (t80) REVERT: 9 104 GLU cc_start: 0.8778 (tm-30) cc_final: 0.7972 (tm-30) REVERT: AA 206 LYS cc_start: 0.8731 (tptp) cc_final: 0.8429 (tptp) REVERT: BA 302 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8903 (tmtt) REVERT: BA 307 PHE cc_start: 0.8826 (t80) cc_final: 0.8474 (t80) outliers start: 97 outliers final: 52 residues processed: 220 average time/residue: 0.3686 time to fit residues: 91.7008 Evaluate side-chains 241 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 160 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 302 LYS Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 102 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.047995 restraints weight = 20593.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.049799 restraints weight = 11217.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051017 restraints weight = 7032.170| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 1.0027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 8.465 Angle : 6.240 58.249 7232 Z= 2.769 Chirality : 0.415 1.058 512 Planarity : 0.028 0.090 960 Dihedral : 25.530 89.681 644 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 198.70 Ramachandran Plot: Outliers : 1.95 % Allowed : 56.64 % Favored : 41.41 % Rotamer: Outliers : 26.30 % Allowed : 31.77 % Favored : 41.93 % Cbeta Deviations : 48.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.12 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.95 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.026 PHE 5 303 *********************** 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 264 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 163 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: A 7 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.9027 (m-10) REVERT: I 102 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8960 (mmtm) REVERT: I 106 LYS cc_start: 0.8972 (tppt) cc_final: 0.8213 (tppt) REVERT: I 107 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: J 206 LYS cc_start: 0.9108 (tttm) cc_final: 0.8729 (ttpp) REVERT: K 306 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8208 (mmmm) REVERT: L 103 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: N 304 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8214 (tm-30) REVERT: N 306 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8288 (mmmm) REVERT: N 307 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8455 (t80) REVERT: O 102 LYS cc_start: 0.9554 (mmtm) cc_final: 0.9343 (mmtm) REVERT: P 206 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8384 (ptmm) REVERT: Q 303 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: Q 304 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8317 (tm-30) REVERT: Q 306 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7813 (mmmm) REVERT: Q 307 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8315 (t80) REVERT: S 202 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.8396 (ttpp) REVERT: S 206 LYS cc_start: 0.8977 (tttm) cc_final: 0.8291 (ttpp) REVERT: T 304 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7549 (tm-30) REVERT: T 306 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8316 (mmtp) REVERT: E 6 LYS cc_start: 0.9311 (mmmm) cc_final: 0.8972 (ttmm) REVERT: U 103 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: U 106 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8839 (tppt) REVERT: V 202 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9002 (ttmm) REVERT: V 206 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8089 (ttpp) REVERT: W 302 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8684 (ttpp) REVERT: W 304 GLU cc_start: 0.8263 (tm-30) cc_final: 0.6915 (tm-30) REVERT: W 306 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8276 (mmtm) REVERT: F 5 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: X 103 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8788 (m-10) REVERT: Z 302 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8407 (tppp) REVERT: Z 304 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8310 (tm-30) REVERT: Z 306 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8158 (mmmm) REVERT: Z 307 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: G 5 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: G 7 PHE cc_start: 0.9517 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: H 4 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5591 (pt0) REVERT: l 102 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9257 (mmtm) REVERT: l 103 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: m 206 LYS cc_start: 0.8923 (tttm) cc_final: 0.8300 (pttm) REVERT: n 304 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8153 (tm-30) REVERT: n 306 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8701 (mmmm) REVERT: a 2 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8557 (mmtt) REVERT: o 107 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8431 (t80) REVERT: p 203 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8496 (t80) REVERT: q 302 LYS cc_start: 0.9324 (tmtt) cc_final: 0.8877 (tmtt) REVERT: q 303 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7353 (t80) REVERT: q 305 PHE cc_start: 0.9111 (t80) cc_final: 0.8898 (t80) REVERT: q 306 LYS cc_start: 0.9131 (tttt) cc_final: 0.8777 (tttp) REVERT: q 307 PHE cc_start: 0.8732 (t80) cc_final: 0.8103 (t80) REVERT: s 202 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8895 (tppp) REVERT: t 303 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7601 (t80) REVERT: v 204 GLU cc_start: 0.8740 (tm-30) cc_final: 0.7980 (tm-30) REVERT: v 207 PHE cc_start: 0.8886 (t80) cc_final: 0.7870 (t80) REVERT: y 203 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8490 (t80) REVERT: z 302 LYS cc_start: 0.9164 (tmtt) cc_final: 0.8683 (tmtt) REVERT: 1 203 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8496 (t80) REVERT: 2 306 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (tmtt) REVERT: f 2 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8539 (mmtt) REVERT: f 5 PHE cc_start: 0.8595 (t80) cc_final: 0.8383 (t80) REVERT: 3 102 LYS cc_start: 0.9161 (tptp) cc_final: 0.8935 (tptp) REVERT: 4 202 LYS cc_start: 0.9199 (tptp) cc_final: 0.8845 (tppp) REVERT: 5 306 LYS cc_start: 0.9007 (tttp) cc_final: 0.8619 (tttp) REVERT: 5 307 PHE cc_start: 0.8900 (t80) cc_final: 0.8589 (t80) REVERT: g 2 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8706 (mmtt) REVERT: 7 202 LYS cc_start: 0.9193 (tptp) cc_final: 0.8791 (tptp) REVERT: 7 203 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8361 (t80) REVERT: 8 307 PHE cc_start: 0.8542 (t80) cc_final: 0.8315 (t80) REVERT: 9 104 GLU cc_start: 0.8807 (tm-30) cc_final: 0.7904 (tm-30) REVERT: AA 206 LYS cc_start: 0.8734 (tptp) cc_final: 0.8467 (tptp) REVERT: BA 307 PHE cc_start: 0.8808 (t80) cc_final: 0.8405 (t80) outliers start: 101 outliers final: 55 residues processed: 225 average time/residue: 0.3647 time to fit residues: 92.8717 Evaluate side-chains 248 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 162 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 302 LYS Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.048164 restraints weight = 20195.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.049951 restraints weight = 10928.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051163 restraints weight = 6858.401| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 1.0067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.476 5568 Z= 8.452 Angle : 6.213 59.478 7232 Z= 2.757 Chirality : 0.413 1.086 512 Planarity : 0.028 0.091 960 Dihedral : 25.490 89.204 644 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 196.18 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.08 % Favored : 42.97 % Rotamer: Outliers : 27.60 % Allowed : 32.29 % Favored : 40.10 % Cbeta Deviations : 47.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.12 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.95 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.025 PHE 5 303 *********************** 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 269 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 163 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8440 (m-10) REVERT: A 7 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.9003 (m-10) REVERT: I 102 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8953 (mmtm) REVERT: I 107 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8662 (m-10) REVERT: J 206 LYS cc_start: 0.9034 (tttm) cc_final: 0.8697 (ttpp) REVERT: K 306 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8249 (mmmm) REVERT: L 103 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (m-80) REVERT: N 304 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8188 (tm-30) REVERT: N 306 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8272 (mmmm) REVERT: N 307 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8432 (t80) REVERT: O 105 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: P 206 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8346 (ptmm) REVERT: Q 303 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: S 202 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.8462 (ttpp) REVERT: S 206 LYS cc_start: 0.8894 (tttm) cc_final: 0.8230 (ttpp) REVERT: T 304 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7585 (tm-30) REVERT: T 306 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8274 (mmtp) REVERT: E 6 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9011 (ttmm) REVERT: U 103 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: V 202 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9088 (ttmm) REVERT: W 302 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8681 (ttpp) REVERT: W 304 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7679 (tm-30) REVERT: F 5 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: X 103 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8777 (m-10) REVERT: X 106 LYS cc_start: 0.9087 (tppt) cc_final: 0.8567 (tppt) REVERT: Z 302 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8479 (tppp) REVERT: Z 306 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8122 (mmmm) REVERT: Z 307 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: G 5 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: H 4 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5395 (pt0) REVERT: l 102 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9241 (mmtm) REVERT: l 103 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: m 206 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8322 (pttm) REVERT: n 304 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8135 (tm-30) REVERT: a 2 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8786 (mtmm) REVERT: o 107 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8315 (t80) REVERT: p 203 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8450 (t80) REVERT: q 302 LYS cc_start: 0.9314 (tmtt) cc_final: 0.8883 (tmtt) REVERT: q 303 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7331 (t80) REVERT: q 305 PHE cc_start: 0.9099 (t80) cc_final: 0.8876 (t80) REVERT: q 306 LYS cc_start: 0.9126 (tttt) cc_final: 0.8744 (tttp) REVERT: q 307 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8096 (t80) REVERT: r 102 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8338 (ttpp) REVERT: s 202 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8880 (tppp) REVERT: t 303 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7552 (t80) REVERT: c 3 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8089 (t80) REVERT: v 204 GLU cc_start: 0.8728 (tm-30) cc_final: 0.7961 (tm-30) REVERT: v 207 PHE cc_start: 0.8867 (t80) cc_final: 0.7851 (t80) REVERT: x 104 GLU cc_start: 0.9127 (pp20) cc_final: 0.8720 (pp20) REVERT: y 203 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8474 (t80) REVERT: z 302 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8671 (tmtt) REVERT: 1 203 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8499 (t80) REVERT: 2 306 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8659 (tmtt) REVERT: f 2 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8486 (mmtt) REVERT: 3 102 LYS cc_start: 0.9126 (tptp) cc_final: 0.8908 (tptp) REVERT: 4 202 LYS cc_start: 0.9207 (tptp) cc_final: 0.8827 (tppp) REVERT: 5 306 LYS cc_start: 0.9008 (tttp) cc_final: 0.8608 (tttp) REVERT: 5 307 PHE cc_start: 0.8911 (t80) cc_final: 0.8625 (t80) REVERT: g 2 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8710 (mmtt) REVERT: 7 202 LYS cc_start: 0.9206 (tptp) cc_final: 0.8863 (tptp) REVERT: 7 203 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8536 (t80) REVERT: 8 307 PHE cc_start: 0.8505 (t80) cc_final: 0.8264 (t80) REVERT: h 2 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (mmtt) REVERT: 9 104 GLU cc_start: 0.8741 (tm-30) cc_final: 0.7852 (tm-30) REVERT: AA 206 LYS cc_start: 0.8726 (tptp) cc_final: 0.8462 (tptp) REVERT: BA 307 PHE cc_start: 0.8791 (t80) cc_final: 0.8389 (t80) outliers start: 106 outliers final: 56 residues processed: 227 average time/residue: 0.3622 time to fit residues: 92.9542 Evaluate side-chains 250 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 161 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 302 LYS Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.048100 restraints weight = 20160.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.049887 restraints weight = 10924.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.051093 restraints weight = 6832.466| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.474 5568 Z= 8.457 Angle : 6.235 58.797 7232 Z= 2.761 Chirality : 0.416 1.079 512 Planarity : 0.028 0.091 960 Dihedral : 25.512 89.116 644 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 198.45 Ramachandran Plot: Outliers : 1.56 % Allowed : 55.86 % Favored : 42.58 % Rotamer: Outliers : 27.34 % Allowed : 33.07 % Favored : 39.58 % Cbeta Deviations : 47.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.10 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE 5 303 *********************** 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 271 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 166 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: A 7 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.9010 (m-10) REVERT: I 102 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8926 (mmtm) REVERT: I 107 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8665 (m-10) REVERT: J 206 LYS cc_start: 0.9052 (tttm) cc_final: 0.8773 (ttpp) REVERT: K 306 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8230 (mmmm) REVERT: L 103 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8941 (m-80) REVERT: N 304 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8216 (tm-30) REVERT: N 306 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8283 (mmmm) REVERT: N 307 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8424 (t80) REVERT: O 102 LYS cc_start: 0.9447 (mmtm) cc_final: 0.9239 (mmtm) REVERT: O 105 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: P 206 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8384 (ptmm) REVERT: Q 302 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8569 (mmmm) REVERT: Q 303 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: Q 307 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8426 (t80) REVERT: S 202 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: S 206 LYS cc_start: 0.8814 (tttm) cc_final: 0.8321 (ttpp) REVERT: T 304 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7597 (tm-30) REVERT: T 306 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (mmtp) REVERT: E 6 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9020 (ttmm) REVERT: U 103 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: U 106 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8853 (tppt) REVERT: V 202 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9187 (ttmm) REVERT: V 206 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8422 (ttpp) REVERT: W 302 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8697 (ttpp) REVERT: W 304 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7197 (tm-30) REVERT: F 5 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: X 106 LYS cc_start: 0.9088 (tppt) cc_final: 0.8586 (tppt) REVERT: Z 302 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8503 (tppp) REVERT: Z 304 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Z 306 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8253 (mmmm) REVERT: Z 307 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: G 5 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: k 303 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: H 4 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5449 (pt0) REVERT: l 102 LYS cc_start: 0.9469 (mmtm) cc_final: 0.9228 (mmtm) REVERT: l 103 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: m 206 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8328 (pttm) REVERT: n 304 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8153 (tm-30) REVERT: a 2 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8797 (mtmm) REVERT: o 107 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8319 (t80) REVERT: p 203 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8462 (t80) REVERT: q 302 LYS cc_start: 0.9315 (tmtt) cc_final: 0.8891 (tmtt) REVERT: q 303 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.7314 (t80) REVERT: q 305 PHE cc_start: 0.9100 (t80) cc_final: 0.8870 (t80) REVERT: q 306 LYS cc_start: 0.9123 (tttt) cc_final: 0.8751 (tttp) REVERT: q 307 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8102 (t80) REVERT: r 102 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8320 (ttpp) REVERT: s 202 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8902 (tppp) REVERT: s 206 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8330 (tptp) REVERT: t 303 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7573 (t80) REVERT: c 3 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8098 (t80) REVERT: v 204 GLU cc_start: 0.8724 (tm-30) cc_final: 0.7952 (tm-30) REVERT: v 207 PHE cc_start: 0.8868 (t80) cc_final: 0.7858 (t80) REVERT: x 104 GLU cc_start: 0.9162 (pp20) cc_final: 0.8722 (pp20) REVERT: y 203 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (t80) REVERT: z 302 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8677 (tmtt) REVERT: 1 203 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8545 (t80) REVERT: 2 306 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8667 (tmtt) REVERT: f 2 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8465 (mmtt) REVERT: 3 102 LYS cc_start: 0.9121 (tptp) cc_final: 0.8915 (tptp) REVERT: 4 202 LYS cc_start: 0.9198 (tptp) cc_final: 0.8826 (tppp) REVERT: 5 306 LYS cc_start: 0.8981 (tttp) cc_final: 0.8595 (tttp) REVERT: 5 307 PHE cc_start: 0.8907 (t80) cc_final: 0.8634 (t80) REVERT: 9 104 GLU cc_start: 0.8732 (tm-30) cc_final: 0.7797 (tm-30) REVERT: AA 206 LYS cc_start: 0.8730 (tptp) cc_final: 0.8486 (tptp) REVERT: BA 307 PHE cc_start: 0.8776 (t80) cc_final: 0.8406 (t80) outliers start: 105 outliers final: 58 residues processed: 229 average time/residue: 0.3772 time to fit residues: 97.5536 Evaluate side-chains 257 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 164 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.055308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.047967 restraints weight = 20207.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049755 restraints weight = 10910.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.050964 restraints weight = 6822.599| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 1.0157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 8.454 Angle : 6.248 59.029 7232 Z= 2.765 Chirality : 0.415 1.085 512 Planarity : 0.028 0.089 960 Dihedral : 25.580 89.725 644 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 198.68 Ramachandran Plot: Outliers : 1.95 % Allowed : 56.25 % Favored : 41.80 % Rotamer: Outliers : 27.08 % Allowed : 36.46 % Favored : 36.46 % Cbeta Deviations : 48.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.09 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.025 PHE P 205 *********************** 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 268 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 164 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: A 7 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.9021 (m-10) REVERT: I 102 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8938 (mmtm) REVERT: I 107 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: J 206 LYS cc_start: 0.9049 (tttm) cc_final: 0.8798 (ttpp) REVERT: K 306 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8345 (mmmm) REVERT: B 6 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8797 (mmmm) REVERT: L 103 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: N 304 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8219 (tm-30) REVERT: N 306 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8293 (mmmm) REVERT: N 307 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8437 (t80) REVERT: O 105 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8468 (m-10) REVERT: P 206 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8502 (ptmm) REVERT: Q 302 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8582 (mtpp) REVERT: Q 303 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: S 202 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8473 (ttpp) REVERT: S 206 LYS cc_start: 0.8812 (tttm) cc_final: 0.8389 (ttpp) REVERT: T 304 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7606 (tm-30) REVERT: T 306 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8259 (mmtp) REVERT: T 307 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: E 6 LYS cc_start: 0.9293 (mmmm) cc_final: 0.8952 (ttmm) REVERT: U 103 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: U 106 LYS cc_start: 0.9046 (tppt) cc_final: 0.8836 (tppt) REVERT: V 202 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9187 (ttmm) REVERT: W 302 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8712 (ttpp) REVERT: W 304 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7283 (tm-30) REVERT: F 5 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: X 103 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8810 (m-10) REVERT: X 106 LYS cc_start: 0.9116 (tppt) cc_final: 0.8623 (tppt) REVERT: Z 302 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8476 (tppp) REVERT: Z 306 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8200 (mmmm) REVERT: Z 307 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: G 5 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: k 303 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: H 4 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5500 (pt0) REVERT: l 102 LYS cc_start: 0.9470 (mmtm) cc_final: 0.9234 (mmtm) REVERT: l 103 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: m 206 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8362 (pttm) REVERT: n 304 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8165 (tm-30) REVERT: a 2 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8800 (mtmm) REVERT: o 107 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8310 (t80) REVERT: p 203 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8479 (t80) REVERT: q 302 LYS cc_start: 0.9322 (tmtt) cc_final: 0.8888 (tmtt) REVERT: q 303 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7322 (t80) REVERT: q 305 PHE cc_start: 0.9098 (t80) cc_final: 0.8874 (t80) REVERT: q 306 LYS cc_start: 0.9119 (tttt) cc_final: 0.8754 (tttp) REVERT: q 307 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8097 (t80) REVERT: r 102 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8351 (ttpp) REVERT: s 202 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8899 (tppp) REVERT: t 303 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7598 (t80) REVERT: c 3 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8094 (t80) REVERT: v 204 GLU cc_start: 0.8743 (tm-30) cc_final: 0.7967 (tm-30) REVERT: v 207 PHE cc_start: 0.8839 (t80) cc_final: 0.7828 (t80) REVERT: x 104 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8847 (pp20) REVERT: y 203 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8515 (t80) REVERT: z 302 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8677 (tmtt) REVERT: 1 203 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8509 (t80) REVERT: 2 306 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8664 (tmtt) REVERT: f 2 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8466 (mmtt) REVERT: f 6 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8883 (ttmt) REVERT: 4 202 LYS cc_start: 0.9199 (tptp) cc_final: 0.8831 (tppp) REVERT: g 2 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8797 (mtmm) REVERT: 7 202 LYS cc_start: 0.9192 (tptp) cc_final: 0.8851 (tptp) REVERT: 8 307 PHE cc_start: 0.8594 (t80) cc_final: 0.8379 (t80) REVERT: 9 104 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7810 (tm-30) REVERT: AA 206 LYS cc_start: 0.8726 (tptp) cc_final: 0.8486 (tptp) REVERT: BA 307 PHE cc_start: 0.8785 (t80) cc_final: 0.8469 (t80) outliers start: 104 outliers final: 60 residues processed: 225 average time/residue: 0.3643 time to fit residues: 92.8155 Evaluate side-chains 258 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 163 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.047217 restraints weight = 20171.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.048992 restraints weight = 10928.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.050189 restraints weight = 6823.319| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 1.0194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 8.456 Angle : 6.262 58.606 7232 Z= 2.770 Chirality : 0.416 1.080 512 Planarity : 0.028 0.088 960 Dihedral : 25.508 88.958 644 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 199.30 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.08 % Favored : 42.97 % Rotamer: Outliers : 26.82 % Allowed : 38.80 % Favored : 34.38 % Cbeta Deviations : 48.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.04 (0.25), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.89 (0.19), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 *********************** 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 269 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 166 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: A 7 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9019 (m-10) REVERT: I 102 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8940 (mmtm) REVERT: I 107 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8685 (m-10) REVERT: J 206 LYS cc_start: 0.9063 (tttm) cc_final: 0.8795 (ttpp) REVERT: K 306 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8211 (mmmm) REVERT: B 6 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8763 (mmmm) REVERT: L 103 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8947 (m-80) REVERT: N 304 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8245 (tm-30) REVERT: N 306 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8287 (mmmm) REVERT: N 307 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8429 (t80) REVERT: O 105 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: P 206 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8474 (ptmm) REVERT: Q 302 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8553 (mmmm) REVERT: Q 303 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: R 106 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8738 (tppt) REVERT: S 202 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.8483 (ttpp) REVERT: T 304 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7591 (tm-30) REVERT: T 306 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (mmtp) REVERT: E 6 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8964 (ttmm) REVERT: U 103 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: U 106 LYS cc_start: 0.9055 (tppt) cc_final: 0.8837 (tppt) REVERT: V 202 LYS cc_start: 0.9571 (ttmm) cc_final: 0.9172 (ttmm) REVERT: W 302 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: W 304 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7225 (tm-30) REVERT: F 5 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: X 106 LYS cc_start: 0.9120 (tppt) cc_final: 0.8633 (tppt) REVERT: Z 302 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8452 (tppp) REVERT: Z 306 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8250 (mmmm) REVERT: Z 307 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: G 5 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: k 303 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: H 4 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5454 (pt0) REVERT: l 102 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9231 (mmtm) REVERT: l 103 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: m 206 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8306 (pttm) REVERT: n 304 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8156 (tm-30) REVERT: a 2 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8803 (mtmm) REVERT: o 107 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8311 (t80) REVERT: p 203 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8478 (t80) REVERT: q 302 LYS cc_start: 0.9318 (tmtt) cc_final: 0.8882 (tmtt) REVERT: q 303 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7317 (t80) REVERT: q 305 PHE cc_start: 0.9104 (t80) cc_final: 0.8883 (t80) REVERT: q 306 LYS cc_start: 0.9128 (tttt) cc_final: 0.8765 (tttp) REVERT: q 307 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8099 (t80) REVERT: r 102 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8361 (ttpp) REVERT: s 202 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8908 (tppp) REVERT: s 206 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8309 (tptp) REVERT: t 303 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7562 (t80) REVERT: c 3 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8100 (t80) REVERT: v 204 GLU cc_start: 0.8746 (tm-30) cc_final: 0.7970 (tm-30) REVERT: v 207 PHE cc_start: 0.8844 (t80) cc_final: 0.7840 (t80) REVERT: x 104 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8848 (pp20) REVERT: y 203 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8516 (t80) REVERT: z 302 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8679 (tmtt) REVERT: 1 203 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8542 (t80) REVERT: 2 306 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (tmtt) REVERT: f 2 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8464 (mmtt) REVERT: f 5 PHE cc_start: 0.8675 (t80) cc_final: 0.8418 (t80) REVERT: f 6 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8690 (ttmt) REVERT: 4 202 LYS cc_start: 0.9207 (tptp) cc_final: 0.8826 (tppp) REVERT: 5 306 LYS cc_start: 0.9010 (tttp) cc_final: 0.8609 (tttp) REVERT: 5 307 PHE cc_start: 0.8946 (t80) cc_final: 0.8638 (t80) REVERT: g 2 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8803 (mtmm) REVERT: 7 202 LYS cc_start: 0.9203 (tptp) cc_final: 0.8811 (tptp) REVERT: h 3 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7700 (t80) REVERT: 9 104 GLU cc_start: 0.8691 (tm-30) cc_final: 0.7792 (tm-30) REVERT: AA 206 LYS cc_start: 0.8719 (tptp) cc_final: 0.8489 (tptp) REVERT: BA 307 PHE cc_start: 0.8790 (t80) cc_final: 0.8499 (t80) outliers start: 103 outliers final: 58 residues processed: 227 average time/residue: 0.3502 time to fit residues: 90.0730 Evaluate side-chains 260 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 165 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 302 LYS Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.047234 restraints weight = 20288.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.049025 restraints weight = 10918.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.050223 restraints weight = 6797.365| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 1.0220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.474 5568 Z= 8.463 Angle : 6.263 58.893 7232 Z= 2.769 Chirality : 0.417 1.081 512 Planarity : 0.027 0.088 960 Dihedral : 25.567 88.801 644 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 200.87 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.86 % Favored : 42.19 % Rotamer: Outliers : 26.82 % Allowed : 39.32 % Favored : 33.85 % Cbeta Deviations : 47.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.05 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.90 (0.19), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 ********************** 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 269 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 166 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8462 (m-10) REVERT: A 7 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.9028 (m-10) REVERT: I 102 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8933 (mmtm) REVERT: I 107 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8682 (m-10) REVERT: J 206 LYS cc_start: 0.9036 (tttm) cc_final: 0.8799 (ttpp) REVERT: K 306 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8219 (mmmm) REVERT: B 6 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8760 (mmmm) REVERT: L 103 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: N 304 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8264 (tm-30) REVERT: N 306 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8309 (mmmm) REVERT: N 307 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8440 (t80) REVERT: O 105 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8466 (m-10) REVERT: P 206 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8460 (ptmm) REVERT: Q 302 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: Q 303 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: R 106 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8731 (tppt) REVERT: S 202 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: T 304 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7620 (tm-30) REVERT: T 306 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8266 (mmtp) REVERT: T 307 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8935 (m-80) REVERT: E 6 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8963 (ttmm) REVERT: U 103 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: U 106 LYS cc_start: 0.9052 (tppt) cc_final: 0.8834 (tppt) REVERT: V 202 LYS cc_start: 0.9571 (ttmm) cc_final: 0.9171 (ttmm) REVERT: W 302 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: F 5 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: X 103 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: X 106 LYS cc_start: 0.9118 (tppt) cc_final: 0.8629 (tppt) REVERT: Z 302 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8489 (tppp) REVERT: Z 306 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8344 (mmmm) REVERT: Z 307 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: G 5 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: k 303 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: H 4 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5496 (pt0) REVERT: l 102 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9239 (mmtm) REVERT: l 103 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: m 206 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8339 (pttm) REVERT: n 304 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8168 (tm-30) REVERT: a 2 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8798 (mtmm) REVERT: o 107 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8302 (t80) REVERT: p 203 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8462 (t80) REVERT: q 302 LYS cc_start: 0.9318 (tmtt) cc_final: 0.8888 (tmtt) REVERT: q 303 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7341 (t80) REVERT: q 305 PHE cc_start: 0.9107 (t80) cc_final: 0.8905 (t80) REVERT: q 306 LYS cc_start: 0.9126 (tttt) cc_final: 0.8763 (tttp) REVERT: q 307 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8097 (t80) REVERT: s 202 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8896 (tppp) REVERT: s 206 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8311 (tptp) REVERT: c 3 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8105 (t80) REVERT: v 204 GLU cc_start: 0.8747 (tm-30) cc_final: 0.7967 (tm-30) REVERT: v 207 PHE cc_start: 0.8840 (t80) cc_final: 0.7834 (t80) REVERT: x 104 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8884 (pp20) REVERT: y 203 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8519 (t80) REVERT: z 302 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8678 (tmtt) REVERT: 1 203 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8556 (t80) REVERT: 2 306 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8659 (tmtt) REVERT: f 2 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8470 (mmtt) REVERT: f 5 PHE cc_start: 0.8667 (t80) cc_final: 0.8446 (t80) REVERT: f 6 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8692 (ttmt) REVERT: 4 202 LYS cc_start: 0.9207 (tptp) cc_final: 0.8829 (tppp) REVERT: g 2 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8801 (mtmm) REVERT: 7 202 LYS cc_start: 0.9199 (tptp) cc_final: 0.8844 (tptp) REVERT: h 3 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7651 (t80) REVERT: 9 104 GLU cc_start: 0.8685 (tm-30) cc_final: 0.7775 (tm-30) REVERT: AA 206 LYS cc_start: 0.8724 (tptp) cc_final: 0.8504 (tptp) REVERT: BA 307 PHE cc_start: 0.8767 (t80) cc_final: 0.8508 (t80) outliers start: 103 outliers final: 60 residues processed: 226 average time/residue: 0.3641 time to fit residues: 93.3851 Evaluate side-chains 263 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 165 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 302 LYS Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 102 LYS Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 102 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain s residue 206 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.047218 restraints weight = 20527.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.049014 restraints weight = 10979.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.050225 restraints weight = 6813.866| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 1.0231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.478 5568 Z= 8.465 Angle : 6.269 58.812 7232 Z= 2.771 Chirality : 0.417 1.081 512 Planarity : 0.027 0.088 960 Dihedral : 25.526 88.746 644 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 201.32 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.86 % Favored : 42.19 % Rotamer: Outliers : 27.60 % Allowed : 38.54 % Favored : 33.85 % Cbeta Deviations : 47.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.08 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.025 PHE P 205 =============================================================================== Job complete usr+sys time: 1742.37 seconds wall clock time: 31 minutes 29.43 seconds (1889.43 seconds total)