Starting phenix.real_space_refine on Thu Oct 22 21:33:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqe_23483/10_2026/7lqe_23483.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 4320 2.51 5 N 792 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6048 Number of models: 1 Model: "" Number of chains: 72 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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 Chain: "CA" 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: "DA" 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: "EA" 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: "FA" 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: "GA" 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: "HA" 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: "IA" 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: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.53, per 1000 atoms: 0.25 Number of scatterers: 6048 At special positions: 0 Unit cell: (87.48, 77.76, 106.92, 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 936 8.00 N 792 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 64.0 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEEA 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE h 5 " --> pdb=" O PHEEA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 8 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE 8 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 2 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHE 2 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE w 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 5 " --> pdb=" O PHE w 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE t 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE a 5 " --> pdb=" O PHE t 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE z 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHE z 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE 5 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHE 5 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEBA 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHEBA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEHA 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE i 5 " --> pdb=" O PHEHA 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'FA' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSGA 302 " --> pdb=" O GMA 9 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 9 206 " --> pdb=" O GLUGA 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAGA 308 " --> pdb=" O LYS 9 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSAA 302 " --> pdb=" O GMA 3 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 3 206 " --> pdb=" O GLUAA 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 4 302 " --> pdb=" O GMA x 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS x 206 " --> pdb=" O GLU 4 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS y 302 " --> pdb=" O GMA u 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS u 206 " --> pdb=" O GLU y 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GMA y 308 " --> pdb=" O LYS u 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS v 302 " --> pdb=" O GMA 0 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS 0 206 " --> pdb=" O GLU v 304 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GMA v 308 " --> pdb=" O LYS 0 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 1 302 " --> pdb=" O GMA 6 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 6 206 " --> pdb=" O GLU 1 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 7 302 " --> pdb=" O GMACA 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSCA 206 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA 7 308 " --> pdb=" O LYSCA 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSDA 302 " --> pdb=" O GMAIA 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSIA 206 " --> pdb=" O GLUDA 304 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 773 1.26 - 1.33: 667 1.33 - 1.41: 1800 1.41 - 1.48: 651 1.48 - 1.56: 2373 Bond restraints: 6264 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 6259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7119 1.98 - 3.96: 795 3.96 - 5.95: 159 5.95 - 7.93: 54 7.93 - 9.91: 9 Bond angle restraints: 8136 Sorted by residual: angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.82 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " pdb=" CAA 5CR h 1 " ideal model delta sigma weight residual 114.91 124.78 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2422 15.26 - 30.52: 395 30.52 - 45.78: 171 45.78 - 61.04: 99 61.04 - 76.30: 9 Dihedral angle restraints: 3096 sinusoidal: 1440 harmonic: 1656 Sorted by residual: dihedral pdb=" CA LYS q 106 " pdb=" CB LYS q 106 " pdb=" CG LYS q 106 " pdb=" CD LYS q 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS Y 106 " pdb=" CB LYS Y 106 " pdb=" CG LYS Y 106 " pdb=" CD LYS Y 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS M 106 " pdb=" CB LYS M 106 " pdb=" CG LYS M 106 " pdb=" CD LYS M 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 191 0.017 - 0.035: 166 0.035 - 0.052: 150 0.052 - 0.070: 53 0.070 - 0.087: 16 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA LYS W 202 " pdb=" N LYS W 202 " pdb=" C LYS W 202 " pdb=" CB LYS W 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.91e-01 chirality pdb=" CA LYS Q 202 " pdb=" N LYS Q 202 " pdb=" C LYS Q 202 " pdb=" CB LYS Q 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.90e-01 chirality pdb=" CA LYS N 202 " pdb=" N LYS N 202 " pdb=" C LYS N 202 " pdb=" CB LYS N 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.87e-01 ... (remaining 573 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 205 " -0.009 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE u 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE u 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 205 " -0.009 2.00e-02 2.50e+03 6.93e-03 8.39e-01 pdb=" CG PHE 6 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 6 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 205 " -0.009 2.00e-02 2.50e+03 6.90e-03 8.33e-01 pdb=" CG PHE x 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE x 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE x 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE x 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2593 2.92 - 3.41: 5352 3.41 - 3.91: 9925 3.91 - 4.40: 12294 4.40 - 4.90: 20848 Nonbonded interactions: 51012 Sorted by model distance: nonbonded pdb=" N GLU D 4 " pdb=" OE1 GLU D 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU A 4 " pdb=" OE1 GLU A 4 " model vdw 2.423 3.120 ... (remaining 51007 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 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.118 6264 Z= 0.782 Angle : 1.417 9.910 8136 Z= 0.592 Chirality : 0.035 0.087 576 Planarity : 0.002 0.009 1080 Dihedral : 20.718 76.296 1944 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.94 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE u 205 Details of bonding type rmsd/Z covalent geometry : bond 0.01603 / 0.78 ( 6264) covalent geometry : angle 1.41685 / 0.59 ( 8136) hydrogen bonds : bond 0.31155 / 17.30 ( 139) hydrogen bonds : angle 15.44596 / 8.43 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.194 Fit side-chains REVERT: A 2 LYS cc_start: 0.8975 (tttt) cc_final: 0.8577 (tptt) REVERT: J 102 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: K 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8709 (ttmt) REVERT: K 206 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8037 (ttmm) REVERT: L 304 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6841 (mm-30) REVERT: L 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8208 (mmmm) REVERT: B 2 LYS cc_start: 0.8950 (tttt) cc_final: 0.8747 (tttp) REVERT: M 102 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: N 202 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8696 (ttmm) REVERT: N 204 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7046 (mt-10) REVERT: O 306 LYS cc_start: 0.8895 (tttt) cc_final: 0.8380 (mmmm) REVERT: C 2 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: P 102 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: P 104 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6835 (mm-30) REVERT: Q 204 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7270 (mt-10) REVERT: R 304 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6963 (mm-30) REVERT: R 306 LYS cc_start: 0.8731 (tttt) cc_final: 0.8295 (mmmm) REVERT: D 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8716 (ttmm) REVERT: S 102 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (ttmt) REVERT: U 304 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6582 (mm-30) REVERT: U 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8236 (mmmm) REVERT: E 4 GLU cc_start: 0.7581 (mp0) cc_final: 0.5848 (mp0) REVERT: V 102 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: V 104 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6989 (mm-30) REVERT: W 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8626 (ttmm) REVERT: W 204 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mt-10) REVERT: W 206 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8144 (ttmm) REVERT: X 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7244 (mm-30) REVERT: X 306 LYS cc_start: 0.8889 (tttt) cc_final: 0.8236 (mmmm) REVERT: F 2 LYS cc_start: 0.8964 (tttt) cc_final: 0.8518 (tttm) REVERT: F 4 GLU cc_start: 0.7595 (mp0) cc_final: 0.7012 (mp0) REVERT: Y 102 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: Z 202 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8683 (ttmm) REVERT: Z 206 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8130 (ttmm) REVERT: j 304 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7285 (mm-30) REVERT: j 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (mmmm) REVERT: G 2 LYS cc_start: 0.8756 (tttt) cc_final: 0.8452 (tttm) REVERT: G 4 GLU cc_start: 0.7496 (mp0) cc_final: 0.6174 (mp0) REVERT: G 6 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7922 (mtmt) REVERT: k 102 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: l 202 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (ttmt) REVERT: l 206 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7935 (ttmm) REVERT: m 302 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mtmt) REVERT: m 304 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7248 (mm-30) REVERT: m 306 LYS cc_start: 0.8693 (tttt) cc_final: 0.8127 (mmmm) REVERT: H 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (ttmt) REVERT: n 102 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: p 306 LYS cc_start: 0.8809 (tttt) cc_final: 0.8244 (mmmm) REVERT: r 202 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: s 306 LYS cc_start: 0.8710 (tttt) cc_final: 0.8340 (tppt) REVERT: a 6 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: w 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: z 105 PHE cc_start: 0.8273 (t80) cc_final: 0.7515 (t80) REVERT: 2 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7759 (t80) REVERT: 4 303 PHE cc_start: 0.8423 (t80) cc_final: 0.8200 (t80) REVERT: 4 307 PHE cc_start: 0.7856 (t80) cc_final: 0.7604 (t80) REVERT: HA 104 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: HA 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7558 (t80) REVERT: JA 303 PHE cc_start: 0.8181 (t80) cc_final: 0.7871 (t80) REVERT: JA 307 PHE cc_start: 0.7572 (t80) cc_final: 0.7215 (t80) outliers start: 63 outliers final: 25 residues processed: 178 average time/residue: 0.1660 time to fit residues: 34.0955 Evaluate side-chains 175 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain V residue 102 LYS Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain k residue 102 LYS Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain m residue 302 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 104 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.092013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078345 restraints weight = 12582.990| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.17 r_work: 0.3232 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6264 Z= 0.138 Angle : 0.632 7.929 8136 Z= 0.291 Chirality : 0.030 0.083 576 Planarity : 0.002 0.011 1080 Dihedral : 16.216 81.450 861 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 21.06 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.63 (0.24), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.18), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE a 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6264) covalent geometry : angle 0.63224 / 0.29 ( 8136) hydrogen bonds : bond 0.02707 / 1.48 ( 139) hydrogen bonds : angle 8.10698 / 4.48 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8663 (ttmt) REVERT: K 204 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7843 (mt-10) REVERT: K 206 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8447 (ttmm) REVERT: L 304 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7543 (mm-30) REVERT: L 306 LYS cc_start: 0.8838 (tttt) cc_final: 0.8358 (mmmm) REVERT: B 2 LYS cc_start: 0.8839 (tttt) cc_final: 0.8517 (tttm) REVERT: N 202 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8700 (ttmm) REVERT: N 204 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7698 (mt-10) REVERT: O 306 LYS cc_start: 0.8989 (tttt) cc_final: 0.8503 (mmmm) REVERT: C 2 LYS cc_start: 0.8730 (tttt) cc_final: 0.8286 (ttmm) REVERT: P 102 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8785 (ttpt) REVERT: P 104 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7587 (mm-30) REVERT: Q 204 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7804 (mt-10) REVERT: R 304 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7506 (mm-30) REVERT: R 306 LYS cc_start: 0.8939 (tttt) cc_final: 0.8520 (mmmm) REVERT: D 2 LYS cc_start: 0.8860 (tttt) cc_final: 0.8378 (ttmm) REVERT: S 102 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8236 (ttpp) REVERT: S 106 LYS cc_start: 0.8487 (tptm) cc_final: 0.8234 (tptm) REVERT: U 306 LYS cc_start: 0.8863 (tttt) cc_final: 0.8376 (mmmm) REVERT: V 102 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8721 (ttmt) REVERT: V 104 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7423 (mm-30) REVERT: W 202 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8577 (ttmm) REVERT: W 204 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7962 (mt-10) REVERT: W 206 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8489 (ttmm) REVERT: X 302 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8652 (ttpt) REVERT: X 306 LYS cc_start: 0.9010 (tttt) cc_final: 0.8362 (mmmm) REVERT: Y 102 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8600 (ttpp) REVERT: Y 104 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7499 (mm-30) REVERT: Y 106 LYS cc_start: 0.8598 (tptm) cc_final: 0.8218 (tptm) REVERT: Z 206 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8435 (ttmm) REVERT: j 304 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7764 (mm-30) REVERT: j 306 LYS cc_start: 0.8826 (tttt) cc_final: 0.8341 (mmmm) REVERT: G 4 GLU cc_start: 0.7795 (mp0) cc_final: 0.6564 (mp0) REVERT: G 6 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8204 (mtmt) REVERT: k 102 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8734 (ttmt) REVERT: l 202 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8483 (ttmt) REVERT: l 206 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8334 (ttmm) REVERT: m 304 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7833 (mm-30) REVERT: m 306 LYS cc_start: 0.8799 (tttt) cc_final: 0.8269 (mmmm) REVERT: H 2 LYS cc_start: 0.9149 (tttt) cc_final: 0.8922 (ttmt) REVERT: o 206 LYS cc_start: 0.5130 (pptt) cc_final: 0.4516 (pttp) REVERT: p 306 LYS cc_start: 0.8925 (tttt) cc_final: 0.8384 (mmmm) REVERT: I 4 GLU cc_start: 0.8064 (mp0) cc_final: 0.7710 (mp0) REVERT: r 202 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8822 (ttmt) REVERT: s 302 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8329 (tppt) REVERT: s 306 LYS cc_start: 0.8980 (tttt) cc_final: 0.8493 (tppt) REVERT: a 5 PHE cc_start: 0.8538 (t80) cc_final: 0.8135 (t80) REVERT: b 3 PHE cc_start: 0.8999 (t80) cc_final: 0.8738 (t80) REVERT: z 105 PHE cc_start: 0.8312 (t80) cc_final: 0.7720 (t80) REVERT: 2 105 PHE cc_start: 0.8381 (t80) cc_final: 0.7515 (t80) REVERT: 6 204 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7267 (tm-30) REVERT: f 7 PHE cc_start: 0.8749 (t80) cc_final: 0.8427 (t80) REVERT: h 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8601 (t80) REVERT: i 3 PHE cc_start: 0.8910 (t80) cc_final: 0.8696 (t80) REVERT: HA 104 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: HA 105 PHE cc_start: 0.8104 (t80) cc_final: 0.7519 (t80) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.1625 time to fit residues: 24.1103 Evaluate side-chains 125 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.088078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075336 restraints weight = 13351.203| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.22 r_work: 0.3117 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.072 6264 Z= 0.695 Angle : 0.980 9.662 8136 Z= 0.457 Chirality : 0.043 0.138 576 Planarity : 0.004 0.017 1080 Dihedral : 16.943 89.062 723 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 5.32 % Allowed : 19.21 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.03 (0.21), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.16), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.004 PHEGA 305 Details of bonding type rmsd/Z covalent geometry : bond 0.01585 / 0.69 ( 6264) covalent geometry : angle 0.98035 / 0.46 ( 8136) hydrogen bonds : bond 0.03535 / 1.98 ( 139) hydrogen bonds : angle 7.11443 / 4.02 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9004 (tttt) cc_final: 0.8577 (ttmt) REVERT: K 202 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8823 (ttmt) REVERT: K 204 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7964 (mt-10) REVERT: K 206 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8340 (ttmm) REVERT: L 304 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7643 (mm-30) REVERT: L 306 LYS cc_start: 0.9015 (tttt) cc_final: 0.8519 (mmmm) REVERT: B 2 LYS cc_start: 0.9151 (tttt) cc_final: 0.8534 (tttp) REVERT: N 204 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7723 (mt-10) REVERT: O 306 LYS cc_start: 0.9012 (tttt) cc_final: 0.8444 (ttmm) REVERT: C 2 LYS cc_start: 0.8831 (tttt) cc_final: 0.8147 (ttmm) REVERT: P 104 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7416 (mm-30) REVERT: Q 204 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 2 LYS cc_start: 0.9027 (tttt) cc_final: 0.8616 (tttt) REVERT: D 4 GLU cc_start: 0.7782 (mp0) cc_final: 0.7157 (mp0) REVERT: D 6 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7843 (mtmt) REVERT: S 106 LYS cc_start: 0.8572 (tptm) cc_final: 0.8303 (tptm) REVERT: U 306 LYS cc_start: 0.9045 (tttt) cc_final: 0.8537 (mtpp) REVERT: V 102 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8700 (ttmt) REVERT: W 204 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7894 (mt-10) REVERT: X 306 LYS cc_start: 0.9124 (tttt) cc_final: 0.8664 (mmmm) REVERT: F 2 LYS cc_start: 0.9181 (tttt) cc_final: 0.8684 (tttm) REVERT: Y 102 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8678 (ttmt) REVERT: Y 106 LYS cc_start: 0.8597 (tptm) cc_final: 0.8207 (tptm) REVERT: Z 203 PHE cc_start: 0.8848 (m-80) cc_final: 0.8292 (m-10) REVERT: Z 206 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8400 (ttmm) REVERT: j 304 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7819 (mm-30) REVERT: j 306 LYS cc_start: 0.9030 (tttt) cc_final: 0.8481 (mmmm) REVERT: G 2 LYS cc_start: 0.8966 (tttt) cc_final: 0.8688 (tttp) REVERT: G 4 GLU cc_start: 0.7835 (mp0) cc_final: 0.7082 (mp0) REVERT: k 102 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8556 (ttpt) REVERT: l 202 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8463 (ttmm) REVERT: l 206 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8443 (ttmm) REVERT: m 304 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7855 (mm-30) REVERT: m 306 LYS cc_start: 0.8921 (tttt) cc_final: 0.8400 (mmmm) REVERT: o 206 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.3282 (pptt) REVERT: p 306 LYS cc_start: 0.9080 (tttt) cc_final: 0.8584 (mmmm) REVERT: I 4 GLU cc_start: 0.8016 (mp0) cc_final: 0.7462 (mp0) REVERT: s 302 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8386 (mmtt) REVERT: a 5 PHE cc_start: 0.8414 (t80) cc_final: 0.8116 (t80) REVERT: a 6 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8142 (ttpp) REVERT: y 302 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: 0 204 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7512 (tm-30) REVERT: 2 105 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7398 (t80) REVERT: 3 204 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7698 (tm-30) REVERT: 4 302 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7969 (tptp) REVERT: 6 204 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7313 (tm-30) REVERT: g 6 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8288 (ttmm) REVERT: HA 104 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: HA 105 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7554 (t80) outliers start: 23 outliers final: 10 residues processed: 142 average time/residue: 0.1709 time to fit residues: 27.8014 Evaluate side-chains 145 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 302 LYS Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain HA residue 105 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.092546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079219 restraints weight = 12868.552| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.36 r_work: 0.3238 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6264 Z= 0.120 Angle : 0.620 8.219 8136 Z= 0.279 Chirality : 0.028 0.084 576 Planarity : 0.002 0.013 1080 Dihedral : 15.496 78.335 723 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.85 % Allowed : 22.69 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.22), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.17), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHEGA 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6264) covalent geometry : angle 0.61951 / 0.28 ( 8136) hydrogen bonds : bond 0.01866 / 1.04 ( 139) hydrogen bonds : angle 6.02314 / 3.39 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8608 (ttmt) REVERT: K 204 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7798 (mt-10) REVERT: K 206 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8483 (ttmm) REVERT: L 304 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7661 (mm-30) REVERT: L 306 LYS cc_start: 0.8914 (tttt) cc_final: 0.8407 (mmmm) REVERT: B 2 LYS cc_start: 0.8882 (tttt) cc_final: 0.8380 (tttp) REVERT: M 102 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8603 (ttpt) REVERT: N 204 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7582 (mt-10) REVERT: O 306 LYS cc_start: 0.8956 (tttt) cc_final: 0.8602 (mmmm) REVERT: P 102 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8610 (ttpt) REVERT: P 104 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7202 (mm-30) REVERT: Q 204 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 2 LYS cc_start: 0.8932 (tttt) cc_final: 0.8632 (ttmm) REVERT: D 4 GLU cc_start: 0.7967 (mp0) cc_final: 0.7601 (mp0) REVERT: S 106 LYS cc_start: 0.8551 (tptm) cc_final: 0.8234 (tptm) REVERT: U 306 LYS cc_start: 0.8888 (tttt) cc_final: 0.8376 (mmmm) REVERT: E 4 GLU cc_start: 0.7703 (mp0) cc_final: 0.5644 (mp0) REVERT: V 102 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8709 (ttmt) REVERT: V 106 LYS cc_start: 0.8529 (tptm) cc_final: 0.7890 (tptm) REVERT: W 202 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8804 (ttmm) REVERT: W 204 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7894 (mt-10) REVERT: W 206 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8504 (ttmm) REVERT: X 302 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8690 (ttpt) REVERT: X 306 LYS cc_start: 0.9009 (tttt) cc_final: 0.8283 (mmmm) REVERT: Y 102 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8784 (ttmt) REVERT: Z 206 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8371 (ttmm) REVERT: j 304 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7952 (mm-30) REVERT: j 306 LYS cc_start: 0.8918 (tttt) cc_final: 0.8276 (mmmm) REVERT: G 4 GLU cc_start: 0.7810 (mp0) cc_final: 0.7180 (mp0) REVERT: k 102 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8596 (ttpt) REVERT: l 202 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8394 (ttmt) REVERT: l 206 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8273 (ttmm) REVERT: m 304 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7827 (mm-30) REVERT: m 306 LYS cc_start: 0.8751 (tttt) cc_final: 0.8271 (mmmm) REVERT: p 306 LYS cc_start: 0.8892 (tttt) cc_final: 0.8431 (mmmm) REVERT: I 4 GLU cc_start: 0.8169 (mp0) cc_final: 0.7304 (mp0) REVERT: q 102 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8861 (ttpt) REVERT: r 202 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8228 (mmtt) REVERT: a 5 PHE cc_start: 0.8273 (t80) cc_final: 0.8030 (t80) REVERT: a 6 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7978 (ttpp) REVERT: v 302 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7619 (tptp) REVERT: z 105 PHE cc_start: 0.8436 (t80) cc_final: 0.7826 (t80) REVERT: 2 105 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7334 (t80) REVERT: 6 204 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7596 (tm-30) REVERT: f 6 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8085 (ttmm) REVERT: AA 302 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (tptp) REVERT: g 6 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8215 (ttmm) REVERT: EA 105 PHE cc_start: 0.8177 (t80) cc_final: 0.7889 (t80) REVERT: i 3 PHE cc_start: 0.8961 (t80) cc_final: 0.8568 (t80) REVERT: HA 104 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: HA 105 PHE cc_start: 0.7769 (t80) cc_final: 0.7145 (t80) outliers start: 8 outliers final: 3 residues processed: 126 average time/residue: 0.1696 time to fit residues: 24.5717 Evaluate side-chains 125 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 302 LYS Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075037 restraints weight = 13670.922| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.33 r_work: 0.3122 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.063 6264 Z= 0.698 Angle : 0.967 8.265 8136 Z= 0.448 Chirality : 0.041 0.127 576 Planarity : 0.004 0.016 1080 Dihedral : 16.093 88.080 723 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.25 % Allowed : 22.22 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.96 (0.22), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.16), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.004 PHE W 203 Details of bonding type rmsd/Z covalent geometry : bond 0.01589 / 0.70 ( 6264) covalent geometry : angle 0.96704 / 0.45 ( 8136) hydrogen bonds : bond 0.03433 / 1.92 ( 139) hydrogen bonds : angle 6.67738 / 3.79 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8981 (tttt) cc_final: 0.8772 (ttmt) REVERT: K 202 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8815 (ttmt) REVERT: K 204 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7976 (mt-10) REVERT: K 206 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8345 (ttmm) REVERT: L 304 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7637 (mm-30) REVERT: L 306 LYS cc_start: 0.9049 (tttt) cc_final: 0.8561 (mmmm) REVERT: B 2 LYS cc_start: 0.8978 (tttt) cc_final: 0.8504 (tttp) REVERT: M 102 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8497 (ttmt) REVERT: N 204 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7681 (mt-10) REVERT: O 306 LYS cc_start: 0.9059 (tttt) cc_final: 0.8500 (ttmm) REVERT: C 2 LYS cc_start: 0.8882 (tttt) cc_final: 0.8469 (ttmm) REVERT: P 104 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7325 (mm-30) REVERT: Q 204 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 4 GLU cc_start: 0.8252 (mp0) cc_final: 0.7466 (mp0) REVERT: D 6 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8064 (mtmt) REVERT: U 306 LYS cc_start: 0.9036 (tttt) cc_final: 0.8564 (mtpp) REVERT: E 4 GLU cc_start: 0.7614 (mp0) cc_final: 0.5738 (mp0) REVERT: V 102 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8802 (mtmt) REVERT: V 106 LYS cc_start: 0.8641 (tptm) cc_final: 0.8106 (tptm) REVERT: W 202 LYS cc_start: 0.9258 (ttmm) cc_final: 0.9055 (ttmm) REVERT: W 204 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7785 (mt-10) REVERT: W 206 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8529 (ttmm) REVERT: X 302 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8749 (mtmt) REVERT: X 306 LYS cc_start: 0.9133 (tttt) cc_final: 0.8572 (mmmm) REVERT: F 2 LYS cc_start: 0.9152 (tttt) cc_final: 0.8703 (tttm) REVERT: Y 102 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8652 (ttmt) REVERT: Y 106 LYS cc_start: 0.8636 (tptm) cc_final: 0.8214 (tptm) REVERT: Z 206 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8401 (ttmm) REVERT: j 304 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7769 (mm-30) REVERT: j 306 LYS cc_start: 0.9069 (tttt) cc_final: 0.8573 (mmmm) REVERT: G 4 GLU cc_start: 0.7813 (mp0) cc_final: 0.7520 (mp0) REVERT: l 202 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8496 (ttmm) REVERT: l 206 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8481 (ttmm) REVERT: m 304 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7894 (mm-30) REVERT: m 306 LYS cc_start: 0.8912 (tttt) cc_final: 0.8435 (mmmm) REVERT: o 202 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8487 (pttm) REVERT: o 206 LYS cc_start: 0.5227 (OUTLIER) cc_final: 0.3111 (pptt) REVERT: p 302 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8228 (pttt) REVERT: p 306 LYS cc_start: 0.9090 (tttt) cc_final: 0.8594 (mmmm) REVERT: s 302 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8421 (mmtt) REVERT: a 5 PHE cc_start: 0.8436 (t80) cc_final: 0.8228 (t80) REVERT: a 6 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8187 (ttpp) REVERT: t 103 PHE cc_start: 0.8563 (t80) cc_final: 0.8276 (t80) REVERT: y 302 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8008 (tptp) REVERT: 0 204 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7486 (tm-30) REVERT: 2 105 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7379 (t80) REVERT: 3 204 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7646 (tm-30) REVERT: 4 305 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7325 (t80) REVERT: 6 204 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7518 (tm-30) REVERT: AA 302 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8062 (tptp) REVERT: g 6 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8343 (ttmm) REVERT: HA 105 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7807 (t80) REVERT: IA 204 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7593 (tm-30) REVERT: JA 302 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8147 (tptp) outliers start: 27 outliers final: 11 residues processed: 141 average time/residue: 0.1735 time to fit residues: 28.1777 Evaluate side-chains 146 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain o residue 202 LYS Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 305 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 302 LYS Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain HA residue 105 PHE Chi-restraints excluded: chain JA residue 302 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080135 restraints weight = 12923.668| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.20 r_work: 0.3249 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6264 Z= 0.128 Angle : 0.633 8.286 8136 Z= 0.287 Chirality : 0.028 0.097 576 Planarity : 0.002 0.010 1080 Dihedral : 14.735 80.345 720 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.62 % Allowed : 28.47 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.44 (0.23), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.18), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE 7 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6264) covalent geometry : angle 0.63279 / 0.29 ( 8136) hydrogen bonds : bond 0.01841 / 1.02 ( 139) hydrogen bonds : angle 5.65722 / 3.20 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8909 (tttt) cc_final: 0.8577 (tttp) REVERT: K 202 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8593 (ttmt) REVERT: K 204 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7840 (mt-10) REVERT: K 206 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8553 (ttmm) REVERT: L 302 LYS cc_start: 0.8926 (tttt) cc_final: 0.8712 (tttt) REVERT: L 304 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7661 (mm-30) REVERT: L 306 LYS cc_start: 0.8903 (tttt) cc_final: 0.8410 (mmmm) REVERT: B 2 LYS cc_start: 0.8914 (tttt) cc_final: 0.8463 (tttp) REVERT: M 102 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8565 (ttmt) REVERT: M 106 LYS cc_start: 0.8586 (tptm) cc_final: 0.8258 (tptm) REVERT: N 204 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7615 (mt-10) REVERT: O 306 LYS cc_start: 0.8977 (tttt) cc_final: 0.8674 (mmmm) REVERT: C 2 LYS cc_start: 0.8636 (tttt) cc_final: 0.8104 (tttt) REVERT: P 104 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7263 (mm-30) REVERT: Q 204 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 2 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8760 (tttp) REVERT: S 102 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8768 (ttpt) REVERT: S 106 LYS cc_start: 0.8419 (tptm) cc_final: 0.8124 (tptm) REVERT: U 306 LYS cc_start: 0.8962 (tttt) cc_final: 0.8538 (mmmm) REVERT: E 4 GLU cc_start: 0.7630 (mp0) cc_final: 0.5774 (mp0) REVERT: V 102 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8783 (ttpt) REVERT: V 106 LYS cc_start: 0.8563 (tptm) cc_final: 0.7974 (tptm) REVERT: W 204 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7773 (mt-10) REVERT: W 206 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8430 (ttmm) REVERT: X 302 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8809 (ttpt) REVERT: X 306 LYS cc_start: 0.8978 (tttt) cc_final: 0.8275 (mmmm) REVERT: Y 106 LYS cc_start: 0.8613 (tptm) cc_final: 0.7971 (tptm) REVERT: Z 202 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8928 (ttmt) REVERT: Z 206 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8375 (ttmm) REVERT: j 304 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7836 (mm-30) REVERT: j 306 LYS cc_start: 0.8963 (tttt) cc_final: 0.8478 (mmmm) REVERT: G 4 GLU cc_start: 0.7892 (mp0) cc_final: 0.7359 (mp0) REVERT: G 6 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8295 (mtmt) REVERT: k 102 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8859 (ttmt) REVERT: l 202 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8494 (ttmt) REVERT: l 206 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8334 (ttmm) REVERT: m 304 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7827 (mm-30) REVERT: m 306 LYS cc_start: 0.8790 (tttt) cc_final: 0.8320 (mmmm) REVERT: H 2 LYS cc_start: 0.9084 (tppt) cc_final: 0.8819 (tppt) REVERT: o 202 LYS cc_start: 0.8914 (tttp) cc_final: 0.8121 (pttm) REVERT: p 302 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8111 (pttt) REVERT: p 306 LYS cc_start: 0.8851 (tttt) cc_final: 0.8410 (mmmm) REVERT: I 2 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8380 (tptt) REVERT: q 102 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8619 (ttpt) REVERT: s 302 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8366 (mmtt) REVERT: a 6 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8075 (ttpp) REVERT: w 104 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7956 (tm-30) REVERT: z 105 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7925 (t80) REVERT: 2 105 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7440 (t80) REVERT: 6 204 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7698 (tm-30) REVERT: g 6 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8216 (ttmm) REVERT: EA 105 PHE cc_start: 0.8169 (t80) cc_final: 0.7818 (t80) REVERT: HA 105 PHE cc_start: 0.7686 (t80) cc_final: 0.7428 (t80) outliers start: 7 outliers final: 2 residues processed: 121 average time/residue: 0.1797 time to fit residues: 24.8807 Evaluate side-chains 122 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076416 restraints weight = 13546.880| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.33 r_work: 0.3144 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.059 6264 Z= 0.558 Angle : 0.872 7.823 8136 Z= 0.402 Chirality : 0.036 0.092 576 Planarity : 0.003 0.015 1080 Dihedral : 15.068 88.125 720 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.40 % Allowed : 26.62 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.70 (0.22), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.17), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.004 PHE b 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.56 ( 6264) covalent geometry : angle 0.87173 / 0.40 ( 8136) hydrogen bonds : bond 0.02928 / 1.62 ( 139) hydrogen bonds : angle 6.36723 / 3.61 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8932 (tttt) cc_final: 0.8588 (ttmt) REVERT: K 206 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8636 (ttmm) REVERT: L 304 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7638 (mm-30) REVERT: L 306 LYS cc_start: 0.8961 (tttt) cc_final: 0.8518 (mmmm) REVERT: B 2 LYS cc_start: 0.8929 (tttt) cc_final: 0.8464 (tttm) REVERT: N 204 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7616 (mt-10) REVERT: O 306 LYS cc_start: 0.9042 (tttt) cc_final: 0.8490 (ttmm) REVERT: C 2 LYS cc_start: 0.8884 (tttt) cc_final: 0.8391 (ttmm) REVERT: P 104 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7361 (mm-30) REVERT: Q 204 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 6 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8062 (mtmt) REVERT: S 106 LYS cc_start: 0.8533 (tptm) cc_final: 0.8208 (tptm) REVERT: U 306 LYS cc_start: 0.9057 (tttt) cc_final: 0.8557 (mtpp) REVERT: E 4 GLU cc_start: 0.7535 (mp0) cc_final: 0.5696 (mp0) REVERT: V 102 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8666 (mtmt) REVERT: V 106 LYS cc_start: 0.8612 (tptm) cc_final: 0.8015 (tptm) REVERT: W 204 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7780 (mt-10) REVERT: W 206 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8429 (ttmm) REVERT: X 302 LYS cc_start: 0.9105 (mtmt) cc_final: 0.8825 (ttpt) REVERT: X 306 LYS cc_start: 0.9063 (tttt) cc_final: 0.8471 (mmmm) REVERT: F 2 LYS cc_start: 0.9117 (tttt) cc_final: 0.8764 (tttp) REVERT: Y 106 LYS cc_start: 0.8604 (tptm) cc_final: 0.8168 (tptm) REVERT: Z 206 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8446 (ttmm) REVERT: j 304 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7855 (mm-30) REVERT: j 306 LYS cc_start: 0.9030 (tttt) cc_final: 0.8521 (mmmm) REVERT: G 4 GLU cc_start: 0.7838 (mp0) cc_final: 0.7463 (mp0) REVERT: G 6 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8376 (mtmt) REVERT: l 202 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8487 (ttmm) REVERT: l 206 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8451 (ttmm) REVERT: m 304 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7897 (mm-30) REVERT: m 306 LYS cc_start: 0.8833 (tttt) cc_final: 0.8363 (mmmm) REVERT: o 206 LYS cc_start: 0.5204 (OUTLIER) cc_final: 0.3215 (pptt) REVERT: p 306 LYS cc_start: 0.9032 (tttt) cc_final: 0.8535 (mmmm) REVERT: I 2 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8580 (tptt) REVERT: s 302 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8290 (mmtt) REVERT: a 6 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8120 (ttmm) REVERT: t 103 PHE cc_start: 0.8468 (t80) cc_final: 0.8180 (t80) REVERT: y 302 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7886 (tptp) REVERT: 0 204 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7411 (tm-30) REVERT: 2 105 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7501 (t80) REVERT: 6 204 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7516 (tm-30) REVERT: HA 105 PHE cc_start: 0.7890 (t80) cc_final: 0.7535 (t80) REVERT: IA 204 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7429 (tm-30) REVERT: JA 302 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8092 (tptp) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.1807 time to fit residues: 27.3110 Evaluate side-chains 136 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 307 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain JA residue 302 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.092804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080040 restraints weight = 13085.810| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.33 r_work: 0.3240 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6264 Z= 0.126 Angle : 0.626 8.202 8136 Z= 0.285 Chirality : 0.028 0.091 576 Planarity : 0.002 0.011 1080 Dihedral : 14.263 85.488 720 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.55 % Allowed : 28.01 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.32 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE b 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6264) covalent geometry : angle 0.62623 / 0.29 ( 8136) hydrogen bonds : bond 0.01761 / 0.98 ( 139) hydrogen bonds : angle 5.58559 / 3.17 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 202 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8497 (ttmt) REVERT: L 304 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7749 (mm-30) REVERT: L 306 LYS cc_start: 0.8898 (tttt) cc_final: 0.8457 (mmmm) REVERT: B 2 LYS cc_start: 0.8801 (tttt) cc_final: 0.8349 (tttp) REVERT: M 102 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8536 (ttpt) REVERT: M 106 LYS cc_start: 0.8650 (tptm) cc_final: 0.8284 (tptm) REVERT: N 204 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7571 (mt-10) REVERT: O 306 LYS cc_start: 0.9007 (tttt) cc_final: 0.8481 (mtpp) REVERT: C 2 LYS cc_start: 0.8603 (tttt) cc_final: 0.8236 (ttmm) REVERT: P 104 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7378 (mm-30) REVERT: P 106 LYS cc_start: 0.8737 (tptt) cc_final: 0.8353 (mptt) REVERT: Q 204 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7819 (mt-10) REVERT: S 102 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8858 (ttpt) REVERT: S 106 LYS cc_start: 0.8466 (tptm) cc_final: 0.8155 (tptm) REVERT: U 306 LYS cc_start: 0.8979 (tttt) cc_final: 0.8611 (mmmm) REVERT: E 4 GLU cc_start: 0.7555 (mp0) cc_final: 0.5876 (mp0) REVERT: V 102 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8720 (ttmt) REVERT: V 106 LYS cc_start: 0.8568 (tptm) cc_final: 0.7986 (tptm) REVERT: W 204 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7735 (mt-10) REVERT: W 206 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8446 (ttmm) REVERT: X 302 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8798 (ttpt) REVERT: X 306 LYS cc_start: 0.8966 (tttt) cc_final: 0.8245 (mmmm) REVERT: Y 106 LYS cc_start: 0.8572 (tptm) cc_final: 0.7939 (tptm) REVERT: Z 202 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8898 (ttmt) REVERT: Z 206 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8491 (ttmm) REVERT: j 304 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7853 (mm-30) REVERT: j 306 LYS cc_start: 0.8965 (tttt) cc_final: 0.8508 (mmmm) REVERT: G 4 GLU cc_start: 0.7882 (mp0) cc_final: 0.7427 (mp0) REVERT: l 202 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8475 (ttmt) REVERT: l 206 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8300 (ttmm) REVERT: m 304 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7953 (mm-30) REVERT: m 306 LYS cc_start: 0.8785 (tttt) cc_final: 0.8305 (mmmm) REVERT: H 4 GLU cc_start: 0.4947 (OUTLIER) cc_final: 0.4634 (pm20) REVERT: n 106 LYS cc_start: 0.8745 (tptm) cc_final: 0.8296 (tptm) REVERT: o 202 LYS cc_start: 0.8975 (tttp) cc_final: 0.8213 (pttm) REVERT: o 206 LYS cc_start: 0.5484 (OUTLIER) cc_final: 0.3743 (pptt) REVERT: p 302 LYS cc_start: 0.8910 (mtpt) cc_final: 0.7984 (pttt) REVERT: p 306 LYS cc_start: 0.8848 (tttt) cc_final: 0.8447 (mmmm) REVERT: I 2 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8460 (tptt) REVERT: I 4 GLU cc_start: 0.8400 (mp0) cc_final: 0.7909 (mp0) REVERT: q 102 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8792 (ttmt) REVERT: s 302 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8173 (tptt) REVERT: a 6 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8057 (ttpp) REVERT: w 104 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7929 (tm-30) REVERT: y 302 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7702 (tptp) REVERT: z 105 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7932 (t80) REVERT: 2 105 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7264 (t80) REVERT: 6 204 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7688 (tm-30) REVERT: EA 104 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7648 (tm-30) REVERT: EA 105 PHE cc_start: 0.8029 (t80) cc_final: 0.7672 (t80) REVERT: i 3 PHE cc_start: 0.8975 (t80) cc_final: 0.8622 (t80) REVERT: HA 105 PHE cc_start: 0.7749 (t80) cc_final: 0.7436 (t80) outliers start: 11 outliers final: 3 residues processed: 126 average time/residue: 0.1701 time to fit residues: 24.5806 Evaluate side-chains 128 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain BA residue 105 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075396 restraints weight = 13772.093| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.35 r_work: 0.3128 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.074 6264 Z= 0.696 Angle : 0.964 7.638 8136 Z= 0.445 Chirality : 0.043 0.111 576 Planarity : 0.004 0.016 1080 Dihedral : 14.858 88.058 720 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.94 % Allowed : 26.16 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.23), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.17), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.004 PHEHA 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01583 / 0.70 ( 6264) covalent geometry : angle 0.96375 / 0.45 ( 8136) hydrogen bonds : bond 0.03477 / 1.94 ( 139) hydrogen bonds : angle 6.58825 / 3.75 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8903 (tttt) cc_final: 0.8647 (tttp) REVERT: K 206 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8735 (ttmm) REVERT: L 304 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7649 (mm-30) REVERT: L 306 LYS cc_start: 0.9003 (tttt) cc_final: 0.8550 (mmmm) REVERT: B 2 LYS cc_start: 0.8956 (tttt) cc_final: 0.8575 (tttp) REVERT: M 102 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8679 (ttpt) REVERT: N 204 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7564 (mt-10) REVERT: O 306 LYS cc_start: 0.9036 (tttt) cc_final: 0.8735 (mmmm) REVERT: C 2 LYS cc_start: 0.8877 (tttt) cc_final: 0.8366 (ttmm) REVERT: P 104 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7411 (mm-30) REVERT: Q 204 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7722 (mt-10) REVERT: D 6 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8093 (mtmt) REVERT: S 106 LYS cc_start: 0.8575 (tptm) cc_final: 0.8215 (tptm) REVERT: U 306 LYS cc_start: 0.9106 (tttt) cc_final: 0.8559 (mtpp) REVERT: E 4 GLU cc_start: 0.7509 (mp0) cc_final: 0.5730 (mp0) REVERT: V 106 LYS cc_start: 0.8604 (tptm) cc_final: 0.8038 (tptm) REVERT: W 204 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7761 (mt-10) REVERT: W 206 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8428 (ttmm) REVERT: X 302 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8848 (ttpt) REVERT: X 306 LYS cc_start: 0.9096 (tttt) cc_final: 0.8496 (mmmm) REVERT: F 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8842 (tttp) REVERT: Y 106 LYS cc_start: 0.8626 (tptm) cc_final: 0.8114 (tptm) REVERT: Z 206 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8471 (ttmm) REVERT: j 304 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7905 (mm-30) REVERT: j 306 LYS cc_start: 0.9081 (tttt) cc_final: 0.8578 (mmmm) REVERT: G 4 GLU cc_start: 0.7904 (mp0) cc_final: 0.7588 (mp0) REVERT: G 6 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8403 (mtmt) REVERT: l 202 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8541 (ttmm) REVERT: l 206 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8438 (ttmm) REVERT: m 304 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7902 (mm-30) REVERT: m 306 LYS cc_start: 0.8869 (tttt) cc_final: 0.8354 (mmmm) REVERT: H 2 LYS cc_start: 0.9209 (tptm) cc_final: 0.9004 (tptt) REVERT: H 4 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5481 (pm20) REVERT: o 206 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3006 (pptt) REVERT: p 306 LYS cc_start: 0.9081 (tttt) cc_final: 0.8595 (mmmm) REVERT: I 4 GLU cc_start: 0.8402 (mp0) cc_final: 0.7820 (mp0) REVERT: s 302 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8276 (mmtt) REVERT: a 6 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8161 (ttmm) REVERT: y 302 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7912 (tptp) REVERT: 0 204 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7442 (tm-30) REVERT: 2 105 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7305 (t80) REVERT: 2 106 LYS cc_start: 0.8379 (tttp) cc_final: 0.8124 (tttm) REVERT: 3 204 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7000 (tm-30) REVERT: 4 305 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7113 (t80) REVERT: 6 204 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7547 (tm-30) REVERT: EA 105 PHE cc_start: 0.8150 (t80) cc_final: 0.7928 (t80) REVERT: IA 204 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7435 (tm-30) REVERT: JA 302 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8089 (tptp) outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 0.1716 time to fit residues: 25.8648 Evaluate side-chains 139 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 307 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain JA residue 302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.092617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.079688 restraints weight = 13034.803| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.36 r_work: 0.3242 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6264 Z= 0.134 Angle : 0.644 8.303 8136 Z= 0.295 Chirality : 0.028 0.103 576 Planarity : 0.002 0.011 1080 Dihedral : 14.062 86.171 720 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.85 % Allowed : 27.55 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.37 (0.24), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.18), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE t 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6264) covalent geometry : angle 0.64362 / 0.29 ( 8136) hydrogen bonds : bond 0.01897 / 1.07 ( 139) hydrogen bonds : angle 5.61756 / 3.21 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8846 (tttt) cc_final: 0.8605 (tttt) REVERT: K 206 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8619 (ttmm) REVERT: L 302 LYS cc_start: 0.8876 (tttt) cc_final: 0.8657 (tttt) REVERT: L 304 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7664 (mm-30) REVERT: L 306 LYS cc_start: 0.8901 (tttt) cc_final: 0.8451 (mmmm) REVERT: B 2 LYS cc_start: 0.8805 (tttt) cc_final: 0.8331 (tttp) REVERT: M 106 LYS cc_start: 0.8711 (tptm) cc_final: 0.8349 (tptm) REVERT: N 204 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7584 (mt-10) REVERT: O 306 LYS cc_start: 0.8984 (tttt) cc_final: 0.8672 (mmmm) REVERT: C 2 LYS cc_start: 0.8534 (tttt) cc_final: 0.8081 (tttt) REVERT: P 104 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7392 (mm-30) REVERT: P 106 LYS cc_start: 0.8679 (tptt) cc_final: 0.8182 (mptt) REVERT: Q 204 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7766 (mt-10) REVERT: S 102 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8567 (ttpp) REVERT: S 106 LYS cc_start: 0.8447 (tptm) cc_final: 0.8138 (tptm) REVERT: T 202 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8702 (tppt) REVERT: U 306 LYS cc_start: 0.8965 (tttt) cc_final: 0.8461 (mmmm) REVERT: E 4 GLU cc_start: 0.7489 (mp0) cc_final: 0.5700 (mp0) REVERT: V 102 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8784 (ttmt) REVERT: V 106 LYS cc_start: 0.8577 (tptm) cc_final: 0.7987 (tptm) REVERT: W 202 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8871 (tttp) REVERT: W 204 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7753 (mt-10) REVERT: W 206 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8405 (ttmm) REVERT: X 302 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8750 (ttpt) REVERT: X 306 LYS cc_start: 0.8953 (tttt) cc_final: 0.8204 (mmmm) REVERT: F 6 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8314 (mtmt) REVERT: Y 106 LYS cc_start: 0.8552 (tptm) cc_final: 0.8176 (tptm) REVERT: Z 202 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8896 (ttmt) REVERT: Z 206 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8488 (ttmm) REVERT: j 304 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7882 (mm-30) REVERT: j 306 LYS cc_start: 0.8987 (tttt) cc_final: 0.8507 (mmmm) REVERT: G 4 GLU cc_start: 0.7929 (mp0) cc_final: 0.7436 (mp0) REVERT: G 6 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8270 (mtmt) REVERT: l 202 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8571 (ttmt) REVERT: l 206 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8334 (ttmm) REVERT: m 304 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7860 (mm-30) REVERT: m 306 LYS cc_start: 0.8768 (tttt) cc_final: 0.8286 (mmmm) REVERT: H 2 LYS cc_start: 0.9009 (tptm) cc_final: 0.8792 (tptt) REVERT: H 4 GLU cc_start: 0.4959 (OUTLIER) cc_final: 0.4631 (pm20) REVERT: n 106 LYS cc_start: 0.8749 (tptm) cc_final: 0.8346 (tptm) REVERT: o 202 LYS cc_start: 0.9111 (tttm) cc_final: 0.8244 (pttm) REVERT: o 206 LYS cc_start: 0.4955 (OUTLIER) cc_final: 0.3436 (pptt) REVERT: p 302 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8067 (pttt) REVERT: p 306 LYS cc_start: 0.8909 (tttt) cc_final: 0.8524 (mmmm) REVERT: I 4 GLU cc_start: 0.8377 (mp0) cc_final: 0.7945 (mp0) REVERT: s 302 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8138 (tptt) REVERT: a 6 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8104 (ttpp) REVERT: w 104 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8046 (tm-30) REVERT: y 302 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7758 (tptp) REVERT: z 105 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8094 (t80) REVERT: 2 105 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7264 (t80) REVERT: 6 204 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7600 (tm-30) REVERT: EA 104 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7847 (tm-30) REVERT: EA 105 PHE cc_start: 0.8046 (t80) cc_final: 0.7631 (t80) outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 0.1705 time to fit residues: 24.1790 Evaluate side-chains 125 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain t residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain BA residue 105 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076464 restraints weight = 13612.920| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.38 r_work: 0.3145 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.056 6264 Z= 0.559 Angle : 0.872 7.715 8136 Z= 0.402 Chirality : 0.037 0.104 576 Planarity : 0.003 0.013 1080 Dihedral : 14.438 87.732 720 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.01 % Allowed : 26.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.70 (0.23), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.17), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.004 PHEGA 305 Details of bonding type rmsd/Z covalent geometry : bond 0.01272 / 0.56 ( 6264) covalent geometry : angle 0.87157 / 0.40 ( 8136) hydrogen bonds : bond 0.02935 / 1.64 ( 139) hydrogen bonds : angle 6.29788 / 3.58 ( 393) =============================================================================== Job complete usr+sys time: 1199.92 seconds wall clock time: 21 minutes 24.86 seconds (1284.86 seconds total)