Starting phenix.real_space_refine on Thu Sep 26 04:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqg_23485/09_2024/7lqg_23485.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 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 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 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: "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: "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: "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: "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: "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: "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: "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: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "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: "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: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "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: "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: "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: "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: "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 Chain: "KA" 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: "LA" 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: "MA" 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: "NA" 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: "OA" 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: "PA" 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: "QA" 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: "RA" 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: "SA" 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: "TA" 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: "UA" 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: "VA" 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: "WA" 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: "XA" 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: "YA" 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: "ZA" 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: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 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: "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: "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: "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 Chain: "kA" 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: "lA" 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: "mA" 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: "nA" 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: "oA" 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: "pA" 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: "qA" 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: "rA" 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: "sA" 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: "tA" 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: "uA" 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: "vA" 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: "wA" 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: "xA" 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: "yA" 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: "zA" 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: "0A" 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: "1A" 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: "2A" 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: "3A" 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: "4A" 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: "5A" 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: "6A" 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: "7A" 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: "8A" 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: "9A" 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: "AB" 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: "BB" 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: "CB" 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: "DB" 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: "EB" 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: "FB" 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: "GB" 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: "HB" 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: "IB" 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: "JB" 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: "KB" 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: "LB" 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: "MB" 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: "NB" 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: "OB" 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: "PB" 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: "QB" 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: "RB" 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: "SB" 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: "TB" 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: 7.81, per 1000 atoms: 0.65 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 108, 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 1872 8.00 N 1584 7.00 C 8640 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 652.6 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 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 'M' and resid 1006 through 1007 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'T' and resid 1006 through 1007 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'j' and resid 1006 through 1007 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'q' and resid 1006 through 1007 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'x' and resid 1006 through 1007 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain '4' and resid 1006 through 1007 Processing sheet with id=AB4, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'BA' and resid 1006 through 1007 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'IA' and resid 1006 through 1007 Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB9, first strand: chain 'PA' and resid 1006 through 1007 Processing sheet with id=AC1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.536A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE f 5 " --> pdb=" O PHE2A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEoA 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHEoA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEaA 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 5 " --> pdb=" O PHEaA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHETA 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 5 " --> pdb=" O PHETA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEhA 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHEhA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEvA 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHEvA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE9A 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHE9A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHENB 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE i 5 " --> pdb=" O PHENB 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSIB 302 " --> pdb=" O GMA3A 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS3A 206 " --> pdb=" O GLUIB 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAIB 308 " --> pdb=" O LYS3A 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS4A 302 " --> pdb=" O GMApA 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSpA 206 " --> pdb=" O GLU4A 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSqA 302 " --> pdb=" O GMAbA 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSbA 206 " --> pdb=" O GLUqA 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYScA 302 " --> pdb=" O GMAUA 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSUA 206 " --> pdb=" O GLUcA 304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAcA 308 " --> pdb=" O LYSUA 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSVA 302 " --> pdb=" O GMAiA 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSiA 206 " --> pdb=" O GLUVA 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAVA 308 " --> pdb=" O LYSiA 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSjA 302 " --> pdb=" O GMAwA 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSwA 206 " --> pdb=" O GLUjA 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSxA 302 " --> pdb=" O GMAAB 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 206 " --> pdb=" O GLUxA 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMAxA 308 " --> pdb=" O LYSAB 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSBB 302 " --> pdb=" O GMAOB 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSOB 206 " --> pdb=" O GLUBB 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'JB' and resid 1002 through 1006 removed outlier: 3.536A pdb=" N PHEKB1105 " --> pdb=" O PHEJB1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEJB1005 " --> pdb=" O PHEKB1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE6A1105 " --> pdb=" O PHE5A1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE5A1005 " --> pdb=" O PHE6A1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEsA1105 " --> pdb=" O PHErA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHErA1005 " --> pdb=" O PHEsA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEeA1105 " --> pdb=" O PHEdA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEdA1005 " --> pdb=" O PHEeA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEXA1105 " --> pdb=" O PHEWA1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEWA1005 " --> pdb=" O PHEXA1103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHElA1105 " --> pdb=" O PHEkA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEkA1005 " --> pdb=" O PHElA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEzA1105 " --> pdb=" O PHEyA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEyA1005 " --> pdb=" O PHEzA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDB1105 " --> pdb=" O PHECB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHECB1005 " --> pdb=" O PHEDB1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHERB1105 " --> pdb=" O PHEQB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEQB1005 " --> pdb=" O PHERB1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N LYSMB1302 " --> pdb=" O GMA7A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS7A1206 " --> pdb=" O GLUMB1304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAMB1308 " --> pdb=" O LYS7A1202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS8A1302 " --> pdb=" O GMAtA1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYStA1206 " --> pdb=" O GLU8A1304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSuA1302 " --> pdb=" O GMAfA1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSfA1206 " --> pdb=" O GLUuA1304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSgA1302 " --> pdb=" O GMAYA1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSYA1206 " --> pdb=" O GLUgA1304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAgA1308 " --> pdb=" O LYSYA1202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSZA1302 " --> pdb=" O GMAmA1208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSmA1206 " --> pdb=" O GLUZA1304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAZA1308 " --> pdb=" O LYSmA1202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSnA1302 " --> pdb=" O GMA0A1208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS0A1206 " --> pdb=" O GLUnA1304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS1A1302 " --> pdb=" O GMAEB1208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSEB1206 " --> pdb=" O GLU1A1304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA1A1308 " --> pdb=" O LYSEB1202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSFB1302 " --> pdb=" O GMASB1208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSB1206 " --> pdb=" O GLUFB1304 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 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: 3.39 Time building geometry restraints manager: 3.61 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: 1530 1.26 - 1.33: 1350 1.33 - 1.41: 3600 1.41 - 1.48: 1300 1.48 - 1.56: 4748 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 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 3.46e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CRQB1001 " pdb=" CAL 5CRQB1001 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14236 1.98 - 3.95: 1586 3.95 - 5.93: 324 5.93 - 7.91: 108 7.91 - 9.88: 18 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " pdb=" CAA 5CR i 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4840 15.26 - 30.52: 794 30.52 - 45.78: 342 45.78 - 61.04: 198 61.04 - 76.30: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 8 106 " pdb=" CB LYS 8 106 " pdb=" CG LYS 8 106 " pdb=" CD LYS 8 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.30 58.70 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 404 0.018 - 0.036: 326 0.036 - 0.054: 308 0.054 - 0.072: 88 0.072 - 0.090: 26 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS l1202 " pdb=" N LYS l1202 " pdb=" C LYS l1202 " pdb=" CB LYS l1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHESB1205 " -0.008 2.00e-02 2.50e+03 6.92e-03 8.39e-01 pdb=" CG PHESB1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHESB1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHESB1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESB1205 " -0.002 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 48 2.45 - 3.07: 6870 3.07 - 3.68: 18066 3.68 - 4.29: 29438 4.29 - 4.90: 49356 Nonbonded interactions: 103778 Sorted by model distance: nonbonded pdb=" CD LYS A 2 " pdb=" OE2 GMADA1208 " model vdw 1.842 2.752 nonbonded pdb=" CD LYS M1002 " pdb=" OE2 GMA 9 208 " model vdw 1.842 2.752 nonbonded pdb=" OE2 GMA V1208 " pdb=" CD LYS H 2 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA R 208 " pdb=" CD LYSIA1002 " model vdw 1.868 2.752 nonbonded pdb=" OE2 GMA l1208 " pdb=" NZ LYS D 2 " model vdw 1.870 2.496 ... (remaining 103773 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 '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' 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 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.760 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.210 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 12528 Z= 0.894 Angle : 1.417 9.883 16272 Z= 0.592 Chirality : 0.035 0.090 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.303 3888 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 31.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 502 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7489 (mp0) cc_final: 0.6990 (pm20) REVERT: A 6 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7960 (mtmt) REVERT: M 1004 GLU cc_start: 0.7511 (mp0) cc_final: 0.7009 (pm20) REVERT: M 1006 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7962 (mtmt) REVERT: P 1302 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8557 (ttmm) REVERT: B 4 GLU cc_start: 0.7387 (mp0) cc_final: 0.6353 (pm20) REVERT: T 1004 GLU cc_start: 0.7416 (mp0) cc_final: 0.6368 (pm20) REVERT: W 1302 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: C 6 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8165 (mtmt) REVERT: Z 306 LYS cc_start: 0.8670 (tttt) cc_final: 0.8389 (tttt) REVERT: j 1006 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8135 (mtmt) REVERT: m 1306 LYS cc_start: 0.8682 (tttt) cc_final: 0.8400 (tttt) REVERT: n 104 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6300 (mm-30) REVERT: p 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8460 (tttt) REVERT: r 1104 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6343 (mm-30) REVERT: t 1306 LYS cc_start: 0.8723 (tttt) cc_final: 0.8465 (tttt) REVERT: E 4 GLU cc_start: 0.7451 (mp0) cc_final: 0.7098 (mp0) REVERT: E 6 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8101 (mtmt) REVERT: u 102 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: u 104 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7138 (mm-30) REVERT: w 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7102 (mm-30) REVERT: w 306 LYS cc_start: 0.8688 (tttt) cc_final: 0.8359 (tttt) REVERT: x 1004 GLU cc_start: 0.7477 (mp0) cc_final: 0.7137 (mp0) REVERT: x 1006 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8120 (mtmt) REVERT: y 1102 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: y 1104 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7164 (mm-30) REVERT: z 1202 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8300 (mtpt) REVERT: 0 1302 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (ttmm) REVERT: 0 1304 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7083 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8386 (tttt) REVERT: F 4 GLU cc_start: 0.7394 (mp0) cc_final: 0.6855 (pm20) REVERT: 2 206 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8190 (ttmm) REVERT: 3 306 LYS cc_start: 0.8751 (tttt) cc_final: 0.8443 (tttt) REVERT: 4 1004 GLU cc_start: 0.7422 (mp0) cc_final: 0.6862 (pm20) REVERT: 6 1206 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8193 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8423 (tttt) REVERT: G 4 GLU cc_start: 0.7500 (mp0) cc_final: 0.6448 (mp0) REVERT: 9 202 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8271 (mtpt) REVERT: 9 204 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6821 (mt-10) REVERT: AA 306 LYS cc_start: 0.8758 (tttt) cc_final: 0.8472 (tttt) REVERT: BA 1004 GLU cc_start: 0.7518 (mp0) cc_final: 0.6466 (mp0) REVERT: DA 1202 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8302 (mtpt) REVERT: DA 1204 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6823 (mt-10) REVERT: EA 1302 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8628 (ttmm) REVERT: EA 1304 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6981 (mm-30) REVERT: EA 1306 LYS cc_start: 0.8759 (tttt) cc_final: 0.8463 (tttt) REVERT: I 4 GLU cc_start: 0.7640 (mp0) cc_final: 0.7418 (mp0) REVERT: OA 306 LYS cc_start: 0.8620 (tttt) cc_final: 0.8202 (tttt) REVERT: RA 1204 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7135 (mt-10) REVERT: SA 1306 LYS cc_start: 0.8631 (tttt) cc_final: 0.8225 (tttt) REVERT: a 3 PHE cc_start: 0.9235 (t80) cc_final: 0.9009 (t80) REVERT: a 5 PHE cc_start: 0.9036 (t80) cc_final: 0.8632 (t80) REVERT: a 7 PHE cc_start: 0.9251 (t80) cc_final: 0.8950 (t80) REVERT: TA 103 PHE cc_start: 0.9011 (t80) cc_final: 0.8762 (t80) REVERT: TA 107 PHE cc_start: 0.8855 (t80) cc_final: 0.8646 (t80) REVERT: UA 202 LYS cc_start: 0.8743 (tttm) cc_final: 0.8497 (mmmm) REVERT: UA 206 LYS cc_start: 0.8907 (tttt) cc_final: 0.8690 (tttt) REVERT: VA 304 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8172 (tm-30) REVERT: WA 1003 PHE cc_start: 0.9235 (t80) cc_final: 0.9018 (t80) REVERT: WA 1005 PHE cc_start: 0.9054 (t80) cc_final: 0.8645 (t80) REVERT: WA 1007 PHE cc_start: 0.9255 (t80) cc_final: 0.8980 (t80) REVERT: XA 1103 PHE cc_start: 0.8981 (t80) cc_final: 0.8746 (t80) REVERT: XA 1107 PHE cc_start: 0.8879 (t80) cc_final: 0.8668 (t80) REVERT: YA 1202 LYS cc_start: 0.8721 (tttm) cc_final: 0.8423 (tttm) REVERT: YA 1206 LYS cc_start: 0.8893 (tttt) cc_final: 0.8671 (tttt) REVERT: ZA 1304 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8173 (tm-30) REVERT: bA 202 LYS cc_start: 0.8657 (tttm) cc_final: 0.8266 (mmmm) REVERT: fA 1202 LYS cc_start: 0.8629 (tttm) cc_final: 0.8364 (tttm) REVERT: hA 103 PHE cc_start: 0.8994 (t80) cc_final: 0.8567 (t80) REVERT: hA 107 PHE cc_start: 0.8728 (t80) cc_final: 0.8372 (t80) REVERT: iA 202 LYS cc_start: 0.8724 (tttm) cc_final: 0.8388 (ttmm) REVERT: iA 204 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6966 (tm-30) REVERT: iA 206 LYS cc_start: 0.8950 (tttt) cc_final: 0.8476 (tttm) REVERT: jA 305 PHE cc_start: 0.8812 (t80) cc_final: 0.8586 (t80) REVERT: lA 1103 PHE cc_start: 0.8962 (t80) cc_final: 0.8549 (t80) REVERT: lA 1107 PHE cc_start: 0.8750 (t80) cc_final: 0.8441 (t80) REVERT: mA 1204 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6925 (tm-30) REVERT: mA 1206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8409 (tttt) REVERT: nA 1305 PHE cc_start: 0.8820 (t80) cc_final: 0.8601 (t80) REVERT: d 5 PHE cc_start: 0.9042 (t80) cc_final: 0.8631 (t80) REVERT: oA 103 PHE cc_start: 0.9060 (t80) cc_final: 0.8390 (t80) REVERT: pA 202 LYS cc_start: 0.8764 (tttm) cc_final: 0.8397 (mmmm) REVERT: pA 206 LYS cc_start: 0.8962 (tttt) cc_final: 0.8485 (tttt) REVERT: rA 1005 PHE cc_start: 0.9060 (t80) cc_final: 0.8811 (t80) REVERT: sA 1103 PHE cc_start: 0.9029 (t80) cc_final: 0.8378 (t80) REVERT: tA 1202 LYS cc_start: 0.8745 (tttm) cc_final: 0.8479 (tttm) REVERT: tA 1206 LYS cc_start: 0.8945 (tttt) cc_final: 0.8470 (tttt) REVERT: e 5 PHE cc_start: 0.9202 (t80) cc_final: 0.8927 (t80) REVERT: wA 202 LYS cc_start: 0.8607 (tttm) cc_final: 0.8262 (tppp) REVERT: wA 206 LYS cc_start: 0.8849 (tttt) cc_final: 0.8513 (tttm) REVERT: xA 303 PHE cc_start: 0.8785 (t80) cc_final: 0.8524 (t80) REVERT: xA 305 PHE cc_start: 0.8647 (t80) cc_final: 0.8384 (t80) REVERT: yA 1005 PHE cc_start: 0.9221 (t80) cc_final: 0.8952 (t80) REVERT: 1A 1303 PHE cc_start: 0.8787 (t80) cc_final: 0.8526 (t80) REVERT: 1A 1305 PHE cc_start: 0.8655 (t80) cc_final: 0.8381 (t80) REVERT: f 3 PHE cc_start: 0.9281 (t80) cc_final: 0.9054 (t80) REVERT: f 7 PHE cc_start: 0.9110 (t80) cc_final: 0.8576 (t80) REVERT: 2A 102 LYS cc_start: 0.8748 (tptm) cc_final: 0.8306 (tptm) REVERT: 2A 106 LYS cc_start: 0.8921 (tttp) cc_final: 0.8703 (tttp) REVERT: 2A 107 PHE cc_start: 0.8737 (t80) cc_final: 0.8278 (t80) REVERT: 3A 202 LYS cc_start: 0.8895 (tttm) cc_final: 0.8665 (tttm) REVERT: 3A 206 LYS cc_start: 0.8908 (tttt) cc_final: 0.8676 (tttm) REVERT: 4A 304 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8244 (tm-30) REVERT: 5A 1003 PHE cc_start: 0.9280 (t80) cc_final: 0.9058 (t80) REVERT: 5A 1007 PHE cc_start: 0.9117 (t80) cc_final: 0.8615 (t80) REVERT: 6A 1102 LYS cc_start: 0.8733 (tptm) cc_final: 0.8313 (tptm) REVERT: 6A 1106 LYS cc_start: 0.8924 (tttp) cc_final: 0.8702 (tttp) REVERT: 6A 1107 PHE cc_start: 0.8759 (t80) cc_final: 0.8326 (t80) REVERT: 7A 1202 LYS cc_start: 0.8870 (tttm) cc_final: 0.8637 (tttm) REVERT: 8A 1304 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8244 (tm-30) REVERT: g 7 PHE cc_start: 0.9090 (t80) cc_final: 0.8841 (t80) REVERT: 9A 102 LYS cc_start: 0.8870 (tptm) cc_final: 0.8366 (tptm) REVERT: 9A 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8562 (tttm) REVERT: 9A 107 PHE cc_start: 0.8870 (t80) cc_final: 0.8327 (t80) REVERT: AB 202 LYS cc_start: 0.8868 (tttm) cc_final: 0.8520 (mtpp) REVERT: AB 206 LYS cc_start: 0.8933 (tttt) cc_final: 0.8727 (tttm) REVERT: BB 304 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8195 (tm-30) REVERT: BB 306 LYS cc_start: 0.8697 (tptp) cc_final: 0.8278 (tptp) REVERT: CB 1003 PHE cc_start: 0.9292 (t80) cc_final: 0.9085 (t80) REVERT: CB 1005 PHE cc_start: 0.9156 (t80) cc_final: 0.8841 (t80) REVERT: CB 1007 PHE cc_start: 0.9095 (t80) cc_final: 0.8865 (t80) REVERT: DB 1106 LYS cc_start: 0.8873 (tttp) cc_final: 0.8662 (tttp) REVERT: DB 1107 PHE cc_start: 0.8889 (t80) cc_final: 0.8278 (t80) REVERT: FB 1304 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8168 (tm-30) REVERT: FB 1306 LYS cc_start: 0.8682 (tptp) cc_final: 0.8280 (tptp) REVERT: GB 102 LYS cc_start: 0.8922 (tptm) cc_final: 0.8611 (tptm) REVERT: GB 106 LYS cc_start: 0.8740 (tttp) cc_final: 0.8378 (tttm) REVERT: HB 202 LYS cc_start: 0.8580 (tttm) cc_final: 0.8274 (mmmm) REVERT: IB 303 PHE cc_start: 0.8740 (t80) cc_final: 0.8458 (t80) REVERT: IB 304 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8502 (tm-30) REVERT: IB 306 LYS cc_start: 0.8770 (tptp) cc_final: 0.8563 (tptp) REVERT: KB 1102 LYS cc_start: 0.8919 (tptm) cc_final: 0.8618 (tptm) REVERT: MB 1303 PHE cc_start: 0.8741 (t80) cc_final: 0.8454 (t80) REVERT: MB 1306 LYS cc_start: 0.8749 (tptp) cc_final: 0.8547 (tptp) REVERT: OB 204 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7337 (tm-30) REVERT: OB 206 LYS cc_start: 0.8959 (tttt) cc_final: 0.8503 (tttt) REVERT: PB 305 PHE cc_start: 0.8500 (t80) cc_final: 0.8208 (t80) REVERT: PB 307 PHE cc_start: 0.8157 (t80) cc_final: 0.7803 (t80) REVERT: SB 1204 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7295 (tm-30) REVERT: SB 1206 LYS cc_start: 0.8938 (tttt) cc_final: 0.8487 (tttt) REVERT: TB 1305 PHE cc_start: 0.8512 (t80) cc_final: 0.8219 (t80) REVERT: TB 1307 PHE cc_start: 0.8172 (t80) cc_final: 0.7811 (t80) outliers start: 126 outliers final: 85 residues processed: 528 average time/residue: 0.4482 time to fit residues: 288.6141 Evaluate side-chains 583 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 492 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain P residue 1302 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain EA residue 1302 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 102 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.317 12528 Z= 5.977 Angle : 3.952 31.986 16272 Z= 1.756 Chirality : 0.299 0.846 1152 Planarity : 0.018 0.055 2160 Dihedral : 21.237 78.266 1786 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 102.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.72 % Favored : 86.28 % Rotamer: Outliers : 13.66 % Allowed : 20.25 % Favored : 66.09 % Cbeta Deviations : 12.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.117 0.018 PHE G 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 447 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 106 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8493 (mmmm) REVERT: K 204 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7922 (mt-10) REVERT: N 1106 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8484 (mmmm) REVERT: O 1204 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8019 (mt-10) REVERT: P 1304 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8164 (mm-30) REVERT: B 6 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8632 (mtmt) REVERT: Q 106 LYS cc_start: 0.8823 (tptm) cc_final: 0.8545 (tptm) REVERT: R 202 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8897 (mtpt) REVERT: R 204 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7552 (mt-10) REVERT: T 1006 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8594 (mtmt) REVERT: U 1106 LYS cc_start: 0.8822 (tptm) cc_final: 0.8454 (tptm) REVERT: V 1202 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8802 (mtpt) REVERT: V 1204 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7557 (mt-10) REVERT: W 1302 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8852 (ttmm) REVERT: C 6 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8627 (mtmt) REVERT: X 106 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8583 (mmmm) REVERT: j 1006 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8640 (mtmt) REVERT: k 1106 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8554 (mmmm) REVERT: l 1202 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8816 (mmmm) REVERT: m 1302 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8925 (ttpt) REVERT: m 1306 LYS cc_start: 0.9209 (tttt) cc_final: 0.8955 (mttt) REVERT: n 106 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8692 (mmmm) REVERT: o 202 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8610 (mmmm) REVERT: p 302 LYS cc_start: 0.9285 (ttpt) cc_final: 0.8715 (ttpp) REVERT: p 304 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7433 (mm-30) REVERT: r 1106 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8683 (mmmm) REVERT: s 1204 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7784 (mt-10) REVERT: s 1206 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8666 (ttmm) REVERT: t 1302 LYS cc_start: 0.9277 (ttpt) cc_final: 0.9022 (ttpp) REVERT: t 1304 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7470 (mm-30) REVERT: u 102 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8603 (ttmm) REVERT: u 104 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7622 (mm-30) REVERT: u 106 LYS cc_start: 0.9146 (tptm) cc_final: 0.8750 (tptm) REVERT: w 302 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8914 (ttmm) REVERT: x 1006 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8240 (mtmt) REVERT: y 1102 LYS cc_start: 0.9182 (ttpt) cc_final: 0.8593 (ttmm) REVERT: y 1104 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7631 (mm-30) REVERT: y 1106 LYS cc_start: 0.9069 (tptm) cc_final: 0.8654 (tptm) REVERT: 0 1302 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8932 (ttmm) REVERT: F 4 GLU cc_start: 0.8009 (mp0) cc_final: 0.7245 (mp0) REVERT: F 6 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8669 (mtmt) REVERT: 2 202 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8862 (mtpt) REVERT: 2 204 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7358 (mt-10) REVERT: 4 1004 GLU cc_start: 0.8047 (mp0) cc_final: 0.7296 (mp0) REVERT: 4 1006 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8683 (mtmt) REVERT: 6 1202 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8847 (mtpt) REVERT: G 6 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8546 (mtmt) REVERT: 8 106 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8366 (mmmm) REVERT: BA 1006 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8423 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: EA 1304 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7888 (mm-30) REVERT: EA 1306 LYS cc_start: 0.8988 (tttt) cc_final: 0.8735 (tttt) REVERT: FA 104 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7646 (mm-30) REVERT: FA 106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8660 (mmmm) REVERT: HA 304 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7356 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7653 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8671 (mmmm) REVERT: I 6 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8075 (mtmt) REVERT: MA 102 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8731 (mmtt) REVERT: NA 202 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8834 (mtpt) REVERT: OA 302 LYS cc_start: 0.9311 (ttpt) cc_final: 0.8821 (tptt) REVERT: OA 304 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8113 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8889 (mtmt) cc_final: 0.7986 (mtmt) REVERT: QA 1102 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8621 (tptt) REVERT: SA 1302 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8712 (mmmt) REVERT: SA 1304 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8104 (mm-30) REVERT: a 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8520 (tp30) REVERT: TA 102 LYS cc_start: 0.9210 (tptm) cc_final: 0.8986 (tptm) REVERT: TA 104 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8272 (tm-30) REVERT: UA 204 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7799 (tp30) REVERT: WA 1004 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8521 (tp30) REVERT: XA 1102 LYS cc_start: 0.9218 (tptm) cc_final: 0.9007 (tptm) REVERT: XA 1104 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8239 (tm-30) REVERT: YA 1204 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7533 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8298 (tm-30) REVERT: ZA 1307 PHE cc_start: 0.9304 (t80) cc_final: 0.9095 (t80) REVERT: b 2 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8845 (ttmt) REVERT: bA 202 LYS cc_start: 0.9233 (tttm) cc_final: 0.8921 (ttmm) REVERT: bA 204 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7851 (tm-30) REVERT: cA 304 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8214 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8854 (ttmt) REVERT: fA 1204 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7820 (tm-30) REVERT: gA 1304 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8182 (tm-30) REVERT: hA 102 LYS cc_start: 0.9360 (tptm) cc_final: 0.9119 (tptm) REVERT: hA 103 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9178 (t80) REVERT: iA 202 LYS cc_start: 0.9297 (tttm) cc_final: 0.8853 (ttmm) REVERT: iA 204 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7747 (tm-30) REVERT: iA 206 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9040 (tttt) REVERT: jA 306 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8529 (ttpp) REVERT: lA 1102 LYS cc_start: 0.9346 (tptm) cc_final: 0.9107 (tptm) REVERT: lA 1103 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.9169 (t80) REVERT: mA 1204 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7629 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8913 (tttm) REVERT: nA 1306 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: qA 304 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8217 (tm-30) REVERT: sA 1103 PHE cc_start: 0.9284 (t80) cc_final: 0.8895 (t80) REVERT: tA 1204 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8125 (tp30) REVERT: uA 1304 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8253 (tm-30) REVERT: e 4 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: vA 104 GLU cc_start: 0.8715 (tm-30) cc_final: 0.7820 (tm-30) REVERT: wA 202 LYS cc_start: 0.9240 (tttm) cc_final: 0.8703 (ttmm) REVERT: wA 204 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7764 (tm-30) REVERT: xA 302 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8730 (tptp) REVERT: xA 304 GLU cc_start: 0.9185 (tm-30) cc_final: 0.7907 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: zA 1102 LYS cc_start: 0.9278 (tptm) cc_final: 0.9043 (tptm) REVERT: 0A 1202 LYS cc_start: 0.9147 (tttm) cc_final: 0.8627 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7176 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8568 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9194 (tm-30) cc_final: 0.7931 (tm-30) REVERT: f 2 LYS cc_start: 0.9184 (ptpt) cc_final: 0.8975 (ptpt) REVERT: 8A 1304 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8524 (tm-30) REVERT: g 4 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: g 6 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8797 (ttpt) REVERT: 9A 102 LYS cc_start: 0.9292 (tptm) cc_final: 0.9017 (tptm) REVERT: 9A 106 LYS cc_start: 0.9107 (tttp) cc_final: 0.8795 (tttm) REVERT: AB 202 LYS cc_start: 0.9287 (tttm) cc_final: 0.8935 (ttmm) REVERT: AB 204 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7757 (tm-30) REVERT: BB 306 LYS cc_start: 0.9136 (tptp) cc_final: 0.8874 (tptp) REVERT: CB 1004 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8466 (tp30) REVERT: DB 1102 LYS cc_start: 0.9283 (tptm) cc_final: 0.9033 (tptm) REVERT: EB 1204 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7732 (tm-30) REVERT: FB 1306 LYS cc_start: 0.9131 (tptp) cc_final: 0.8913 (tptp) REVERT: h 4 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: GB 102 LYS cc_start: 0.9237 (tptm) cc_final: 0.8874 (tptm) REVERT: HB 202 LYS cc_start: 0.9278 (tttm) cc_final: 0.8874 (ttmm) REVERT: JB 1004 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: KB 1102 LYS cc_start: 0.9215 (tptm) cc_final: 0.8853 (tptm) REVERT: i 4 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7710 (tp30) REVERT: i 5 PHE cc_start: 0.9232 (t80) cc_final: 0.8541 (t80) REVERT: OB 204 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8046 (tm-30) REVERT: OB 206 LYS cc_start: 0.9239 (tttt) cc_final: 0.8959 (tttm) REVERT: PB 307 PHE cc_start: 0.9392 (t80) cc_final: 0.9126 (t80) REVERT: QB 1002 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8983 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9236 (t80) cc_final: 0.8855 (t80) REVERT: SB 1204 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8015 (tm-30) REVERT: TB 1307 PHE cc_start: 0.9391 (t80) cc_final: 0.9140 (t80) outliers start: 118 outliers final: 67 residues processed: 490 average time/residue: 0.4782 time to fit residues: 282.6156 Evaluate side-chains 539 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 447 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain m residue 1302 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.317 12528 Z= 5.989 Angle : 4.143 65.073 16272 Z= 1.827 Chirality : 0.298 0.851 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.532 89.142 1526 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 106.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 18.52 % Allowed : 22.34 % Favored : 59.14 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.99 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.105 0.018 PHE9A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 438 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7660 (mm-30) REVERT: J 106 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8520 (mmmm) REVERT: K 204 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8002 (mt-10) REVERT: N 1106 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8558 (mmmm) REVERT: O 1204 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7997 (mt-10) REVERT: P 1304 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 4 GLU cc_start: 0.8182 (mp0) cc_final: 0.7657 (mp0) REVERT: B 6 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8697 (mtmt) REVERT: Q 106 LYS cc_start: 0.8906 (tptm) cc_final: 0.8364 (tptm) REVERT: R 202 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8801 (mtpt) REVERT: S 302 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8906 (ttmm) REVERT: T 1004 GLU cc_start: 0.8284 (mp0) cc_final: 0.7627 (mp0) REVERT: T 1006 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8681 (mtmt) REVERT: U 1106 LYS cc_start: 0.8895 (tptm) cc_final: 0.8360 (tptm) REVERT: V 1202 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8836 (mtpt) REVERT: W 1302 LYS cc_start: 0.9281 (ttpt) cc_final: 0.8896 (ttmm) REVERT: C 4 GLU cc_start: 0.7463 (mp0) cc_final: 0.6844 (mp0) REVERT: C 6 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8582 (mtmt) REVERT: X 106 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8730 (mmmm) REVERT: Y 202 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8804 (mtpp) REVERT: Z 302 LYS cc_start: 0.9379 (ttpt) cc_final: 0.8903 (ttmm) REVERT: j 1004 GLU cc_start: 0.7370 (mp0) cc_final: 0.7123 (mp0) REVERT: j 1006 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8646 (mtmt) REVERT: k 1106 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8724 (mmmm) REVERT: D 4 GLU cc_start: 0.8184 (mp0) cc_final: 0.7239 (mp0) REVERT: n 104 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7622 (mm-30) REVERT: n 106 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8644 (mmmm) REVERT: r 1104 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7527 (mm-30) REVERT: r 1106 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8655 (mmmm) REVERT: t 1302 LYS cc_start: 0.9277 (ttpt) cc_final: 0.8983 (ttpp) REVERT: E 6 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8517 (mtmt) REVERT: u 102 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8612 (ttmm) REVERT: u 104 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7519 (mm-30) REVERT: u 106 LYS cc_start: 0.9131 (tptm) cc_final: 0.8722 (tptm) REVERT: w 302 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8863 (ttmm) REVERT: x 1006 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8500 (mtmt) REVERT: y 1104 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7601 (mm-30) REVERT: y 1106 LYS cc_start: 0.9098 (tptm) cc_final: 0.8697 (tptm) REVERT: 0 1302 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8921 (ttmm) REVERT: F 4 GLU cc_start: 0.8007 (mp0) cc_final: 0.7483 (mp0) REVERT: F 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8734 (mtmt) REVERT: 1 104 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7463 (mm-30) REVERT: 1 106 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8665 (mmmm) REVERT: 2 202 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8844 (mtpt) REVERT: 2 204 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8004 (mt-10) REVERT: 4 1004 GLU cc_start: 0.8053 (mp0) cc_final: 0.7422 (mp0) REVERT: 5 1106 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8677 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8826 (mtpt) REVERT: G 4 GLU cc_start: 0.7917 (mp0) cc_final: 0.6689 (mp0) REVERT: G 6 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8558 (mtmt) REVERT: 8 106 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8374 (mmmm) REVERT: BA 1004 GLU cc_start: 0.7980 (mp0) cc_final: 0.6868 (mp0) REVERT: BA 1006 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8557 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8356 (mmmm) REVERT: FA 104 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7742 (mm-30) REVERT: FA 106 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8653 (mmmm) REVERT: GA 202 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8546 (mtpt) REVERT: JA 1104 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7636 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8666 (mmmm) REVERT: I 6 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8207 (mtmt) REVERT: OA 302 LYS cc_start: 0.9290 (ttpt) cc_final: 0.8861 (tptt) REVERT: OA 304 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8171 (mm-30) REVERT: PA 1006 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8097 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9283 (ttpt) cc_final: 0.8697 (mmmt) REVERT: SA 1304 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8298 (mm-30) REVERT: a 4 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8580 (tp30) REVERT: UA 202 LYS cc_start: 0.9326 (tttm) cc_final: 0.9046 (tttm) REVERT: UA 204 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7829 (tp30) REVERT: VA 304 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8651 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8541 (tp30) REVERT: XA 1104 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8296 (tm-30) REVERT: YA 1204 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7590 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8436 (tm-30) REVERT: b 2 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8894 (ttmt) REVERT: aA 105 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9034 (t80) REVERT: bA 202 LYS cc_start: 0.9251 (tttm) cc_final: 0.8926 (ttmm) REVERT: cA 304 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8476 (tm-30) REVERT: cA 305 PHE cc_start: 0.9256 (t80) cc_final: 0.8988 (t80) REVERT: dA 1002 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8906 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9071 (t80) REVERT: eA 1106 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8768 (ptmm) REVERT: fA 1204 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7583 (tp30) REVERT: gA 1304 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8392 (tm-30) REVERT: hA 102 LYS cc_start: 0.9336 (tptm) cc_final: 0.9121 (tptm) REVERT: iA 202 LYS cc_start: 0.9317 (tttm) cc_final: 0.9097 (tttm) REVERT: iA 204 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7956 (tp30) REVERT: iA 206 LYS cc_start: 0.9272 (tttt) cc_final: 0.9038 (tttm) REVERT: jA 306 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8473 (ttpp) REVERT: jA 307 PHE cc_start: 0.9516 (OUTLIER) cc_final: 0.9012 (t80) REVERT: lA 1102 LYS cc_start: 0.9324 (tptm) cc_final: 0.9093 (tptm) REVERT: mA 1204 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7645 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9270 (tttt) cc_final: 0.8972 (tttm) REVERT: nA 1306 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8452 (ttpp) REVERT: oA 103 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8998 (t80) REVERT: qA 304 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8471 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9131 (ptpt) cc_final: 0.8915 (ptpt) REVERT: uA 1304 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8545 (tm-30) REVERT: wA 202 LYS cc_start: 0.9235 (tttm) cc_final: 0.8706 (ttmm) REVERT: wA 204 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7661 (tm-30) REVERT: xA 302 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8786 (tptp) REVERT: xA 304 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8186 (tm-30) REVERT: zA 1102 LYS cc_start: 0.9266 (tptm) cc_final: 0.8998 (tptm) REVERT: zA 1105 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.9036 (t80) REVERT: 0A 1202 LYS cc_start: 0.9175 (tttm) cc_final: 0.8778 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7096 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8493 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8248 (tm-30) REVERT: f 2 LYS cc_start: 0.9188 (ptpt) cc_final: 0.8971 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8553 (tm-30) REVERT: 5A 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: 8A 1304 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8588 (tm-30) REVERT: g 4 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: AB 202 LYS cc_start: 0.9318 (tttm) cc_final: 0.8946 (ttmm) REVERT: AB 204 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7857 (tm-30) REVERT: BB 302 LYS cc_start: 0.8944 (tptp) cc_final: 0.8705 (tptp) REVERT: CB 1004 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: DB 1102 LYS cc_start: 0.9309 (tptm) cc_final: 0.9085 (tptm) REVERT: EB 1204 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7814 (tm-30) REVERT: h 2 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8954 (pptt) REVERT: i 4 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: i 5 PHE cc_start: 0.9214 (t80) cc_final: 0.8715 (t80) REVERT: OB 206 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: QB 1004 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9224 (t80) cc_final: 0.8957 (t80) REVERT: SB 1206 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (pttt) outliers start: 160 outliers final: 103 residues processed: 498 average time/residue: 0.4945 time to fit residues: 300.3805 Evaluate side-chains 568 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 440 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain SB residue 1206 LYS Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.321 12528 Z= 5.986 Angle : 4.177 54.085 16272 Z= 1.848 Chirality : 0.297 0.784 1152 Planarity : 0.017 0.051 2160 Dihedral : 20.486 78.142 1514 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 108.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.15 % Favored : 83.68 % Rotamer: Outliers : 21.53 % Allowed : 22.69 % Favored : 55.79 % Cbeta Deviations : 15.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.07 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.111 0.017 PHEPB 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 437 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8313 (mp0) cc_final: 0.8093 (mp0) REVERT: A 6 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8705 (mmmt) REVERT: J 106 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8530 (mmmm) REVERT: K 204 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7985 (mt-10) REVERT: M 1004 GLU cc_start: 0.8427 (mp0) cc_final: 0.8009 (mp0) REVERT: M 1006 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8730 (mmmt) REVERT: N 1106 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8556 (mmmm) REVERT: O 1204 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 4 GLU cc_start: 0.8257 (mp0) cc_final: 0.7770 (mp0) REVERT: B 6 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8670 (mtmt) REVERT: Q 106 LYS cc_start: 0.8918 (tptm) cc_final: 0.8371 (tptm) REVERT: R 202 LYS cc_start: 0.9241 (mtpt) cc_final: 0.8868 (mtpt) REVERT: S 302 LYS cc_start: 0.9273 (ttpt) cc_final: 0.8869 (mtpp) REVERT: T 1004 GLU cc_start: 0.8251 (mp0) cc_final: 0.7716 (mp0) REVERT: T 1006 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8713 (mtmt) REVERT: V 1202 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8854 (mtpt) REVERT: W 1302 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8930 (mtpp) REVERT: C 6 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8634 (mtmt) REVERT: X 106 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8728 (mmmm) REVERT: Y 202 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8795 (mtpp) REVERT: Z 302 LYS cc_start: 0.9394 (ttpt) cc_final: 0.8931 (ttmm) REVERT: j 1006 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8688 (mtmt) REVERT: k 1106 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8701 (mmmm) REVERT: m 1302 LYS cc_start: 0.9330 (ttpt) cc_final: 0.8659 (ttpp) REVERT: D 4 GLU cc_start: 0.8076 (mp0) cc_final: 0.7792 (mp0) REVERT: n 104 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7768 (mm-30) REVERT: n 106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8664 (mmmm) REVERT: o 202 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8810 (mtpp) REVERT: p 302 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8914 (ttpp) REVERT: q 1002 LYS cc_start: 0.7798 (tttt) cc_final: 0.7508 (tptm) REVERT: q 1004 GLU cc_start: 0.8245 (mp0) cc_final: 0.7327 (mp0) REVERT: r 1104 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7729 (mm-30) REVERT: r 1106 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8655 (mmmm) REVERT: t 1302 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8961 (ttpp) REVERT: E 6 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8596 (mtmt) REVERT: u 102 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8638 (ttpt) REVERT: u 104 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7849 (mm-30) REVERT: u 106 LYS cc_start: 0.9111 (tptm) cc_final: 0.8697 (tptm) REVERT: w 302 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8858 (ttmm) REVERT: x 1002 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6438 (mmtp) REVERT: x 1006 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8531 (mtmt) REVERT: y 1104 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7830 (mm-30) REVERT: y 1106 LYS cc_start: 0.9124 (tptm) cc_final: 0.8701 (tptm) REVERT: 0 1302 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8900 (ttmm) REVERT: F 4 GLU cc_start: 0.7988 (mp0) cc_final: 0.7347 (mp0) REVERT: F 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8769 (mtmt) REVERT: 1 104 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7347 (mm-30) REVERT: 1 106 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8584 (mmmm) REVERT: 2 206 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8624 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8023 (mp0) cc_final: 0.7245 (mp0) REVERT: 5 1104 GLU cc_start: 0.8329 (mm-30) cc_final: 0.6881 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8565 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8973 (mtpt) REVERT: G 4 GLU cc_start: 0.7941 (mp0) cc_final: 0.6950 (mp0) REVERT: G 6 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8586 (mtmt) REVERT: BA 1004 GLU cc_start: 0.7982 (mp0) cc_final: 0.7094 (mp0) REVERT: BA 1006 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8585 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8486 (mmmm) REVERT: FA 104 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7815 (mm-30) REVERT: FA 106 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8720 (mmmm) REVERT: GA 202 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8549 (mtpt) REVERT: HA 304 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8292 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7734 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8741 (mmmm) REVERT: MA 106 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5394 (tptp) REVERT: OA 302 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8849 (tptt) REVERT: OA 304 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8328 (mm-30) REVERT: OA 306 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5628 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8567 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9274 (ttpt) cc_final: 0.8674 (mmmt) REVERT: SA 1304 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8393 (mm-30) REVERT: SA 1306 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5533 (mmmt) REVERT: a 4 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8559 (tp30) REVERT: UA 204 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7607 (tm-30) REVERT: VA 304 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8676 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8558 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9204 (tptp) cc_final: 0.8965 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8425 (tm-30) REVERT: b 2 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8884 (ttmt) REVERT: aA 105 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9026 (t80) REVERT: bA 202 LYS cc_start: 0.9249 (tttm) cc_final: 0.8928 (ttmm) REVERT: bA 204 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7881 (tp30) REVERT: cA 304 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8304 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8907 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8304 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8000 (tm-30) REVERT: gA 1304 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8609 (tm-30) REVERT: iA 202 LYS cc_start: 0.9332 (tttm) cc_final: 0.9093 (tttm) REVERT: iA 204 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8087 (tp30) REVERT: iA 206 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8652 (ttpp) REVERT: jA 306 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8406 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7760 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8543 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8387 (ttpp) REVERT: nA 1307 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9128 (t80) REVERT: pA 206 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8957 (pttt) REVERT: qA 304 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8645 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9160 (ptpt) cc_final: 0.8958 (ptpt) REVERT: uA 1304 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8504 (tm-30) REVERT: e 2 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8761 (ttpt) REVERT: vA 104 GLU cc_start: 0.8743 (tm-30) cc_final: 0.7942 (tm-30) REVERT: wA 202 LYS cc_start: 0.9251 (tttm) cc_final: 0.8747 (ttmm) REVERT: wA 204 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7045 (tm-30) REVERT: xA 302 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8560 (tptp) REVERT: xA 304 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8299 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8853 (tppt) REVERT: yA 1004 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: 0A 1202 LYS cc_start: 0.9149 (tttm) cc_final: 0.8761 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7053 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8485 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8360 (tm-30) REVERT: f 2 LYS cc_start: 0.9184 (ptpt) cc_final: 0.8967 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8542 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8821 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8799 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8581 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9071 (tptp) cc_final: 0.8804 (tptp) REVERT: g 4 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: AB 202 LYS cc_start: 0.9321 (tttm) cc_final: 0.8945 (ttmm) REVERT: AB 204 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: EB 1204 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7891 (tm-30) REVERT: h 2 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8943 (pptt) REVERT: i 4 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: i 5 PHE cc_start: 0.9222 (t80) cc_final: 0.8674 (t80) REVERT: i 6 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8854 (ttpt) REVERT: OB 206 LYS cc_start: 0.9244 (tttt) cc_final: 0.8996 (tttm) REVERT: QB 1004 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9225 (t80) cc_final: 0.9002 (t80) REVERT: QB 1006 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8887 (ttpt) outliers start: 186 outliers final: 127 residues processed: 505 average time/residue: 0.5008 time to fit residues: 307.7775 Evaluate side-chains 601 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 438 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.310 12528 Z= 5.989 Angle : 4.207 51.119 16272 Z= 1.857 Chirality : 0.297 0.773 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.546 88.368 1506 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 109.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 23.73 % Allowed : 24.07 % Favored : 52.20 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.115 0.017 PHE V1207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 437 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8726 (mmmt) REVERT: J 106 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8522 (mmmm) REVERT: L 304 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8119 (mm-30) REVERT: N 1106 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8542 (mmmm) REVERT: B 4 GLU cc_start: 0.8254 (mp0) cc_final: 0.7829 (mp0) REVERT: B 6 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8711 (mtmt) REVERT: Q 106 LYS cc_start: 0.8913 (tptm) cc_final: 0.8391 (tptm) REVERT: R 202 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8923 (mtpt) REVERT: S 302 LYS cc_start: 0.9256 (ttpt) cc_final: 0.8880 (mtpp) REVERT: T 1004 GLU cc_start: 0.8271 (mp0) cc_final: 0.7799 (mp0) REVERT: T 1006 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8726 (mtmt) REVERT: V 1202 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8863 (mtpt) REVERT: W 1302 LYS cc_start: 0.9291 (ttpt) cc_final: 0.8937 (mtpp) REVERT: C 6 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8618 (mtmt) REVERT: X 106 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8738 (mmmm) REVERT: Y 202 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8743 (mtpp) REVERT: Z 302 LYS cc_start: 0.9413 (ttpt) cc_final: 0.8984 (ttpp) REVERT: j 1004 GLU cc_start: 0.7718 (mp0) cc_final: 0.7450 (mp0) REVERT: j 1006 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8704 (mtmt) REVERT: k 1106 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8675 (mmmm) REVERT: m 1302 LYS cc_start: 0.9337 (ttpt) cc_final: 0.8915 (ttmm) REVERT: D 4 GLU cc_start: 0.8120 (mp0) cc_final: 0.7826 (mp0) REVERT: n 104 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7766 (mm-30) REVERT: n 106 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8653 (mmmm) REVERT: o 202 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8819 (mtpp) REVERT: p 302 LYS cc_start: 0.9247 (ttpt) cc_final: 0.8900 (ttpp) REVERT: q 1002 LYS cc_start: 0.7830 (tttt) cc_final: 0.7607 (tptm) REVERT: q 1004 GLU cc_start: 0.8278 (mp0) cc_final: 0.7715 (mp0) REVERT: r 1104 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7806 (mm-30) REVERT: r 1106 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8691 (mmmm) REVERT: t 1302 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8957 (ttpp) REVERT: u 102 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8844 (ttpt) REVERT: u 106 LYS cc_start: 0.9104 (tptm) cc_final: 0.8687 (tptm) REVERT: w 302 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: x 1002 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6432 (mmtp) REVERT: x 1006 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8441 (mtmt) REVERT: y 1106 LYS cc_start: 0.9124 (tptm) cc_final: 0.8710 (tptm) REVERT: 0 1302 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8893 (ttmm) REVERT: F 4 GLU cc_start: 0.7942 (mp0) cc_final: 0.7532 (mp0) REVERT: F 6 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8768 (mtmt) REVERT: 1 106 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8548 (mmmm) REVERT: 4 1004 GLU cc_start: 0.8008 (mp0) cc_final: 0.7185 (mp0) REVERT: 5 1104 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7903 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8575 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8943 (mtpt) REVERT: G 4 GLU cc_start: 0.7949 (mp0) cc_final: 0.7063 (mp0) REVERT: G 6 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8574 (mtmt) REVERT: BA 1004 GLU cc_start: 0.7967 (mp0) cc_final: 0.7161 (mp0) REVERT: BA 1006 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8603 (mtmt) REVERT: CA 1106 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8499 (mmmm) REVERT: FA 106 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8781 (mmmm) REVERT: GA 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8559 (mtpt) REVERT: GA 204 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.4202 (pm20) REVERT: JA 1104 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7622 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9056 (tttt) cc_final: 0.8848 (tttt) REVERT: MA 106 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5268 (tptp) REVERT: OA 302 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8822 (tptt) REVERT: OA 304 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8365 (mm-30) REVERT: OA 306 LYS cc_start: 0.5248 (OUTLIER) cc_final: 0.4795 (mmmt) REVERT: PA 1006 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8548 (mtmt) REVERT: SA 1302 LYS cc_start: 0.9268 (ttpt) cc_final: 0.8659 (mmmt) REVERT: SA 1306 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.5420 (mmmt) REVERT: a 4 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (tp30) REVERT: TA 107 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8063 (t80) REVERT: UA 204 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7862 (tp30) REVERT: VA 304 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8695 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8541 (tp30) REVERT: YA 1204 GLU cc_start: 0.8069 (tp30) cc_final: 0.7810 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9243 (tptp) cc_final: 0.8880 (tptp) REVERT: ZA 1303 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8600 (t80) REVERT: ZA 1304 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8378 (tm-30) REVERT: b 2 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8884 (ttmt) REVERT: aA 105 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9036 (t80) REVERT: bA 202 LYS cc_start: 0.9257 (tttm) cc_final: 0.8928 (ttmm) REVERT: bA 204 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8002 (tp30) REVERT: cA 304 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8592 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8898 (ttmt) REVERT: eA 1105 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.9012 (t80) REVERT: eA 1106 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8289 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7849 (tp30) REVERT: gA 1304 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8627 (tm-30) REVERT: iA 202 LYS cc_start: 0.9319 (tttm) cc_final: 0.9090 (tttm) REVERT: iA 204 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8133 (tp30) REVERT: iA 206 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8680 (ttpp) REVERT: jA 306 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8403 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7807 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8510 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8364 (ttpp) REVERT: nA 1307 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.8981 (t80) REVERT: pA 206 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8951 (pttt) REVERT: qA 304 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8619 (tm-30) REVERT: rA 1002 LYS cc_start: 0.9163 (ptpt) cc_final: 0.8962 (ptpt) REVERT: tA 1206 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8942 (pttt) REVERT: uA 1304 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8675 (tm-30) REVERT: vA 104 GLU cc_start: 0.8748 (tm-30) cc_final: 0.7971 (tm-30) REVERT: wA 202 LYS cc_start: 0.9260 (tttm) cc_final: 0.8758 (ttmm) REVERT: wA 204 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7028 (tm-30) REVERT: xA 302 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8558 (tptp) REVERT: xA 304 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8386 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8831 (tppt) REVERT: 0A 1202 LYS cc_start: 0.9168 (tttm) cc_final: 0.8765 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7011 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8474 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8417 (tm-30) REVERT: f 2 LYS cc_start: 0.9185 (ptpt) cc_final: 0.8965 (ptpt) REVERT: 4A 304 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8572 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8816 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8585 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8834 (ttpp) REVERT: g 4 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: 9A 102 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9073 (tptm) REVERT: AB 204 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8437 (tp30) REVERT: EB 1204 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: h 2 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8937 (pptt) REVERT: i 4 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: i 5 PHE cc_start: 0.9200 (t80) cc_final: 0.8683 (t80) REVERT: i 6 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8859 (ttpt) REVERT: OB 206 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8509 (ttpp) REVERT: QB 1004 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9226 (t80) cc_final: 0.9005 (t80) REVERT: QB 1006 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8871 (ttpt) outliers start: 205 outliers final: 146 residues processed: 514 average time/residue: 0.4525 time to fit residues: 283.0146 Evaluate side-chains 626 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 437 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 203 PHE Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.308 12528 Z= 5.994 Angle : 4.224 51.200 16272 Z= 1.863 Chirality : 0.298 0.768 1152 Planarity : 0.017 0.054 2160 Dihedral : 20.682 82.222 1506 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 110.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 26.04 % Allowed : 24.07 % Favored : 49.88 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.116 0.017 PHE R 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 434 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8402 (mp0) cc_final: 0.8100 (mp0) REVERT: A 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8728 (mmmt) REVERT: J 106 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8525 (mmmm) REVERT: M 1004 GLU cc_start: 0.8577 (mp0) cc_final: 0.8299 (mp0) REVERT: N 1106 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8545 (mmmm) REVERT: B 4 GLU cc_start: 0.8261 (mp0) cc_final: 0.7848 (mp0) REVERT: B 6 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8722 (mtmt) REVERT: Q 106 LYS cc_start: 0.8911 (tptm) cc_final: 0.8390 (tptm) REVERT: R 202 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8943 (mtpt) REVERT: S 302 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8869 (mtpp) REVERT: T 1004 GLU cc_start: 0.8246 (mp0) cc_final: 0.7819 (mp0) REVERT: T 1006 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8737 (mtmt) REVERT: V 1202 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8882 (mtpt) REVERT: W 1302 LYS cc_start: 0.9301 (ttpt) cc_final: 0.8913 (mtpp) REVERT: C 6 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8614 (mtmt) REVERT: X 106 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8741 (mmmm) REVERT: Y 202 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8738 (mtpp) REVERT: Z 302 LYS cc_start: 0.9359 (ttpt) cc_final: 0.8942 (ttpp) REVERT: j 1006 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8690 (mtmt) REVERT: k 1106 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8683 (mmmm) REVERT: m 1302 LYS cc_start: 0.9348 (ttpt) cc_final: 0.8982 (ttpp) REVERT: m 1306 LYS cc_start: 0.9328 (tttt) cc_final: 0.8937 (mttt) REVERT: D 4 GLU cc_start: 0.8235 (mp0) cc_final: 0.7966 (mp0) REVERT: n 104 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7751 (mm-30) REVERT: n 106 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8615 (mmmm) REVERT: o 202 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8822 (mtpp) REVERT: p 302 LYS cc_start: 0.9245 (ttpt) cc_final: 0.8883 (ttpp) REVERT: q 1004 GLU cc_start: 0.8228 (mp0) cc_final: 0.7847 (mp0) REVERT: r 1104 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7765 (mm-30) REVERT: r 1106 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8655 (mmmm) REVERT: t 1302 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8945 (ttpp) REVERT: u 102 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8774 (mtpp) REVERT: u 106 LYS cc_start: 0.9116 (tptm) cc_final: 0.8686 (tptm) REVERT: w 302 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8850 (ttmm) REVERT: x 1002 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6450 (mmtp) REVERT: x 1006 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8440 (mtmt) REVERT: y 1102 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8958 (ttpp) REVERT: y 1106 LYS cc_start: 0.9127 (tptm) cc_final: 0.8706 (tptm) REVERT: 0 1302 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8893 (ttmm) REVERT: 1 104 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7917 (mm-30) REVERT: 1 106 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8548 (mmmm) REVERT: 2 206 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8632 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8078 (mp0) cc_final: 0.7293 (mp0) REVERT: 5 1104 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7978 (mm-30) REVERT: 5 1106 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8533 (mmmm) REVERT: G 4 GLU cc_start: 0.8270 (mp0) cc_final: 0.7917 (mp0) REVERT: G 6 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8560 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8202 (mp0) cc_final: 0.7907 (mp0) REVERT: BA 1006 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8558 (mtmt) REVERT: GA 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8537 (mtpt) REVERT: GA 204 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4232 (pm20) REVERT: HA 304 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8004 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7604 (mm-30) REVERT: LA 1304 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8033 (mm-30) REVERT: MA 106 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5214 (tptp) REVERT: OA 302 LYS cc_start: 0.9294 (ttpt) cc_final: 0.8810 (tptt) REVERT: SA 1302 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8812 (tptt) REVERT: SA 1306 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5388 (mmmt) REVERT: a 4 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8602 (tp30) REVERT: UA 204 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7798 (tp30) REVERT: VA 304 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8519 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: YA 1204 GLU cc_start: 0.8019 (tp30) cc_final: 0.7779 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9229 (tptp) cc_final: 0.8834 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8588 (tm-30) REVERT: b 2 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8879 (ttmt) REVERT: bA 202 LYS cc_start: 0.9249 (tttm) cc_final: 0.8907 (ttmm) REVERT: bA 204 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7990 (tp30) REVERT: cA 304 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8569 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8906 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7841 (tp30) REVERT: gA 1304 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8652 (tm-30) REVERT: iA 204 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7965 (tm-30) REVERT: iA 206 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8651 (ttpp) REVERT: jA 306 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8394 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7996 (tp30) REVERT: mA 1206 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8546 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8381 (ttpp) REVERT: pA 206 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8952 (pttt) REVERT: qA 304 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8627 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (pttt) REVERT: uA 1304 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8687 (tm-30) REVERT: vA 104 GLU cc_start: 0.8758 (tm-30) cc_final: 0.7976 (tm-30) REVERT: wA 202 LYS cc_start: 0.9252 (tttm) cc_final: 0.8760 (ttmm) REVERT: wA 204 GLU cc_start: 0.8018 (tm-30) cc_final: 0.6955 (tm-30) REVERT: wA 206 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8668 (ttpp) REVERT: xA 302 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8517 (tptp) REVERT: xA 304 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8380 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8812 (tppt) REVERT: 0A 1202 LYS cc_start: 0.9168 (tttm) cc_final: 0.8784 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7985 (tm-30) cc_final: 0.6958 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8496 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8447 (tm-30) REVERT: 4A 304 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8575 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8827 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8815 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8577 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8842 (ttpp) REVERT: g 4 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: 9A 102 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9088 (tptm) REVERT: AB 204 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: EB 1204 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: i 4 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: i 5 PHE cc_start: 0.9196 (t80) cc_final: 0.8689 (t80) REVERT: i 6 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8866 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9224 (t80) cc_final: 0.8998 (t80) REVERT: QB 1006 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8873 (ttpt) outliers start: 225 outliers final: 163 residues processed: 520 average time/residue: 0.4652 time to fit residues: 293.5925 Evaluate side-chains 633 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 435 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.355 12528 Z= 5.990 Angle : 4.234 50.970 16272 Z= 1.867 Chirality : 0.298 0.766 1152 Planarity : 0.017 0.056 2160 Dihedral : 20.775 92.567 1506 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 112.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 26.74 % Allowed : 24.07 % Favored : 49.19 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.17 (0.21), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.119 0.017 PHE V1207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 435 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8766 (mmmt) REVERT: J 106 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8529 (mmmm) REVERT: M 1004 GLU cc_start: 0.8598 (mp0) cc_final: 0.8104 (mp0) REVERT: N 1106 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8542 (mmmm) REVERT: O 1202 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8978 (mtpt) REVERT: P 1304 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: B 4 GLU cc_start: 0.8245 (mp0) cc_final: 0.7853 (mp0) REVERT: B 6 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8706 (mtmt) REVERT: Q 106 LYS cc_start: 0.8935 (tptm) cc_final: 0.8337 (tptm) REVERT: R 202 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8985 (mtpt) REVERT: S 302 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8851 (mtpp) REVERT: T 1004 GLU cc_start: 0.8252 (mp0) cc_final: 0.7828 (mp0) REVERT: T 1006 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8672 (mtmt) REVERT: V 1202 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8904 (mtpt) REVERT: W 1302 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8904 (mtpp) REVERT: C 6 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8681 (mtmt) REVERT: X 106 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8741 (mmmm) REVERT: Y 202 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8708 (mtpp) REVERT: Z 302 LYS cc_start: 0.9354 (ttpt) cc_final: 0.8972 (ttpp) REVERT: j 1006 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8684 (mtmt) REVERT: k 1106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8675 (mmmm) REVERT: m 1302 LYS cc_start: 0.9353 (ttpt) cc_final: 0.8971 (ttpp) REVERT: m 1306 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8946 (mttt) REVERT: D 4 GLU cc_start: 0.8167 (mp0) cc_final: 0.7811 (mm-30) REVERT: n 104 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7742 (mm-30) REVERT: n 106 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8643 (mmmm) REVERT: o 202 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8809 (mtpp) REVERT: p 302 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8881 (ttpp) REVERT: q 1002 LYS cc_start: 0.7754 (tptm) cc_final: 0.7306 (tptm) REVERT: q 1004 GLU cc_start: 0.8248 (mp0) cc_final: 0.7889 (mp0) REVERT: r 1104 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7786 (mm-30) REVERT: r 1106 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8661 (mmmm) REVERT: t 1302 LYS cc_start: 0.9261 (ttpt) cc_final: 0.8924 (ttpp) REVERT: u 102 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8734 (mtpp) REVERT: u 106 LYS cc_start: 0.9099 (tptm) cc_final: 0.8678 (tptm) REVERT: w 302 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8854 (ttmm) REVERT: x 1002 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6496 (mmtp) REVERT: x 1006 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8436 (mtmt) REVERT: y 1106 LYS cc_start: 0.9105 (tptm) cc_final: 0.8682 (tptm) REVERT: 0 1302 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8897 (ttmm) REVERT: F 6 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8741 (mtmt) REVERT: 1 104 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7720 (mm-30) REVERT: 1 106 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8547 (mmmm) REVERT: 2 206 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8623 (ptmm) REVERT: 4 1004 GLU cc_start: 0.8110 (mp0) cc_final: 0.7474 (mp0) REVERT: 5 1106 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8432 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8742 (ptmm) REVERT: G 4 GLU cc_start: 0.8054 (mp0) cc_final: 0.7583 (mp0) REVERT: G 6 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8572 (mtmt) REVERT: BA 1004 GLU cc_start: 0.8056 (mp0) cc_final: 0.7583 (mp0) REVERT: BA 1006 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8582 (mtmt) REVERT: EA 1302 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8781 (ttmm) REVERT: GA 202 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8541 (mtpt) REVERT: GA 204 GLU cc_start: 0.5145 (OUTLIER) cc_final: 0.4442 (pm20) REVERT: HA 304 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8139 (mm-30) REVERT: KA 1204 GLU cc_start: 0.5036 (OUTLIER) cc_final: 0.4133 (pm20) REVERT: LA 1304 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9066 (tttt) cc_final: 0.8862 (tttt) REVERT: I 2 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8628 (tttt) REVERT: MA 106 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5168 (tptp) REVERT: OA 302 LYS cc_start: 0.9304 (ttpt) cc_final: 0.8814 (tptt) REVERT: SA 1302 LYS cc_start: 0.9278 (ttpt) cc_final: 0.8816 (tptt) REVERT: SA 1306 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4898 (mmmt) REVERT: a 4 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: UA 204 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7812 (tp30) REVERT: VA 304 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8518 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: YA 1204 GLU cc_start: 0.8038 (tp30) cc_final: 0.7741 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9230 (tptp) cc_final: 0.8852 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8605 (tm-30) REVERT: b 2 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8894 (ttmt) REVERT: bA 202 LYS cc_start: 0.9255 (tttm) cc_final: 0.8927 (ttmm) REVERT: bA 204 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7986 (tp30) REVERT: cA 304 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8578 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8906 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7825 (tp30) REVERT: gA 1304 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8605 (tm-30) REVERT: iA 204 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7975 (tm-30) REVERT: iA 206 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8669 (ttpp) REVERT: jA 306 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8422 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8000 (tp30) REVERT: mA 1206 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8554 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8374 (ttpp) REVERT: pA 206 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8963 (pttt) REVERT: qA 304 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8634 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8931 (pttt) REVERT: uA 1304 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8716 (tm-30) REVERT: vA 104 GLU cc_start: 0.8764 (tm-30) cc_final: 0.7998 (tm-30) REVERT: wA 202 LYS cc_start: 0.9241 (tttm) cc_final: 0.8747 (ttmm) REVERT: wA 204 GLU cc_start: 0.8022 (tm-30) cc_final: 0.6968 (tm-30) REVERT: xA 302 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8508 (tptp) REVERT: xA 304 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8408 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8811 (tppt) REVERT: zA 1105 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8942 (t80) REVERT: 0A 1202 LYS cc_start: 0.9168 (tttm) cc_final: 0.8692 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7974 (tm-30) cc_final: 0.6886 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8486 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8449 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9000 (tppp) REVERT: 4A 306 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8817 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8816 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8580 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8838 (ttpp) REVERT: g 4 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: 9A 102 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9105 (tptm) REVERT: AB 204 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: DB 1102 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9113 (tptm) REVERT: EB 1204 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: i 4 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: i 5 PHE cc_start: 0.9193 (t80) cc_final: 0.8695 (t80) REVERT: i 6 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8859 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9222 (t80) cc_final: 0.8997 (t80) REVERT: QB 1006 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8881 (ttpt) outliers start: 231 outliers final: 170 residues processed: 521 average time/residue: 0.4531 time to fit residues: 287.7425 Evaluate side-chains 648 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 435 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.326 12528 Z= 5.987 Angle : 4.231 51.111 16272 Z= 1.868 Chirality : 0.299 0.773 1152 Planarity : 0.017 0.052 2160 Dihedral : 20.772 103.859 1506 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 112.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.53 % Favored : 82.47 % Rotamer: Outliers : 26.39 % Allowed : 25.35 % Favored : 48.26 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.16 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.16), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.114 0.017 PHE R 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 433 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8733 (mmmt) REVERT: J 106 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8526 (mmmm) REVERT: M 1004 GLU cc_start: 0.8637 (mp0) cc_final: 0.8210 (mp0) REVERT: N 1106 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8546 (mmmm) REVERT: O 1202 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8995 (mtpt) REVERT: B 4 GLU cc_start: 0.8251 (mp0) cc_final: 0.7864 (mp0) REVERT: B 6 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8712 (mtmt) REVERT: Q 106 LYS cc_start: 0.8942 (tptm) cc_final: 0.8328 (tptm) REVERT: R 202 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8985 (mtpt) REVERT: S 302 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8847 (mtpp) REVERT: T 1006 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8671 (mtmt) REVERT: V 1202 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8911 (mtpt) REVERT: W 1302 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8904 (mtpp) REVERT: C 6 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8671 (mtmt) REVERT: X 106 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8743 (mmmm) REVERT: Y 202 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8713 (mtpp) REVERT: Z 302 LYS cc_start: 0.9356 (ttpt) cc_final: 0.8964 (ttpp) REVERT: j 1006 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8678 (mtmt) REVERT: k 1106 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8685 (mmmm) REVERT: m 1302 LYS cc_start: 0.9348 (ttpt) cc_final: 0.8963 (ttpp) REVERT: m 1306 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8957 (mttt) REVERT: D 4 GLU cc_start: 0.8198 (mp0) cc_final: 0.7898 (mp0) REVERT: n 106 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8617 (mmmm) REVERT: o 202 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8811 (mtpp) REVERT: p 302 LYS cc_start: 0.9244 (ttpt) cc_final: 0.8874 (ttpp) REVERT: q 1002 LYS cc_start: 0.7731 (tptm) cc_final: 0.7317 (tptm) REVERT: q 1004 GLU cc_start: 0.8191 (mp0) cc_final: 0.7765 (mp0) REVERT: r 1106 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8654 (mmmm) REVERT: t 1302 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8915 (ttpp) REVERT: u 102 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8769 (mtpp) REVERT: u 106 LYS cc_start: 0.9121 (tptm) cc_final: 0.8690 (tptm) REVERT: w 302 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8856 (ttmm) REVERT: x 1002 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6494 (mmtp) REVERT: x 1006 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8446 (mtmt) REVERT: y 1106 LYS cc_start: 0.9127 (tptm) cc_final: 0.8700 (tptm) REVERT: 0 1302 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8903 (ttmm) REVERT: F 6 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8737 (mtmt) REVERT: 1 106 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8409 (mmmm) REVERT: 2 206 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8640 (ptmm) REVERT: 5 1106 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8425 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8743 (ptmm) REVERT: G 4 GLU cc_start: 0.8140 (mp0) cc_final: 0.7860 (mp0) REVERT: G 6 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8591 (mtmt) REVERT: BA 1006 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8607 (mtmt) REVERT: EA 1302 LYS cc_start: 0.9257 (ttpt) cc_final: 0.8815 (ttmm) REVERT: GA 202 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8541 (mtpt) REVERT: GA 204 GLU cc_start: 0.5145 (OUTLIER) cc_final: 0.4513 (pm20) REVERT: KA 1204 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4132 (pm20) REVERT: LA 1304 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9073 (tttt) cc_final: 0.8861 (tttt) REVERT: I 2 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8614 (tttt) REVERT: MA 106 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.4919 (tptp) REVERT: OA 302 LYS cc_start: 0.9244 (ttpt) cc_final: 0.8812 (tptt) REVERT: SA 1302 LYS cc_start: 0.9294 (ttpt) cc_final: 0.8811 (tptt) REVERT: a 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: UA 202 LYS cc_start: 0.9335 (mttm) cc_final: 0.9017 (mmmm) REVERT: UA 204 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7846 (tp30) REVERT: VA 304 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8536 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8548 (tp30) REVERT: YA 1204 GLU cc_start: 0.8006 (tp30) cc_final: 0.7692 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9228 (tptp) cc_final: 0.8821 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8595 (tm-30) REVERT: b 2 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8893 (ttmt) REVERT: bA 202 LYS cc_start: 0.9255 (tttm) cc_final: 0.8933 (ttmm) REVERT: bA 204 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8006 (tp30) REVERT: cA 304 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8571 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8907 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8313 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7884 (tp30) REVERT: gA 1304 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8627 (tm-30) REVERT: iA 204 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7987 (tm-30) REVERT: iA 206 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: jA 306 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8386 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7999 (tp30) REVERT: mA 1206 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8526 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8305 (ttpp) REVERT: pA 206 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8960 (pttt) REVERT: qA 304 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8630 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8927 (pttt) REVERT: uA 1304 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8725 (tm-30) REVERT: vA 104 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8001 (tm-30) REVERT: wA 202 LYS cc_start: 0.9236 (tttm) cc_final: 0.8754 (ttmm) REVERT: wA 204 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7002 (tm-30) REVERT: wA 206 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8652 (ttpp) REVERT: xA 302 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8504 (tptp) REVERT: xA 304 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8408 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8818 (tppt) REVERT: zA 1105 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8977 (t80) REVERT: 0A 1202 LYS cc_start: 0.9151 (tttm) cc_final: 0.8781 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7988 (tm-30) cc_final: 0.6980 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8459 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9001 (tppp) REVERT: 4A 306 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8816 (ttpp) REVERT: 5A 1004 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: 6A 1102 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8817 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8574 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: g 4 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: 9A 102 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9117 (tptm) REVERT: AB 204 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8365 (tp30) REVERT: DB 1102 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9115 (tptm) REVERT: EB 1204 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: i 4 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: i 5 PHE cc_start: 0.9215 (t80) cc_final: 0.8734 (t80) REVERT: i 6 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8870 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: QB 1005 PHE cc_start: 0.9222 (t80) cc_final: 0.8980 (t80) REVERT: QB 1006 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8883 (ttpt) outliers start: 228 outliers final: 170 residues processed: 521 average time/residue: 0.4735 time to fit residues: 300.2900 Evaluate side-chains 646 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 434 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1002 LYS Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.109 0.341 12528 Z= 5.986 Angle : 4.236 50.968 16272 Z= 1.871 Chirality : 0.299 0.773 1152 Planarity : 0.017 0.056 2160 Dihedral : 20.830 119.704 1506 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 112.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.71 % Favored : 82.29 % Rotamer: Outliers : 26.97 % Allowed : 26.04 % Favored : 46.99 % Cbeta Deviations : 14.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.120 0.017 PHE Q 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 430 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8770 (mmmt) REVERT: J 106 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8530 (mmmm) REVERT: L 304 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: M 1004 GLU cc_start: 0.8656 (mp0) cc_final: 0.8325 (mp0) REVERT: N 1106 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8548 (mmmm) REVERT: O 1202 LYS cc_start: 0.9223 (mtpt) cc_final: 0.9006 (mtpt) REVERT: B 4 GLU cc_start: 0.8236 (mp0) cc_final: 0.7923 (mp0) REVERT: B 6 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8711 (mtmt) REVERT: Q 106 LYS cc_start: 0.8935 (tptm) cc_final: 0.8324 (tptm) REVERT: R 202 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8985 (mtpt) REVERT: S 302 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8850 (mtpp) REVERT: T 1006 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8686 (mtmt) REVERT: V 1202 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8927 (mtpt) REVERT: W 1302 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8901 (mtpp) REVERT: C 6 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8604 (mtmt) REVERT: X 106 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8747 (mmmm) REVERT: Y 202 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8706 (mtpp) REVERT: Z 302 LYS cc_start: 0.9354 (ttpt) cc_final: 0.8962 (ttpp) REVERT: j 1006 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8674 (mtmt) REVERT: k 1106 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8684 (mmmm) REVERT: m 1302 LYS cc_start: 0.9350 (ttpt) cc_final: 0.8956 (ttpp) REVERT: m 1306 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8959 (mttt) REVERT: n 106 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8586 (mmmm) REVERT: o 202 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8800 (mtpp) REVERT: p 302 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8884 (ttpp) REVERT: q 1002 LYS cc_start: 0.7765 (tttm) cc_final: 0.7318 (tptm) REVERT: r 1106 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8630 (mmmm) REVERT: t 1302 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8905 (ttpp) REVERT: u 102 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8733 (mtpp) REVERT: u 106 LYS cc_start: 0.9106 (tptm) cc_final: 0.8680 (tptm) REVERT: w 302 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8852 (ttmm) REVERT: x 1002 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6432 (mmtp) REVERT: x 1006 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8451 (mtmt) REVERT: y 1106 LYS cc_start: 0.9102 (tptm) cc_final: 0.8683 (tptm) REVERT: 0 1302 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8897 (ttmm) REVERT: F 4 GLU cc_start: 0.8414 (mp0) cc_final: 0.7865 (mp0) REVERT: F 6 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8709 (mtmt) REVERT: 1 106 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8388 (mmmm) REVERT: 2 206 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8637 (ptmm) REVERT: 5 1106 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8424 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8745 (ptmm) REVERT: G 4 GLU cc_start: 0.8097 (mp0) cc_final: 0.7772 (mp0) REVERT: G 6 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8600 (mtmt) REVERT: BA 1006 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8598 (mtmt) REVERT: GA 202 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8535 (mtpt) REVERT: GA 204 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4683 (pm20) REVERT: KA 1204 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4319 (pm20) REVERT: LA 1304 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9076 (tttt) cc_final: 0.8860 (tttt) REVERT: I 2 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (tttt) REVERT: MA 106 LYS cc_start: 0.5550 (OUTLIER) cc_final: 0.4957 (tptp) REVERT: OA 302 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8818 (tptt) REVERT: RA 1202 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8513 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8775 (tptt) REVERT: SA 1306 LYS cc_start: 0.3247 (OUTLIER) cc_final: 0.2454 (mmmt) REVERT: a 4 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: UA 202 LYS cc_start: 0.9338 (mttm) cc_final: 0.9041 (mmmm) REVERT: UA 204 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7873 (tp30) REVERT: VA 304 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8544 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: YA 1204 GLU cc_start: 0.8033 (tp30) cc_final: 0.7719 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9225 (tptp) cc_final: 0.8822 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8448 (tm-30) REVERT: b 2 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8889 (ttmt) REVERT: bA 202 LYS cc_start: 0.9259 (tttm) cc_final: 0.8938 (ttmm) REVERT: bA 204 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7980 (tp30) REVERT: cA 304 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8579 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8909 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7921 (tp30) REVERT: gA 1304 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8627 (tm-30) REVERT: iA 202 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9027 (ttmm) REVERT: iA 204 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8003 (tm-30) REVERT: iA 206 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8674 (ttpp) REVERT: jA 306 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8405 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7848 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8496 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8346 (ttpp) REVERT: pA 206 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8943 (pttt) REVERT: qA 304 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8660 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8956 (pttt) REVERT: uA 1304 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8741 (tm-30) REVERT: vA 104 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8004 (tm-30) REVERT: wA 202 LYS cc_start: 0.9249 (tttm) cc_final: 0.8749 (ttmm) REVERT: wA 204 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7074 (tm-30) REVERT: xA 302 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8502 (tptp) REVERT: xA 304 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8407 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8812 (tppt) REVERT: zA 1102 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9041 (tptm) REVERT: zA 1105 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.9010 (t80) REVERT: 0A 1202 LYS cc_start: 0.9156 (tttm) cc_final: 0.8793 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7960 (tm-30) cc_final: 0.6933 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8488 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8465 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8990 (tppp) REVERT: 4A 306 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8814 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8957 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8570 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8839 (ttpp) REVERT: g 4 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: 9A 102 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9106 (tptm) REVERT: AB 204 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: CB 1004 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: EB 1204 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: i 5 PHE cc_start: 0.9263 (t80) cc_final: 0.8918 (t80) REVERT: i 6 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8868 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: QB 1006 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8872 (ttpt) outliers start: 233 outliers final: 175 residues processed: 517 average time/residue: 0.4570 time to fit residues: 287.9464 Evaluate side-chains 647 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 430 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain T residue 1002 LYS Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain XA residue 1107 PHE Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1102 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.334 12528 Z= 5.992 Angle : 4.245 50.983 16272 Z= 1.877 Chirality : 0.299 0.776 1152 Planarity : 0.017 0.053 2160 Dihedral : 20.844 125.987 1506 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 112.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.71 % Favored : 82.29 % Rotamer: Outliers : 26.16 % Allowed : 27.08 % Favored : 46.76 % Cbeta Deviations : 15.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.17 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.115 0.017 PHE U1105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 431 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8785 (mmmt) REVERT: J 106 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8533 (mmmm) REVERT: M 1004 GLU cc_start: 0.8666 (mp0) cc_final: 0.8344 (mp0) REVERT: N 1106 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8550 (mmmm) REVERT: O 1202 LYS cc_start: 0.9219 (mtpt) cc_final: 0.9003 (mtpt) REVERT: B 4 GLU cc_start: 0.8250 (mp0) cc_final: 0.7976 (mp0) REVERT: B 6 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8710 (mtmt) REVERT: Q 106 LYS cc_start: 0.8942 (tptm) cc_final: 0.8328 (tptm) REVERT: R 202 LYS cc_start: 0.9196 (mtpt) cc_final: 0.8990 (mtpt) REVERT: S 302 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8861 (mtpp) REVERT: T 1006 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8689 (mtmt) REVERT: V 1202 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8934 (mtpt) REVERT: W 1302 LYS cc_start: 0.9294 (ttpt) cc_final: 0.8903 (mtpp) REVERT: C 6 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8611 (mtmt) REVERT: X 106 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8743 (mmmm) REVERT: Y 202 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8704 (mtpp) REVERT: Z 302 LYS cc_start: 0.9353 (ttpt) cc_final: 0.8962 (ttpp) REVERT: j 1006 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8680 (mtmt) REVERT: k 1106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8684 (mmmm) REVERT: m 1302 LYS cc_start: 0.9351 (ttpt) cc_final: 0.8956 (ttpp) REVERT: m 1306 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8957 (mttt) REVERT: n 106 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8608 (mmmm) REVERT: o 202 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8794 (mtpp) REVERT: p 302 LYS cc_start: 0.9257 (ttpt) cc_final: 0.8893 (ttpp) REVERT: q 1002 LYS cc_start: 0.7726 (tttm) cc_final: 0.7360 (tptm) REVERT: r 1106 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8643 (mmmm) REVERT: t 1302 LYS cc_start: 0.9254 (ttpt) cc_final: 0.8902 (ttpp) REVERT: u 102 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8726 (mtpp) REVERT: u 106 LYS cc_start: 0.9120 (tptm) cc_final: 0.8699 (tptm) REVERT: w 302 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: x 1002 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6473 (mmtp) REVERT: x 1006 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8453 (mtmt) REVERT: y 1106 LYS cc_start: 0.9104 (tptm) cc_final: 0.8689 (tptm) REVERT: 0 1302 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8898 (ttmm) REVERT: F 4 GLU cc_start: 0.8412 (mp0) cc_final: 0.7957 (mp0) REVERT: F 6 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8708 (mtmt) REVERT: 1 106 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8380 (mmmm) REVERT: 2 206 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8638 (ptmm) REVERT: 5 1106 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8426 (mmmm) REVERT: 6 1206 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8744 (ptmm) REVERT: G 4 GLU cc_start: 0.8107 (mp0) cc_final: 0.7854 (mp0) REVERT: G 6 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8468 (mtmt) REVERT: 8 106 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8531 (tmmm) REVERT: BA 1006 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8631 (mtmt) REVERT: GA 202 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8523 (mtpt) REVERT: KA 1204 GLU cc_start: 0.5111 (OUTLIER) cc_final: 0.4382 (pm20) REVERT: LA 1304 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9077 (tttt) cc_final: 0.8861 (tttt) REVERT: I 2 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8612 (tttt) REVERT: MA 106 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4950 (tptp) REVERT: OA 302 LYS cc_start: 0.9229 (ttpt) cc_final: 0.8799 (tptt) REVERT: RA 1202 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8550 (ttmm) REVERT: SA 1302 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8773 (tptt) REVERT: a 4 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: UA 202 LYS cc_start: 0.9340 (mttm) cc_final: 0.9007 (mmmm) REVERT: UA 204 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7856 (tp30) REVERT: VA 304 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8542 (tm-30) REVERT: WA 1004 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: YA 1204 GLU cc_start: 0.8040 (tp30) cc_final: 0.7759 (tp30) REVERT: ZA 1302 LYS cc_start: 0.9225 (tptp) cc_final: 0.8835 (tptp) REVERT: ZA 1304 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8459 (tm-30) REVERT: b 2 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8888 (ttmt) REVERT: bA 202 LYS cc_start: 0.9257 (tttm) cc_final: 0.8938 (ttmm) REVERT: bA 204 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7972 (tp30) REVERT: cA 304 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8571 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8911 (ttmt) REVERT: eA 1106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8310 (ttpp) REVERT: fA 1204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7877 (tp30) REVERT: gA 1304 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8635 (tm-30) REVERT: iA 202 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9032 (ttmm) REVERT: iA 204 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8006 (tm-30) REVERT: iA 206 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: jA 306 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8398 (ttpp) REVERT: mA 1204 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7852 (tm-30) REVERT: mA 1206 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8505 (ttpp) REVERT: nA 1306 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8346 (ttpp) REVERT: pA 206 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8947 (pttt) REVERT: qA 304 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8655 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8979 (pttt) REVERT: uA 1304 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8763 (tm-30) REVERT: vA 104 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8008 (tm-30) REVERT: wA 202 LYS cc_start: 0.9259 (tttm) cc_final: 0.8769 (ttmm) REVERT: wA 204 GLU cc_start: 0.8000 (tm-30) cc_final: 0.6936 (tm-30) REVERT: xA 302 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: xA 304 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8410 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8798 (tppt) REVERT: zA 1102 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9039 (tptm) REVERT: zA 1105 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.9002 (t80) REVERT: 0A 1202 LYS cc_start: 0.9162 (tttm) cc_final: 0.8793 (ttmm) REVERT: 0A 1204 GLU cc_start: 0.7978 (tm-30) cc_final: 0.6971 (tm-30) REVERT: 1A 1302 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8478 (tptp) REVERT: 1A 1304 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8466 (tm-30) REVERT: 3A 202 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8997 (tppp) REVERT: 4A 306 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8816 (ttpp) REVERT: 6A 1102 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8956 (tptm) REVERT: 8A 1304 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8568 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8839 (ttpp) REVERT: g 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: AB 204 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: CB 1002 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8969 (ptpt) REVERT: CB 1004 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: EB 1204 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: i 5 PHE cc_start: 0.9284 (t80) cc_final: 0.8904 (t80) REVERT: i 6 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8876 (ttpt) REVERT: QB 1004 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: QB 1006 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8853 (ttpt) REVERT: SB 1206 LYS cc_start: 0.9238 (pttt) cc_final: 0.8417 (ttpp) outliers start: 226 outliers final: 177 residues processed: 516 average time/residue: 0.4597 time to fit residues: 288.6192 Evaluate side-chains 648 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 431 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1002 LYS Chi-restraints excluded: chain M residue 1006 LYS Chi-restraints excluded: chain P residue 1304 GLU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 304 GLU Chi-restraints excluded: chain U residue 1104 GLU Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1304 GLU Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 207 PHE Chi-restraints excluded: chain Z residue 304 GLU Chi-restraints excluded: chain k residue 1104 GLU Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 307 PHE Chi-restraints excluded: chain s residue 1207 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1302 LYS Chi-restraints excluded: chain 0 residue 1306 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain BA residue 1006 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain IA residue 1004 GLU Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain NA residue 207 PHE Chi-restraints excluded: chain OA residue 306 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1306 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 103 PHE Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain TA residue 107 PHE Chi-restraints excluded: chain UA residue 206 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 103 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain eA residue 1106 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain hA residue 102 LYS Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain iA residue 202 LYS Chi-restraints excluded: chain iA residue 206 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 306 LYS Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 206 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain vA residue 106 LYS Chi-restraints excluded: chain xA residue 302 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1102 LYS Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1206 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 2A residue 102 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 202 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1306 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 204 GLU Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1204 GLU Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1305 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 303 PHE Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 105 PHE Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain OB residue 206 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 306 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1306 LYS Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061365 restraints weight = 33454.804| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.01 r_work: 0.2693 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.337 12528 Z= 5.992 Angle : 4.244 50.971 16272 Z= 1.875 Chirality : 0.299 0.779 1152 Planarity : 0.017 0.053 2160 Dihedral : 20.854 128.812 1506 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 112.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.36 % Favored : 82.64 % Rotamer: Outliers : 26.27 % Allowed : 27.20 % Favored : 46.53 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.19 (0.22), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.111 0.017 PHE U1105 =============================================================================== Job complete usr+sys time: 4085.40 seconds wall clock time: 73 minutes 58.22 seconds (4438.22 seconds total)