Starting phenix.real_space_refine on Fri Jul 19 01:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/07_2024/7lqf_23484.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3840 2.51 5 N 704 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 304": "OE1" <-> "OE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "r PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 304": "OE1" <-> "OE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 304": "OE1" <-> "OE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 104": "OE1" <-> "OE2" Residue "x PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 304": "OE1" <-> "OE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 104": "OE1" <-> "OE2" Residue "0 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 304": "OE1" <-> "OE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 104": "OE1" <-> "OE2" Residue "3 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 304": "OE1" <-> "OE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 104": "OE1" <-> "OE2" Residue "6 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 304": "OE1" <-> "OE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 104": "OE1" <-> "OE2" Residue "9 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 304": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5376 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.42, per 1000 atoms: 0.64 Number of scatterers: 5376 At special positions: 0 Unit cell: (70.2, 87.48, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 832 8.00 N 704 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 427.8 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.813A pdb=" N LYS A 6 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 6 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 6 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 305 through 306 removed outlier: 6.248A pdb=" N PHE j 205 " --> pdb=" O LYS k 306 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE W 305 " --> pdb=" O LYS j 206 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE V 205 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE Q 305 " --> pdb=" O LYS V 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE P 205 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE K 305 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 205 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE M 205 " --> pdb=" O LYS N 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE S 205 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE Y 205 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE m 205 " --> pdb=" O LYS n 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'a' and resid 4 through 6 removed outlier: 3.879A pdb=" N GLU a 4 " --> pdb=" O LYS r 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS r 106 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU r 104 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 104 through 106 removed outlier: 3.582A pdb=" N GLU o 104 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS o 106 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU c 4 " --> pdb=" O LYS o 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'y' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHE z 305 " --> pdb=" O PHE y 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE y 205 " --> pdb=" O PHE z 303 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU s 204 " --> pdb=" O LYS z 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GMA z 308 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS s 202 " --> pdb=" O GMA z 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE t 305 " --> pdb=" O PHE s 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE s 205 " --> pdb=" O PHE t 303 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS p 206 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU p 204 " --> pdb=" O LYS t 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE q 305 " --> pdb=" O PHE p 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE p 205 " --> pdb=" O PHE q 303 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU v 204 " --> pdb=" O LYS q 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GMA q 308 " --> pdb=" O LYS v 202 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS v 202 " --> pdb=" O GMA q 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE w 305 " --> pdb=" O PHE v 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE v 205 " --> pdb=" O PHE w 303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 1 206 " --> pdb=" O GLU w 304 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 1 204 " --> pdb=" O LYS w 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GMA w 308 " --> pdb=" O LYS 1 202 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS 1 202 " --> pdb=" O GMA w 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE 2 305 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE 1 205 " --> pdb=" O PHE 2 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS 7 206 " --> pdb=" O GLU 2 304 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU 7 204 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GMA 2 308 " --> pdb=" O LYS 7 202 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 7 202 " --> pdb=" O GMA 2 308 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 8 305 " --> pdb=" O PHE 7 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 7 205 " --> pdb=" O PHE 8 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 4 through 6 removed outlier: 3.815A pdb=" N GLU b 4 " --> pdb=" O LYS x 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'u' and resid 104 through 106 removed outlier: 3.578A pdb=" N GLU u 104 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS u 106 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 4 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.865A pdb=" N GLU d 4 " --> pdb=" O LYS 3 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 3 106 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 3 104 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 104 through 106 removed outlier: 3.619A pdb=" N GLU 0 104 " --> pdb=" O LYS g 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS 0 106 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU g 4 " --> pdb=" O LYS 0 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.795A pdb=" N GLU f 4 " --> pdb=" O LYS 9 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU 9 104 " --> pdb=" O LYS f 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 202 through 205 removed outlier: 3.693A pdb=" N PHE 5 305 " --> pdb=" O PHE 4 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 4 205 " --> pdb=" O PHE 5 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AA' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHEBA 305 " --> pdb=" O PHEAA 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHEAA 205 " --> pdb=" O PHEBA 303 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 649 1.25 - 1.33: 411 1.33 - 1.40: 1820 1.40 - 1.47: 576 1.47 - 1.54: 2112 Bond restraints: 5568 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 105.49 - 109.76: 526 109.76 - 114.03: 1763 114.03 - 118.30: 915 118.30 - 122.57: 3299 122.57 - 126.84: 729 Bond angle restraints: 7232 Sorted by residual: angle pdb=" C 5CR q 301 " pdb=" CA 5CR q 301 " pdb=" CB 5CR q 301 " ideal model delta sigma weight residual 110.10 116.12 -6.02 1.90e+00 2.77e-01 1.00e+01 angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.41 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C 5CR t 301 " pdb=" CA 5CR t 301 " pdb=" CB 5CR t 301 " ideal model delta sigma weight residual 110.10 116.11 -6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C 5CR 5 301 " pdb=" CA 5CR 5 301 " pdb=" CB 5CR 5 301 " ideal model delta sigma weight residual 110.10 116.10 -6.00 1.90e+00 2.77e-01 9.99e+00 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.39 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 7227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.80: 1977 10.80 - 21.61: 416 21.61 - 32.41: 159 32.41 - 43.21: 144 43.21 - 54.01: 56 Dihedral angle restraints: 2752 sinusoidal: 1280 harmonic: 1472 Sorted by residual: dihedral pdb=" CA LYS r 106 " pdb=" CB LYS r 106 " pdb=" CG LYS r 106 " pdb=" CD LYS r 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS 9 106 " pdb=" CB LYS 9 106 " pdb=" CG LYS 9 106 " pdb=" CD LYS 9 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS u 106 " pdb=" CB LYS u 106 " pdb=" CG LYS u 106 " pdb=" CD LYS u 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.017: 172 0.017 - 0.034: 140 0.034 - 0.051: 124 0.051 - 0.067: 60 0.067 - 0.084: 16 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PHE j 203 " pdb=" N PHE j 203 " pdb=" C PHE j 203 " pdb=" CB PHE j 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PHE Y 203 " pdb=" N PHE Y 203 " pdb=" C PHE Y 203 " pdb=" CB PHE Y 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.73e-01 chirality pdb=" CA PHE m 203 " pdb=" N PHE m 203 " pdb=" C PHE m 203 " pdb=" CB PHE m 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.71e-01 ... (remaining 509 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE p 203 " 0.009 2.00e-02 2.50e+03 6.10e-03 6.51e-01 pdb=" CG PHE p 203 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE p 203 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE p 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE p 203 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE p 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE p 203 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEBA 303 " 0.005 2.00e-02 2.50e+03 5.92e-03 6.14e-01 pdb=" CG PHEBA 303 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHEBA 303 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEBA 303 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEBA 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEBA 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHEBA 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 203 " -0.009 2.00e-02 2.50e+03 5.91e-03 6.11e-01 pdb=" CG PHE 4 203 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 203 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 203 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 203 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 4 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1729 2.79 - 3.31: 4534 3.31 - 3.84: 8714 3.84 - 4.37: 11165 4.37 - 4.90: 19430 Nonbonded interactions: 45572 Sorted by model distance: nonbonded pdb=" O GMA I 108 " pdb=" N 5CR J 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA i 108 " pdb=" N 5CR j 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA X 108 " pdb=" N 5CR Y 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA l 108 " pdb=" N 5CR m 201 " model vdw 2.258 2.520 nonbonded pdb=" O GMA R 108 " pdb=" N 5CR S 201 " model vdw 2.258 2.520 ... (remaining 45567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.110 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.116 5568 Z= 0.863 Angle : 1.461 9.501 7232 Z= 0.602 Chirality : 0.035 0.084 512 Planarity : 0.002 0.007 960 Dihedral : 18.365 54.014 1728 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8811 (tptm) REVERT: A 7 PHE cc_start: 0.8216 (m-10) cc_final: 0.7886 (m-10) REVERT: J 202 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7898 (ttmm) REVERT: K 306 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7586 (mmmm) REVERT: B 2 LYS cc_start: 0.9157 (tttt) cc_final: 0.8892 (tptm) REVERT: B 6 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7432 (mmmm) REVERT: L 102 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8600 (mmtt) REVERT: M 204 GLU cc_start: 0.8113 (pt0) cc_final: 0.7204 (pm20) REVERT: N 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Q 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7608 (mmmm) REVERT: D 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8722 (tptm) REVERT: D 3 PHE cc_start: 0.8401 (m-80) cc_final: 0.8172 (m-80) REVERT: D 6 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7546 (mmmm) REVERT: R 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6923 (tm-30) REVERT: S 204 GLU cc_start: 0.8108 (pt0) cc_final: 0.7535 (pm20) REVERT: T 305 PHE cc_start: 0.8456 (m-80) cc_final: 0.8254 (m-10) REVERT: T 306 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7671 (mmmm) REVERT: E 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8717 (tptm) REVERT: U 104 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7072 (tm-30) REVERT: V 204 GLU cc_start: 0.8325 (pt0) cc_final: 0.7746 (pm20) REVERT: W 302 LYS cc_start: 0.8301 (tppp) cc_final: 0.7719 (tppp) REVERT: W 306 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7862 (mmmm) REVERT: F 2 LYS cc_start: 0.9090 (tttt) cc_final: 0.8422 (tmtt) REVERT: X 104 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7017 (tm-30) REVERT: X 106 LYS cc_start: 0.7894 (tppt) cc_final: 0.7561 (tppt) REVERT: Y 204 GLU cc_start: 0.8371 (pt0) cc_final: 0.7350 (pp20) REVERT: Z 306 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7335 (mmmm) REVERT: G 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7868 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8357 (mmtt) REVERT: i 104 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7020 (tm-30) REVERT: i 106 LYS cc_start: 0.7678 (tppt) cc_final: 0.7407 (tppt) REVERT: j 204 GLU cc_start: 0.8071 (pt0) cc_final: 0.7744 (pm20) REVERT: k 304 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6755 (tm-30) REVERT: H 3 PHE cc_start: 0.8404 (m-80) cc_final: 0.8026 (m-80) REVERT: l 102 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8558 (mmtt) REVERT: m 204 GLU cc_start: 0.7905 (pt0) cc_final: 0.7370 (pm20) REVERT: m 205 PHE cc_start: 0.8286 (m-80) cc_final: 0.8052 (m-80) REVERT: n 306 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7577 (mmmm) REVERT: p 203 PHE cc_start: 0.7511 (t80) cc_final: 0.7309 (t80) REVERT: q 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7808 (t80) REVERT: q 307 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80) REVERT: r 105 PHE cc_start: 0.9015 (p90) cc_final: 0.8791 (p90) REVERT: t 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7770 (t80) REVERT: t 305 PHE cc_start: 0.7586 (t80) cc_final: 0.7183 (t80) REVERT: v 204 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7051 (tm-30) REVERT: w 302 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8490 (tmtt) REVERT: x 105 PHE cc_start: 0.8978 (p90) cc_final: 0.8358 (p90) REVERT: x 107 PHE cc_start: 0.8027 (t80) cc_final: 0.7191 (t80) REVERT: z 305 PHE cc_start: 0.7904 (t80) cc_final: 0.7476 (t80) REVERT: e 6 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8167 (ttmm) REVERT: e 7 PHE cc_start: 0.9053 (t80) cc_final: 0.8752 (t80) REVERT: 1 202 LYS cc_start: 0.8057 (tptp) cc_final: 0.7783 (tptp) REVERT: 2 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7673 (t80) REVERT: f 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8382 (t80) REVERT: 3 105 PHE cc_start: 0.8867 (p90) cc_final: 0.8660 (p90) REVERT: 3 106 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8356 (ttpp) REVERT: 4 204 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 5 303 PHE cc_start: 0.8146 (t80) cc_final: 0.7910 (t80) REVERT: g 2 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8492 (mmtt) REVERT: 6 106 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8435 (ttpp) REVERT: 7 204 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 8 302 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8593 (tmtt) REVERT: 8 307 PHE cc_start: 0.7753 (t80) cc_final: 0.7394 (t80) REVERT: 9 107 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) outliers start: 8 outliers final: 0 residues processed: 164 average time/residue: 0.3607 time to fit residues: 67.4099 Evaluate side-chains 161 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain G residue 6 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.5980 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: 0.8356 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.153 0.473 5568 Z= 8.405 Angle : 6.035 58.890 7232 Z= 2.682 Chirality : 0.410 1.078 512 Planarity : 0.031 0.095 960 Dihedral : 24.922 84.557 652 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 204.58 Ramachandran Plot: Outliers : 8.98 % Allowed : 37.50 % Favored : 53.52 % Rotamer: Outliers : 14.58 % Allowed : 29.69 % Favored : 55.73 % Cbeta Deviations : 46.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.81 (0.25), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.71 (0.19), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.191 0.029 PHE 3 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 156 time to evaluate : 0.548 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: I 103 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: I 107 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8360 (m-10) REVERT: J 206 LYS cc_start: 0.8971 (tttm) cc_final: 0.7683 (ttpp) REVERT: K 306 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8158 (mmmm) REVERT: L 103 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: M 202 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8847 (ttmm) REVERT: M 206 LYS cc_start: 0.8661 (tttm) cc_final: 0.8023 (tttm) REVERT: N 302 LYS cc_start: 0.8813 (tppp) cc_final: 0.8519 (tppp) REVERT: N 304 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8140 (tm-30) REVERT: N 306 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8085 (mmmm) REVERT: N 307 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8332 (t80) REVERT: Q 302 LYS cc_start: 0.8831 (tppp) cc_final: 0.8193 (tppp) REVERT: Q 303 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: S 206 LYS cc_start: 0.8882 (tttm) cc_final: 0.8431 (tttm) REVERT: T 304 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8177 (tm-30) REVERT: T 306 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8075 (mmmm) REVERT: E 6 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8537 (ttmm) REVERT: V 202 LYS cc_start: 0.9364 (ttmm) cc_final: 0.8777 (ttmm) REVERT: W 302 LYS cc_start: 0.8877 (tppp) cc_final: 0.8474 (tppp) REVERT: W 304 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7190 (tm-30) REVERT: Y 206 LYS cc_start: 0.8527 (tttm) cc_final: 0.8145 (tttm) REVERT: Z 306 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8030 (mmmm) REVERT: Z 307 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: G 2 LYS cc_start: 0.9293 (tptt) cc_final: 0.8971 (tptm) REVERT: G 6 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8199 (ttmm) REVERT: G 7 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: i 102 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8757 (mmmt) REVERT: i 106 LYS cc_start: 0.5049 (tppt) cc_final: 0.4342 (tptt) REVERT: j 206 LYS cc_start: 0.8839 (tttm) cc_final: 0.8202 (ttpp) REVERT: H 6 LYS cc_start: 0.9378 (mmmm) cc_final: 0.9163 (mmmm) REVERT: l 103 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: l 106 LYS cc_start: 0.8900 (tppt) cc_final: 0.8460 (tppt) REVERT: m 202 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8829 (ttmm) REVERT: m 204 GLU cc_start: 0.8969 (pt0) cc_final: 0.8570 (pt0) REVERT: n 302 LYS cc_start: 0.8866 (tppp) cc_final: 0.8615 (tppp) REVERT: n 304 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7948 (tm-30) REVERT: n 306 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8307 (mmmm) REVERT: n 307 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8622 (t80) REVERT: o 106 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8799 (ttmt) REVERT: p 204 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8373 (tm-30) REVERT: p 206 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8249 (tptp) REVERT: s 202 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8671 (ttmm) REVERT: t 302 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8443 (tmtt) REVERT: t 306 LYS cc_start: 0.8846 (tmtt) cc_final: 0.7972 (tmtt) REVERT: c 2 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8602 (mmtt) REVERT: v 204 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7978 (tm-30) REVERT: d 7 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8879 (t80) REVERT: z 306 LYS cc_start: 0.8939 (tttt) cc_final: 0.7944 (tmtt) REVERT: z 307 PHE cc_start: 0.8868 (t80) cc_final: 0.8616 (t80) REVERT: 0 106 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: 1 206 LYS cc_start: 0.8511 (tptp) cc_final: 0.7999 (tptp) REVERT: 3 102 LYS cc_start: 0.9072 (tptp) cc_final: 0.8778 (tptp) REVERT: 3 103 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8231 (p90) REVERT: 3 107 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8414 (t80) REVERT: 4 204 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7863 (tm-30) REVERT: 5 302 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8654 (tmtt) REVERT: 5 307 PHE cc_start: 0.8811 (t80) cc_final: 0.8544 (t80) REVERT: g 2 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8516 (mmtt) REVERT: 6 102 LYS cc_start: 0.9102 (tptp) cc_final: 0.8898 (tptp) REVERT: 7 202 LYS cc_start: 0.9045 (tptp) cc_final: 0.8760 (tptp) REVERT: 8 307 PHE cc_start: 0.8630 (t80) cc_final: 0.8384 (t80) REVERT: AA 206 LYS cc_start: 0.8734 (tptp) cc_final: 0.8431 (tptp) REVERT: BA 307 PHE cc_start: 0.8866 (t80) cc_final: 0.8618 (t80) outliers start: 56 outliers final: 28 residues processed: 195 average time/residue: 0.3790 time to fit residues: 82.9975 Evaluate side-chains 197 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 106 LYS Chi-restraints excluded: chain p residue 206 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain c residue 7 PHE Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.9702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.485 5568 Z= 8.474 Angle : 6.148 59.236 7232 Z= 2.731 Chirality : 0.414 1.055 512 Planarity : 0.030 0.091 960 Dihedral : 24.767 88.590 648 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 200.04 Ramachandran Plot: Outliers : 2.73 % Allowed : 59.38 % Favored : 37.89 % Rotamer: Outliers : 22.14 % Allowed : 34.11 % Favored : 43.75 % Cbeta Deviations : 47.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.42 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.18 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.182 0.027 PHE N 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 153 time to evaluate : 0.585 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: A 2 LYS cc_start: 0.9333 (tptt) cc_final: 0.9024 (tptt) REVERT: A 5 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: A 7 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8859 (m-10) REVERT: I 107 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: J 206 LYS cc_start: 0.8879 (tttm) cc_final: 0.8338 (ttpp) REVERT: K 302 LYS cc_start: 0.9012 (tppp) cc_final: 0.8732 (tppp) REVERT: K 306 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8280 (mmmm) REVERT: M 202 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8828 (ttmm) REVERT: N 302 LYS cc_start: 0.8936 (tppp) cc_final: 0.8703 (tppp) REVERT: N 304 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8207 (tm-30) REVERT: N 306 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8208 (mmmm) REVERT: N 307 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8351 (t80) REVERT: Q 303 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: S 206 LYS cc_start: 0.8827 (tttm) cc_final: 0.8185 (ttpp) REVERT: T 304 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7484 (tm-30) REVERT: T 306 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8063 (mmtp) REVERT: E 6 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8467 (ttmm) REVERT: V 202 LYS cc_start: 0.9393 (ttmm) cc_final: 0.9000 (ttmm) REVERT: W 302 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8581 (tppp) REVERT: X 103 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8661 (m-10) REVERT: Y 206 LYS cc_start: 0.8504 (tttm) cc_final: 0.8204 (tttm) REVERT: Z 302 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8474 (tppp) REVERT: Z 304 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8251 (tm-30) REVERT: Z 306 LYS cc_start: 0.8571 (mmmm) cc_final: 0.7759 (mmmm) REVERT: Z 307 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: G 2 LYS cc_start: 0.9279 (tptt) cc_final: 0.9078 (tptm) REVERT: G 5 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: G 7 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: i 102 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8683 (mmmt) REVERT: i 103 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8823 (m-10) REVERT: j 206 LYS cc_start: 0.8784 (tttm) cc_final: 0.8565 (ttpp) REVERT: H 6 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9098 (mmmm) REVERT: l 102 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9090 (mmtt) REVERT: l 103 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: l 106 LYS cc_start: 0.9018 (tppt) cc_final: 0.8625 (tppt) REVERT: m 202 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8908 (ttmm) REVERT: m 207 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7144 (t80) REVERT: n 302 LYS cc_start: 0.8930 (tppp) cc_final: 0.8627 (tppp) REVERT: n 304 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8011 (tm-30) REVERT: n 306 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8465 (mmmm) REVERT: a 2 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8340 (mmtt) REVERT: p 206 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8177 (tptp) REVERT: q 306 LYS cc_start: 0.8899 (tttt) cc_final: 0.8442 (tttp) REVERT: q 307 PHE cc_start: 0.8705 (t80) cc_final: 0.8042 (t80) REVERT: r 106 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: t 302 LYS cc_start: 0.8972 (tmtt) cc_final: 0.8130 (tmtt) REVERT: t 303 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7122 (t80) REVERT: c 2 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8672 (mmtt) REVERT: v 204 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8189 (tm-30) REVERT: d 7 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8940 (t80) REVERT: y 202 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8855 (ttmm) REVERT: y 203 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8325 (t80) REVERT: 1 206 LYS cc_start: 0.8428 (tptp) cc_final: 0.7906 (tptp) REVERT: 3 102 LYS cc_start: 0.9176 (tptp) cc_final: 0.8915 (tptp) REVERT: 3 103 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8364 (p90) REVERT: 3 107 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8424 (t80) REVERT: 4 204 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8190 (tm-30) REVERT: 5 306 LYS cc_start: 0.8704 (tttt) cc_final: 0.8370 (tttt) REVERT: 5 307 PHE cc_start: 0.8900 (t80) cc_final: 0.8320 (t80) REVERT: 8 307 PHE cc_start: 0.8590 (t80) cc_final: 0.8295 (t80) REVERT: 9 104 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7459 (tm-30) REVERT: AA 206 LYS cc_start: 0.8703 (tptp) cc_final: 0.8147 (tptp) REVERT: BA 307 PHE cc_start: 0.8850 (t80) cc_final: 0.8508 (t80) outliers start: 85 outliers final: 46 residues processed: 210 average time/residue: 0.3528 time to fit residues: 83.9540 Evaluate side-chains 219 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 151 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 206 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.9906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.482 5568 Z= 8.457 Angle : 6.174 59.630 7232 Z= 2.743 Chirality : 0.415 1.031 512 Planarity : 0.029 0.087 960 Dihedral : 24.815 84.553 648 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 201.57 Ramachandran Plot: Outliers : 1.17 % Allowed : 61.72 % Favored : 37.11 % Rotamer: Outliers : 24.74 % Allowed : 36.72 % Favored : 38.54 % Cbeta Deviations : 46.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.45 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.20 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.183 0.026 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 156 time to evaluate : 0.508 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 5 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8017 (m-10) REVERT: A 7 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8871 (m-10) REVERT: I 107 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: J 206 LYS cc_start: 0.8969 (tttm) cc_final: 0.8434 (ttpp) REVERT: K 306 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8236 (mmmm) REVERT: L 103 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: M 202 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8836 (ttmm) REVERT: N 302 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8803 (tppp) REVERT: N 304 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8161 (tm-30) REVERT: N 306 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8190 (mmmm) REVERT: N 307 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8338 (t80) REVERT: Q 306 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7908 (mmmm) REVERT: Q 307 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7879 (t80) REVERT: S 202 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8631 (ttpp) REVERT: S 206 LYS cc_start: 0.8808 (tttm) cc_final: 0.8473 (ttpp) REVERT: T 304 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7442 (tm-30) REVERT: T 306 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8081 (mmtp) REVERT: V 202 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9083 (ttmm) REVERT: V 206 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7919 (ttpp) REVERT: W 302 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8567 (tppp) REVERT: X 106 LYS cc_start: 0.8984 (tppt) cc_final: 0.8377 (tppt) REVERT: Y 206 LYS cc_start: 0.8495 (tttm) cc_final: 0.8221 (tttm) REVERT: Z 302 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8361 (tppp) REVERT: Z 307 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: G 5 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: G 7 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: i 102 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8652 (mmmt) REVERT: i 103 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8766 (m-10) REVERT: j 206 LYS cc_start: 0.8605 (tttm) cc_final: 0.8278 (ttpp) REVERT: H 6 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9100 (mmmm) REVERT: l 103 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: m 202 LYS cc_start: 0.9228 (ttmm) cc_final: 0.9021 (ttmm) REVERT: m 207 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6837 (t80) REVERT: n 302 LYS cc_start: 0.8933 (tppp) cc_final: 0.8678 (tppp) REVERT: n 304 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8004 (tm-30) REVERT: n 306 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8604 (mmmm) REVERT: a 2 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8313 (mmtt) REVERT: o 107 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8301 (t80) REVERT: p 203 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8091 (t80) REVERT: q 307 PHE cc_start: 0.8714 (t80) cc_final: 0.8215 (t80) REVERT: r 102 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: r 106 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8658 (ttpp) REVERT: t 303 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7240 (t80) REVERT: c 2 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8635 (mmtt) REVERT: v 204 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8149 (tm-30) REVERT: y 203 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8417 (t80) REVERT: 1 206 LYS cc_start: 0.8429 (tptp) cc_final: 0.7932 (tptp) REVERT: 2 306 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8386 (tmtt) REVERT: 2 307 PHE cc_start: 0.8731 (t80) cc_final: 0.8481 (t80) REVERT: f 2 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8424 (mmtt) REVERT: 3 102 LYS cc_start: 0.9124 (tptp) cc_final: 0.8880 (tptp) REVERT: 3 103 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8359 (p90) REVERT: 4 204 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8146 (tm-30) REVERT: 5 306 LYS cc_start: 0.8727 (tttp) cc_final: 0.8300 (tttt) REVERT: 5 307 PHE cc_start: 0.8917 (t80) cc_final: 0.8326 (t80) REVERT: g 2 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8448 (mmtt) REVERT: 7 202 LYS cc_start: 0.9063 (tptp) cc_final: 0.8776 (tptp) REVERT: 7 203 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8271 (t80) REVERT: 8 307 PHE cc_start: 0.8563 (t80) cc_final: 0.8269 (t80) REVERT: 9 104 GLU cc_start: 0.8717 (tm-30) cc_final: 0.7670 (tm-30) REVERT: AA 206 LYS cc_start: 0.8714 (tptp) cc_final: 0.8131 (tptp) REVERT: BA 307 PHE cc_start: 0.8858 (t80) cc_final: 0.8427 (t80) outliers start: 95 outliers final: 52 residues processed: 210 average time/residue: 0.3615 time to fit residues: 85.6983 Evaluate side-chains 235 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 155 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 102 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.9983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.478 5568 Z= 8.451 Angle : 6.176 59.756 7232 Z= 2.740 Chirality : 0.415 1.041 512 Planarity : 0.029 0.093 960 Dihedral : 24.828 85.067 644 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 200.54 Ramachandran Plot: Outliers : 1.95 % Allowed : 63.28 % Favored : 34.77 % Rotamer: Outliers : 26.04 % Allowed : 36.46 % Favored : 37.50 % Cbeta Deviations : 47.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.46 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.21 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.182 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 156 time to evaluate : 0.557 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 5 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: A 7 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8879 (m-10) REVERT: I 106 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8106 (tppt) REVERT: I 107 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: J 206 LYS cc_start: 0.9000 (tttm) cc_final: 0.8515 (ttpp) REVERT: K 302 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8633 (tppp) REVERT: K 306 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8275 (mmmm) REVERT: M 202 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8808 (ttmm) REVERT: N 302 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8809 (tppp) REVERT: N 304 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8220 (tm-30) REVERT: N 306 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8186 (mmmm) REVERT: N 307 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8335 (t80) REVERT: Q 302 LYS cc_start: 0.8846 (tppp) cc_final: 0.8592 (mmmm) REVERT: Q 303 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: Q 306 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7857 (mmmm) REVERT: S 202 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8263 (ttpp) REVERT: S 206 LYS cc_start: 0.8713 (tttm) cc_final: 0.7845 (ttpp) REVERT: T 304 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7482 (tm-30) REVERT: T 306 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: V 202 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9071 (ttmm) REVERT: V 206 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7866 (ttpp) REVERT: W 302 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8577 (tppp) REVERT: X 103 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: X 106 LYS cc_start: 0.8990 (tppt) cc_final: 0.8415 (tppt) REVERT: Y 206 LYS cc_start: 0.8507 (tttm) cc_final: 0.8242 (tttm) REVERT: Z 302 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8248 (tppp) REVERT: Z 306 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8033 (mmmm) REVERT: Z 307 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: G 5 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: G 7 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: i 102 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8640 (mmmt) REVERT: i 103 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8758 (m-10) REVERT: j 206 LYS cc_start: 0.8526 (tttm) cc_final: 0.8186 (ttpp) REVERT: k 304 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7365 (tm-30) REVERT: H 6 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9033 (mmmm) REVERT: l 102 LYS cc_start: 0.9413 (mmtt) cc_final: 0.9174 (mmtm) REVERT: l 103 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: l 106 LYS cc_start: 0.9018 (tppt) cc_final: 0.8602 (tppt) REVERT: m 207 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.6829 (t80) REVERT: n 302 LYS cc_start: 0.8929 (tppp) cc_final: 0.8688 (tppp) REVERT: n 304 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7994 (tm-30) REVERT: a 2 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8281 (mmtt) REVERT: o 107 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8042 (t80) REVERT: p 203 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8189 (t80) REVERT: q 307 PHE cc_start: 0.8732 (t80) cc_final: 0.8167 (t80) REVERT: b 2 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8532 (mmtt) REVERT: r 106 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8670 (ttpp) REVERT: s 207 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8348 (t80) REVERT: t 303 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7209 (t80) REVERT: u 102 LYS cc_start: 0.9067 (tptp) cc_final: 0.8859 (tptp) REVERT: v 204 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8161 (tm-30) REVERT: d 7 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8895 (t80) REVERT: y 203 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8416 (t80) REVERT: 1 206 LYS cc_start: 0.8426 (tptp) cc_final: 0.7924 (tptp) REVERT: 2 306 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8567 (tmtt) REVERT: 3 102 LYS cc_start: 0.9119 (tptp) cc_final: 0.8897 (tptp) REVERT: 3 103 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8406 (p90) REVERT: 4 204 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8130 (tm-30) REVERT: 5 306 LYS cc_start: 0.8710 (tttp) cc_final: 0.8288 (tttp) REVERT: 5 307 PHE cc_start: 0.8904 (t80) cc_final: 0.8461 (t80) REVERT: g 2 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8451 (mmtt) REVERT: 7 203 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8425 (t80) REVERT: 8 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8271 (t80) REVERT: 9 104 GLU cc_start: 0.8682 (tm-30) cc_final: 0.7569 (tm-30) REVERT: AA 206 LYS cc_start: 0.8652 (tptp) cc_final: 0.8026 (tptp) REVERT: BA 307 PHE cc_start: 0.8859 (t80) cc_final: 0.8387 (t80) outliers start: 100 outliers final: 55 residues processed: 216 average time/residue: 0.3525 time to fit residues: 86.1035 Evaluate side-chains 243 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 156 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain 9 residue 107 PHE Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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: 0.8302 moved from start: 1.0037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.476 5568 Z= 8.463 Angle : 6.198 59.658 7232 Z= 2.749 Chirality : 0.416 1.053 512 Planarity : 0.029 0.092 960 Dihedral : 24.737 82.049 644 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 201.49 Ramachandran Plot: Outliers : 1.95 % Allowed : 62.11 % Favored : 35.94 % Rotamer: Outliers : 28.39 % Allowed : 35.16 % Favored : 36.46 % Cbeta Deviations : 47.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.47 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.21 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.180 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 156 time to evaluate : 0.576 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 5 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: A 7 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8876 (m-10) REVERT: I 103 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: I 106 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8113 (tppt) REVERT: I 107 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: J 206 LYS cc_start: 0.8994 (tttm) cc_final: 0.8503 (ttpp) REVERT: K 302 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8687 (tppp) REVERT: K 306 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8314 (mmmm) REVERT: M 202 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8797 (ttmm) REVERT: N 302 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8810 (tppp) REVERT: N 304 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8238 (tm-30) REVERT: N 306 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8184 (mmmm) REVERT: N 307 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8331 (t80) REVERT: Q 302 LYS cc_start: 0.8803 (tppp) cc_final: 0.8567 (mmmm) REVERT: Q 303 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: Q 306 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7789 (mmmm) REVERT: S 202 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8236 (ttpp) REVERT: S 206 LYS cc_start: 0.8699 (tttm) cc_final: 0.7898 (ttpp) REVERT: T 304 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7476 (tm-30) REVERT: T 306 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8101 (mmtp) REVERT: U 106 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8341 (tppt) REVERT: V 202 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9051 (ttmm) REVERT: V 206 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7826 (ttpp) REVERT: W 302 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8584 (tppp) REVERT: F 5 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: X 103 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8713 (m-10) REVERT: X 106 LYS cc_start: 0.8987 (tppt) cc_final: 0.8399 (tppt) REVERT: Y 206 LYS cc_start: 0.8520 (tttm) cc_final: 0.8273 (tttm) REVERT: Z 302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8237 (tppp) REVERT: Z 306 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8026 (mmmm) REVERT: Z 307 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: G 5 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: G 7 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: i 102 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8634 (mmmt) REVERT: i 103 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8756 (m-10) REVERT: k 304 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7402 (tm-30) REVERT: H 6 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9032 (mmmm) REVERT: l 102 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9178 (mmtm) REVERT: l 103 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: l 106 LYS cc_start: 0.8987 (tppt) cc_final: 0.8578 (tppt) REVERT: m 207 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6836 (t80) REVERT: n 304 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8023 (tm-30) REVERT: a 2 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8287 (mmtt) REVERT: o 107 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8058 (t80) REVERT: p 203 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8198 (t80) REVERT: q 306 LYS cc_start: 0.8878 (tttp) cc_final: 0.8460 (tttp) REVERT: q 307 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7974 (t80) REVERT: r 106 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: s 207 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8248 (t80) REVERT: t 303 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7230 (t80) REVERT: c 2 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8473 (mmtt) REVERT: c 3 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7850 (t80) REVERT: u 102 LYS cc_start: 0.9120 (tptp) cc_final: 0.8913 (tptp) REVERT: v 204 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8190 (tm-30) REVERT: y 203 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8410 (t80) REVERT: 1 203 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8408 (t80) REVERT: 1 206 LYS cc_start: 0.8442 (tptp) cc_final: 0.7951 (tptp) REVERT: 2 306 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8586 (tmtt) REVERT: 3 102 LYS cc_start: 0.9108 (tptp) cc_final: 0.8877 (tptp) REVERT: 3 103 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8384 (p90) REVERT: 4 202 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8710 (tppp) REVERT: 4 204 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8124 (tm-30) REVERT: 5 306 LYS cc_start: 0.8726 (tttp) cc_final: 0.8286 (tttp) REVERT: 5 307 PHE cc_start: 0.8893 (t80) cc_final: 0.8429 (t80) REVERT: g 2 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8451 (mmtt) REVERT: 7 202 LYS cc_start: 0.9194 (tptp) cc_final: 0.8749 (tptp) REVERT: 7 203 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8271 (t80) REVERT: 9 104 GLU cc_start: 0.8712 (tm-30) cc_final: 0.7598 (tm-30) REVERT: AA 206 LYS cc_start: 0.8663 (tptp) cc_final: 0.8026 (tptp) REVERT: BA 307 PHE cc_start: 0.8883 (t80) cc_final: 0.8430 (t80) outliers start: 109 outliers final: 59 residues processed: 219 average time/residue: 0.3629 time to fit residues: 89.9906 Evaluate side-chains 252 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 156 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain 9 residue 107 PHE Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.0084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 8.461 Angle : 6.210 59.604 7232 Z= 2.756 Chirality : 0.417 1.104 512 Planarity : 0.029 0.093 960 Dihedral : 24.737 83.127 644 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 201.16 Ramachandran Plot: Outliers : 2.73 % Allowed : 61.72 % Favored : 35.55 % Rotamer: Outliers : 29.95 % Allowed : 35.16 % Favored : 34.90 % Cbeta Deviations : 47.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.49 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.23 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.181 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 157 time to evaluate : 0.537 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 5 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: A 7 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8878 (m-10) REVERT: I 103 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: I 106 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8108 (tppt) REVERT: I 107 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: J 206 LYS cc_start: 0.8988 (tttm) cc_final: 0.8492 (ttpp) REVERT: K 302 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8667 (tppp) REVERT: K 306 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8228 (mmmm) REVERT: M 202 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8767 (ttmm) REVERT: N 302 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8813 (tppp) REVERT: N 306 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8186 (mmmm) REVERT: N 307 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8335 (t80) REVERT: Q 302 LYS cc_start: 0.8821 (tppp) cc_final: 0.8597 (mmmm) REVERT: Q 303 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: S 202 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: S 206 LYS cc_start: 0.8761 (tttm) cc_final: 0.7800 (ttpp) REVERT: T 304 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7487 (tm-30) REVERT: T 306 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8124 (mmtp) REVERT: E 6 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8570 (ttmm) REVERT: U 106 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8404 (tppt) REVERT: V 202 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: V 206 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8136 (ttpp) REVERT: W 302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8208 (ttpp) REVERT: W 307 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8074 (t80) REVERT: F 5 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: X 103 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: X 106 LYS cc_start: 0.8982 (tppt) cc_final: 0.8440 (tppt) REVERT: Y 206 LYS cc_start: 0.8528 (tttm) cc_final: 0.8273 (tttm) REVERT: Z 302 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8360 (tppp) REVERT: Z 306 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8026 (mmmm) REVERT: Z 307 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: G 5 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: G 7 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: i 102 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8633 (mmmt) REVERT: i 103 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8745 (m-10) REVERT: k 304 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7409 (tm-30) REVERT: H 6 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9030 (mmmm) REVERT: l 102 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9167 (mmtm) REVERT: l 103 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: l 106 LYS cc_start: 0.8972 (tppt) cc_final: 0.8571 (tppt) REVERT: n 302 LYS cc_start: 0.8773 (tppp) cc_final: 0.8553 (tppp) REVERT: n 304 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8081 (tm-30) REVERT: a 2 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8284 (mmtt) REVERT: o 107 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8060 (t80) REVERT: p 203 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8215 (t80) REVERT: q 307 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8164 (t80) REVERT: r 102 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8340 (ttpp) REVERT: r 106 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: s 207 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8124 (t80) REVERT: t 303 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7222 (t80) REVERT: c 2 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8496 (mmtt) REVERT: c 3 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7876 (t80) REVERT: u 102 LYS cc_start: 0.9075 (tptp) cc_final: 0.8865 (tptp) REVERT: v 204 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8212 (tm-30) REVERT: v 207 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8154 (t80) REVERT: d 7 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8851 (t80) REVERT: y 203 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8411 (t80) REVERT: 1 206 LYS cc_start: 0.8440 (tptp) cc_final: 0.7957 (tptp) REVERT: 2 306 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8483 (tmtt) REVERT: 3 102 LYS cc_start: 0.9121 (tptp) cc_final: 0.8916 (tptp) REVERT: 3 103 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8471 (p90) REVERT: 4 204 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8114 (tm-30) REVERT: 5 306 LYS cc_start: 0.8740 (tttp) cc_final: 0.8329 (tttp) REVERT: 5 307 PHE cc_start: 0.8882 (t80) cc_final: 0.8443 (t80) REVERT: g 2 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8453 (mmtt) REVERT: 7 202 LYS cc_start: 0.9114 (tptp) cc_final: 0.8647 (tptp) REVERT: 7 203 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8094 (t80) REVERT: 8 306 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7369 (pttm) REVERT: 8 307 PHE cc_start: 0.8537 (t80) cc_final: 0.8130 (t80) REVERT: 9 104 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7596 (tm-30) REVERT: AA 206 LYS cc_start: 0.8660 (tptp) cc_final: 0.8026 (tptp) REVERT: BA 307 PHE cc_start: 0.8850 (t80) cc_final: 0.8398 (t80) outliers start: 115 outliers final: 62 residues processed: 224 average time/residue: 0.3425 time to fit residues: 87.0447 Evaluate side-chains 259 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 157 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 307 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 8 residue 304 GLU Chi-restraints excluded: chain 8 residue 306 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain 9 residue 107 PHE Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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: 0.8302 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 8.457 Angle : 6.240 59.762 7232 Z= 2.765 Chirality : 0.417 1.070 512 Planarity : 0.029 0.091 960 Dihedral : 24.747 82.513 644 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 202.50 Ramachandran Plot: Outliers : 2.34 % Allowed : 61.72 % Favored : 35.94 % Rotamer: Outliers : 27.86 % Allowed : 38.28 % Favored : 33.85 % Cbeta Deviations : 47.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.52 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.25 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.181 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 156 time to evaluate : 0.475 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 5 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: A 7 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8872 (m-10) REVERT: I 103 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: I 106 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: I 107 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: J 206 LYS cc_start: 0.8989 (tttm) cc_final: 0.8501 (ttpp) REVERT: K 302 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8642 (tppp) REVERT: K 306 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8304 (mmmm) REVERT: B 6 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8702 (mmmm) REVERT: M 202 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8759 (ttmm) REVERT: M 206 LYS cc_start: 0.8708 (tttm) cc_final: 0.8235 (tttm) REVERT: N 302 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8818 (tppp) REVERT: N 306 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8172 (mmmm) REVERT: N 307 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8334 (t80) REVERT: Q 302 LYS cc_start: 0.8794 (tppp) cc_final: 0.8589 (mmmm) REVERT: Q 303 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: S 202 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: S 206 LYS cc_start: 0.8694 (tttm) cc_final: 0.7754 (ttpp) REVERT: T 304 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7476 (tm-30) REVERT: T 306 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8058 (mmtp) REVERT: U 106 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8423 (tppt) REVERT: V 202 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.8345 (ttmm) REVERT: V 206 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8132 (ttpp) REVERT: W 302 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8206 (ttpp) REVERT: F 5 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: X 103 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: X 106 LYS cc_start: 0.9005 (tppt) cc_final: 0.8465 (tppt) REVERT: Y 206 LYS cc_start: 0.8535 (tttm) cc_final: 0.8300 (tttm) REVERT: Z 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8321 (tppp) REVERT: Z 306 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8020 (mmmm) REVERT: Z 307 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: G 5 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: G 7 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: i 102 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8633 (mmmt) REVERT: i 103 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8747 (m-10) REVERT: j 206 LYS cc_start: 0.8788 (ttpp) cc_final: 0.7805 (ttpp) REVERT: k 304 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7416 (tm-30) REVERT: H 6 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9036 (mmmm) REVERT: l 102 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9162 (mmtm) REVERT: l 103 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: l 106 LYS cc_start: 0.8974 (tppt) cc_final: 0.8576 (tppt) REVERT: m 207 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7126 (t80) REVERT: n 302 LYS cc_start: 0.8968 (tppp) cc_final: 0.8713 (tppp) REVERT: n 304 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8077 (tm-30) REVERT: a 2 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8279 (mmtt) REVERT: o 107 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8093 (t80) REVERT: p 203 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8213 (t80) REVERT: q 307 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8186 (t80) REVERT: r 102 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8316 (ttpp) REVERT: r 106 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8645 (ttpp) REVERT: s 207 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8138 (t80) REVERT: t 303 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7194 (t80) REVERT: c 2 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8589 (mmtt) REVERT: c 3 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7868 (t80) REVERT: v 204 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8176 (tm-30) REVERT: v 207 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8153 (t80) REVERT: y 203 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8416 (t80) REVERT: 1 206 LYS cc_start: 0.8438 (tptp) cc_final: 0.7944 (tptp) REVERT: 2 306 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8464 (tmtt) REVERT: 3 102 LYS cc_start: 0.9126 (tptp) cc_final: 0.8897 (tptp) REVERT: 3 103 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8401 (p90) REVERT: 4 204 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8111 (tm-30) REVERT: 5 306 LYS cc_start: 0.8744 (tttp) cc_final: 0.8312 (tttp) REVERT: 5 307 PHE cc_start: 0.8873 (t80) cc_final: 0.8454 (t80) REVERT: g 2 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8457 (mmtt) REVERT: 7 202 LYS cc_start: 0.9080 (tptp) cc_final: 0.8666 (tptp) REVERT: 7 203 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8189 (t80) REVERT: 8 306 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7367 (pttm) REVERT: 8 307 PHE cc_start: 0.8446 (t80) cc_final: 0.7994 (t80) REVERT: 9 104 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7587 (tm-30) REVERT: AA 206 LYS cc_start: 0.8666 (tptp) cc_final: 0.8037 (tptp) REVERT: BA 307 PHE cc_start: 0.8853 (t80) cc_final: 0.8406 (t80) outliers start: 107 outliers final: 59 residues processed: 220 average time/residue: 0.3500 time to fit residues: 87.3188 Evaluate side-chains 255 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 156 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 8 residue 304 GLU Chi-restraints excluded: chain 8 residue 306 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain 9 residue 107 PHE Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.0140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.477 5568 Z= 8.462 Angle : 6.234 59.723 7232 Z= 2.761 Chirality : 0.418 1.096 512 Planarity : 0.029 0.093 960 Dihedral : 24.692 84.446 644 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 201.75 Ramachandran Plot: Outliers : 1.95 % Allowed : 62.11 % Favored : 35.94 % Rotamer: Outliers : 28.12 % Allowed : 38.54 % Favored : 33.33 % Cbeta Deviations : 47.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.50 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.24 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.180 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 157 time to evaluate : 0.558 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: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8066 (m-10) REVERT: A 7 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8874 (m-10) REVERT: I 103 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: I 106 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8127 (tppt) REVERT: I 107 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: J 206 LYS cc_start: 0.8992 (tttm) cc_final: 0.8509 (ttpp) REVERT: K 302 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8672 (tppp) REVERT: K 306 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8236 (mmmm) REVERT: B 6 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8699 (mmmm) REVERT: M 202 LYS cc_start: 0.9165 (ttmm) cc_final: 0.8769 (ttmm) REVERT: M 206 LYS cc_start: 0.8711 (tttm) cc_final: 0.8232 (tttm) REVERT: N 302 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8801 (tppp) REVERT: N 306 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8158 (mmmm) REVERT: N 307 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8332 (t80) REVERT: Q 302 LYS cc_start: 0.8799 (tppp) cc_final: 0.8598 (tppp) REVERT: Q 303 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: S 202 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8665 (ttpp) REVERT: S 206 LYS cc_start: 0.8634 (tttm) cc_final: 0.7895 (ttpp) REVERT: T 304 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7498 (tm-30) REVERT: T 306 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8076 (mmtp) REVERT: U 106 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8428 (tppt) REVERT: V 202 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9112 (ttmm) REVERT: V 206 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8166 (ttpp) REVERT: F 5 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: X 103 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8669 (m-10) REVERT: Y 206 LYS cc_start: 0.8557 (tttm) cc_final: 0.8342 (tttm) REVERT: Z 302 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8359 (tppp) REVERT: Z 306 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8020 (mmmm) REVERT: Z 307 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: G 5 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: G 7 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: i 102 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8632 (mmmt) REVERT: i 103 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8742 (m-10) REVERT: k 304 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7150 (tm-30) REVERT: H 6 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9032 (mmmm) REVERT: l 102 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9164 (mmtm) REVERT: l 103 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: l 106 LYS cc_start: 0.8971 (tppt) cc_final: 0.8571 (tppt) REVERT: m 207 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7084 (t80) REVERT: n 302 LYS cc_start: 0.8929 (tppp) cc_final: 0.8711 (tppp) REVERT: n 304 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8081 (tm-30) REVERT: a 2 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8465 (mtmm) REVERT: o 107 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8080 (t80) REVERT: p 203 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8215 (t80) REVERT: q 307 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8182 (t80) REVERT: r 102 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: r 106 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: s 207 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8160 (t80) REVERT: t 303 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7226 (t80) REVERT: c 2 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8569 (mmtt) REVERT: c 3 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7865 (t80) REVERT: v 204 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8086 (tm-30) REVERT: v 207 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8102 (t80) REVERT: x 104 GLU cc_start: 0.8813 (pp20) cc_final: 0.8407 (pp20) REVERT: y 203 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8463 (t80) REVERT: 1 206 LYS cc_start: 0.8436 (tptp) cc_final: 0.7943 (tptp) REVERT: 2 306 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8464 (tmtt) REVERT: 3 102 LYS cc_start: 0.9121 (tptp) cc_final: 0.8893 (tptp) REVERT: 3 103 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8408 (p90) REVERT: 4 204 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8109 (tm-30) REVERT: 5 307 PHE cc_start: 0.8871 (t80) cc_final: 0.8651 (t80) REVERT: g 2 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8467 (mmtt) REVERT: 7 202 LYS cc_start: 0.9060 (tptp) cc_final: 0.8675 (tptp) REVERT: 7 203 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8183 (t80) REVERT: 8 306 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7381 (pttm) REVERT: 8 307 PHE cc_start: 0.8467 (t80) cc_final: 0.7968 (t80) REVERT: 9 104 GLU cc_start: 0.8649 (tm-30) cc_final: 0.7558 (tm-30) REVERT: AA 206 LYS cc_start: 0.8673 (tptp) cc_final: 0.8053 (tptp) REVERT: BA 307 PHE cc_start: 0.8839 (t80) cc_final: 0.8426 (t80) outliers start: 108 outliers final: 61 residues processed: 221 average time/residue: 0.3575 time to fit residues: 89.8540 Evaluate side-chains 257 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 157 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 8 residue 304 GLU Chi-restraints excluded: chain 8 residue 306 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain 9 residue 107 PHE Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.0158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.477 5568 Z= 8.465 Angle : 6.250 60.275 7232 Z= 2.767 Chirality : 0.417 1.089 512 Planarity : 0.029 0.091 960 Dihedral : 24.659 85.642 644 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 204.00 Ramachandran Plot: Outliers : 1.95 % Allowed : 60.94 % Favored : 37.11 % Rotamer: Outliers : 26.56 % Allowed : 40.36 % Favored : 33.07 % Cbeta Deviations : 46.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.49 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.23 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.181 0.025 PHE 5 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 157 time to evaluate : 0.567 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: symmetry clash REVERT: A 5 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: A 7 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8873 (m-10) REVERT: I 103 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: I 106 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8135 (tppt) REVERT: I 107 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8567 (m-10) REVERT: J 206 LYS cc_start: 0.8991 (tttm) cc_final: 0.8502 (ttpp) REVERT: K 302 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8670 (tppp) REVERT: K 306 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8291 (mmmm) REVERT: B 6 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (mmmm) REVERT: M 202 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8765 (ttmm) REVERT: M 206 LYS cc_start: 0.8706 (tttm) cc_final: 0.8234 (tttm) REVERT: N 302 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8811 (tppp) REVERT: N 306 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8187 (mmmm) REVERT: N 307 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8273 (t80) REVERT: Q 303 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: S 202 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8667 (ttpp) REVERT: S 206 LYS cc_start: 0.8634 (tttm) cc_final: 0.7920 (ttpp) REVERT: T 304 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7492 (tm-30) REVERT: T 306 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8078 (mmtp) REVERT: U 106 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8432 (tppt) REVERT: V 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8379 (ttmm) REVERT: V 206 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: W 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8214 (ttpp) REVERT: F 5 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: X 103 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8672 (m-10) REVERT: Y 206 LYS cc_start: 0.8563 (tttm) cc_final: 0.8346 (tttm) REVERT: Z 302 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8360 (tppp) REVERT: Z 306 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8016 (mmmm) REVERT: Z 307 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: G 5 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: G 7 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: i 102 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8631 (mmmt) REVERT: i 103 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8742 (m-10) REVERT: k 304 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7163 (tm-30) REVERT: H 6 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9035 (mmmm) REVERT: l 102 LYS cc_start: 0.9408 (mmtm) cc_final: 0.9160 (mmtm) REVERT: l 103 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: l 106 LYS cc_start: 0.8967 (tppt) cc_final: 0.8568 (tppt) REVERT: m 207 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7127 (t80) REVERT: n 302 LYS cc_start: 0.8949 (tppp) cc_final: 0.8730 (tppp) REVERT: n 304 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8073 (tm-30) REVERT: a 2 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8467 (mtmm) REVERT: o 107 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8088 (t80) REVERT: p 203 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8188 (t80) REVERT: q 307 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8180 (t80) REVERT: r 102 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8314 (ttpp) REVERT: r 106 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8639 (ttpp) REVERT: s 207 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8156 (t80) REVERT: t 303 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7215 (t80) REVERT: c 2 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8576 (mmtt) REVERT: c 3 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7868 (t80) REVERT: v 204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8137 (tm-30) REVERT: v 207 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8089 (t80) REVERT: y 203 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8439 (t80) REVERT: 1 206 LYS cc_start: 0.8441 (tptp) cc_final: 0.7942 (tptp) REVERT: 2 306 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8454 (tmtt) REVERT: 3 102 LYS cc_start: 0.9127 (tptp) cc_final: 0.8896 (tptp) REVERT: 3 103 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8419 (p90) REVERT: 4 204 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8109 (tm-30) REVERT: 5 307 PHE cc_start: 0.8868 (t80) cc_final: 0.8650 (t80) REVERT: g 2 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8466 (mmtt) REVERT: 7 202 LYS cc_start: 0.9060 (tptp) cc_final: 0.8692 (tptp) REVERT: 7 203 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8197 (t80) REVERT: 8 306 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7375 (pttm) REVERT: 8 307 PHE cc_start: 0.8459 (t80) cc_final: 0.7953 (t80) REVERT: 9 104 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7536 (tm-30) REVERT: AA 206 LYS cc_start: 0.8664 (tptp) cc_final: 0.8057 (tptp) REVERT: BA 307 PHE cc_start: 0.8834 (t80) cc_final: 0.8424 (t80) outliers start: 102 outliers final: 60 residues processed: 215 average time/residue: 0.3627 time to fit residues: 88.7896 Evaluate side-chains 257 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 157 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 202 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain m residue 207 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain r residue 106 LYS Chi-restraints excluded: chain s residue 207 PHE Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain v residue 207 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 304 GLU Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 106 LYS Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 202 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 202 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 304 GLU Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 8 residue 304 GLU Chi-restraints excluded: chain 8 residue 306 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.047587 restraints weight = 20268.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.049369 restraints weight = 10852.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050608 restraints weight = 6786.059| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 1.0170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.477 5568 Z= 8.469 Angle : 6.248 59.983 7232 Z= 2.766 Chirality : 0.417 1.090 512 Planarity : 0.029 0.092 960 Dihedral : 24.628 87.109 644 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 204.33 Ramachandran Plot: Outliers : 1.95 % Allowed : 61.33 % Favored : 36.72 % Rotamer: Outliers : 27.08 % Allowed : 40.10 % Favored : 32.81 % Cbeta Deviations : 47.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.51 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.25 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.180 0.025 PHE 5 303 =============================================================================== Job complete usr+sys time: 1357.75 seconds wall clock time: 25 minutes 29.54 seconds (1529.54 seconds total)