Starting phenix.real_space_refine on Fri Jul 19 02:44:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqe_23483/07_2024/7lqe_23483.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4320 2.51 5 N 792 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 304": "OE1" <-> "OE2" Residue "L PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 304": "OE1" <-> "OE2" Residue "O PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 204": "OE1" <-> "OE2" Residue "Q PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 304": "OE1" <-> "OE2" Residue "R PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 204": "OE1" <-> "OE2" Residue "T PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 304": "OE1" <-> "OE2" Residue "U PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 204": "OE1" <-> "OE2" Residue "W PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 304": "OE1" <-> "OE2" Residue "X PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "Z PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 304": "OE1" <-> "OE2" Residue "j PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "l PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 304": "OE1" <-> "OE2" Residue "m PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 204": "OE1" <-> "OE2" Residue "o PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 304": "OE1" <-> "OE2" Residue "p PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 204": "OE1" <-> "OE2" Residue "r PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 304": "OE1" <-> "OE2" Residue "s PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 204": "OE1" <-> "OE2" Residue "u PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 304": "OE1" <-> "OE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 204": "OE1" <-> "OE2" Residue "x PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 304": "OE1" <-> "OE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 204": "OE1" <-> "OE2" Residue "0 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 304": "OE1" <-> "OE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 204": "OE1" <-> "OE2" Residue "3 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 304": "OE1" <-> "OE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 204": "OE1" <-> "OE2" Residue "6 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 304": "OE1" <-> "OE2" Residue "f PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 204": "OE1" <-> "OE2" Residue "9 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 304": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 204": "OE1" <-> "OE2" Residue "CA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 304": "OE1" <-> "OE2" Residue "h PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA GLU 204": "OE1" <-> "OE2" Residue "FA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA GLU 304": "OE1" <-> "OE2" Residue "i PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA GLU 204": "OE1" <-> "OE2" Residue "IA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA 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: 6048 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.77, per 1000 atoms: 0.62 Number of scatterers: 6048 At special positions: 0 Unit cell: (87.48, 77.76, 106.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 936 8.00 N 792 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.57 Conformation dependent library (CDL) restraints added in 603.5 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEEA 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE h 5 " --> pdb=" O PHEEA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 8 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE 8 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 2 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHE 2 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE w 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 5 " --> pdb=" O PHE w 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE t 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE a 5 " --> pdb=" O PHE t 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE z 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHE z 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE 5 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHE 5 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEBA 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHEBA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEHA 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE i 5 " --> pdb=" O PHEHA 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'FA' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSGA 302 " --> pdb=" O GMA 9 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 9 206 " --> pdb=" O GLUGA 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAGA 308 " --> pdb=" O LYS 9 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSAA 302 " --> pdb=" O GMA 3 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 3 206 " --> pdb=" O GLUAA 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 4 302 " --> pdb=" O GMA x 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS x 206 " --> pdb=" O GLU 4 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS y 302 " --> pdb=" O GMA u 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS u 206 " --> pdb=" O GLU y 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GMA y 308 " --> pdb=" O LYS u 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS v 302 " --> pdb=" O GMA 0 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS 0 206 " --> pdb=" O GLU v 304 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GMA v 308 " --> pdb=" O LYS 0 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 1 302 " --> pdb=" O GMA 6 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 6 206 " --> pdb=" O GLU 1 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 7 302 " --> pdb=" O GMACA 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSCA 206 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA 7 308 " --> pdb=" O LYSCA 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSDA 302 " --> pdb=" O GMAIA 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSIA 206 " --> pdb=" O GLUDA 304 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 773 1.26 - 1.33: 667 1.33 - 1.41: 1800 1.41 - 1.48: 651 1.48 - 1.56: 2373 Bond restraints: 6264 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 6259 not shown) Histogram of bond angle deviations from ideal: 105.43 - 109.76: 572 109.76 - 114.08: 2036 114.08 - 118.41: 1064 118.41 - 122.73: 3735 122.73 - 127.06: 729 Bond angle restraints: 8136 Sorted by residual: angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.82 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " pdb=" CAA 5CR h 1 " ideal model delta sigma weight residual 114.91 124.78 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2422 15.26 - 30.52: 395 30.52 - 45.78: 171 45.78 - 61.04: 99 61.04 - 76.30: 9 Dihedral angle restraints: 3096 sinusoidal: 1440 harmonic: 1656 Sorted by residual: dihedral pdb=" CA LYS q 106 " pdb=" CB LYS q 106 " pdb=" CG LYS q 106 " pdb=" CD LYS q 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS Y 106 " pdb=" CB LYS Y 106 " pdb=" CG LYS Y 106 " pdb=" CD LYS Y 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS M 106 " pdb=" CB LYS M 106 " pdb=" CG LYS M 106 " pdb=" CD LYS M 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 191 0.017 - 0.035: 166 0.035 - 0.052: 150 0.052 - 0.070: 53 0.070 - 0.087: 16 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA LYS W 202 " pdb=" N LYS W 202 " pdb=" C LYS W 202 " pdb=" CB LYS W 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.91e-01 chirality pdb=" CA LYS Q 202 " pdb=" N LYS Q 202 " pdb=" C LYS Q 202 " pdb=" CB LYS Q 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.90e-01 chirality pdb=" CA LYS N 202 " pdb=" N LYS N 202 " pdb=" C LYS N 202 " pdb=" CB LYS N 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.87e-01 ... (remaining 573 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 205 " -0.009 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE u 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE u 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 205 " -0.009 2.00e-02 2.50e+03 6.93e-03 8.39e-01 pdb=" CG PHE 6 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 6 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 205 " -0.009 2.00e-02 2.50e+03 6.90e-03 8.33e-01 pdb=" CG PHE x 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE x 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE x 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE x 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2593 2.92 - 3.41: 5352 3.41 - 3.91: 9925 3.91 - 4.40: 12294 4.40 - 4.90: 20848 Nonbonded interactions: 51012 Sorted by model distance: nonbonded pdb=" N GLU D 4 " pdb=" OE1 GLU D 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.423 2.520 nonbonded pdb=" N GLU A 4 " pdb=" OE1 GLU A 4 " model vdw 2.423 2.520 ... (remaining 51007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.118 6264 Z= 0.833 Angle : 1.417 9.910 8136 Z= 0.592 Chirality : 0.035 0.087 576 Planarity : 0.002 0.009 1080 Dihedral : 20.718 76.296 1944 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE u 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 143 time to evaluate : 0.617 Fit side-chains REVERT: A 2 LYS cc_start: 0.8975 (tttt) cc_final: 0.8577 (tptt) REVERT: J 102 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: K 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8709 (ttmt) REVERT: K 206 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8037 (ttmm) REVERT: L 304 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6841 (mm-30) REVERT: L 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8208 (mmmm) REVERT: B 2 LYS cc_start: 0.8950 (tttt) cc_final: 0.8747 (tttp) REVERT: M 102 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: N 202 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8696 (ttmm) REVERT: N 204 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7046 (mt-10) REVERT: O 306 LYS cc_start: 0.8895 (tttt) cc_final: 0.8380 (mmmm) REVERT: C 2 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: P 102 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: P 104 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6835 (mm-30) REVERT: Q 204 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7270 (mt-10) REVERT: R 304 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6963 (mm-30) REVERT: R 306 LYS cc_start: 0.8731 (tttt) cc_final: 0.8294 (mmmm) REVERT: D 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8716 (ttmm) REVERT: S 102 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (ttmt) REVERT: U 304 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6582 (mm-30) REVERT: U 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8235 (mmmm) REVERT: E 4 GLU cc_start: 0.7580 (mp0) cc_final: 0.5848 (mp0) REVERT: V 102 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: V 104 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6989 (mm-30) REVERT: W 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8626 (ttmm) REVERT: W 204 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mt-10) REVERT: W 206 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8144 (ttmm) REVERT: X 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7245 (mm-30) REVERT: X 306 LYS cc_start: 0.8889 (tttt) cc_final: 0.8236 (mmmm) REVERT: F 2 LYS cc_start: 0.8964 (tttt) cc_final: 0.8518 (tttm) REVERT: F 4 GLU cc_start: 0.7595 (mp0) cc_final: 0.7012 (mp0) REVERT: Y 102 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: Z 202 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8683 (ttmm) REVERT: Z 206 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8130 (ttmm) REVERT: j 304 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7285 (mm-30) REVERT: j 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (mmmm) REVERT: G 2 LYS cc_start: 0.8756 (tttt) cc_final: 0.8452 (tttm) REVERT: G 4 GLU cc_start: 0.7496 (mp0) cc_final: 0.6174 (mp0) REVERT: G 6 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7922 (mtmt) REVERT: k 102 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: l 202 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (ttmt) REVERT: l 206 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7935 (ttmm) REVERT: m 302 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mtmt) REVERT: m 304 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7248 (mm-30) REVERT: m 306 LYS cc_start: 0.8693 (tttt) cc_final: 0.8127 (mmmm) REVERT: H 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (ttmt) REVERT: n 102 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: p 306 LYS cc_start: 0.8809 (tttt) cc_final: 0.8244 (mmmm) REVERT: r 202 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: s 306 LYS cc_start: 0.8710 (tttt) cc_final: 0.8340 (tppt) REVERT: a 6 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: w 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: z 105 PHE cc_start: 0.8273 (t80) cc_final: 0.7515 (t80) REVERT: 2 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7759 (t80) REVERT: 4 303 PHE cc_start: 0.8424 (t80) cc_final: 0.8200 (t80) REVERT: 4 307 PHE cc_start: 0.7856 (t80) cc_final: 0.7604 (t80) REVERT: HA 104 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: HA 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7558 (t80) REVERT: JA 303 PHE cc_start: 0.8181 (t80) cc_final: 0.7871 (t80) REVERT: JA 307 PHE cc_start: 0.7572 (t80) cc_final: 0.7215 (t80) outliers start: 63 outliers final: 25 residues processed: 178 average time/residue: 0.3609 time to fit residues: 73.6534 Evaluate side-chains 175 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain V residue 102 LYS Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain k residue 102 LYS Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain m residue 302 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 104 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.148 0.425 6264 Z= 8.149 Angle : 4.879 41.839 8136 Z= 2.270 Chirality : 0.381 1.029 576 Planarity : 0.025 0.083 1080 Dihedral : 23.836 127.566 861 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 127.48 Ramachandran Plot: Outliers : 3.82 % Allowed : 19.10 % Favored : 77.08 % Rotamer: Outliers : 20.83 % Allowed : 18.98 % Favored : 60.19 % Cbeta Deviations : 38.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.93 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.28 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.026 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 138 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8394 (mp0) cc_final: 0.7612 (mp0) REVERT: K 206 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8757 (ttmm) REVERT: L 304 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8407 (mm-30) REVERT: L 306 LYS cc_start: 0.9128 (tttt) cc_final: 0.8877 (mmmm) REVERT: B 2 LYS cc_start: 0.9271 (tttt) cc_final: 0.8985 (tttp) REVERT: M 104 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8122 (mm-30) REVERT: M 106 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8766 (mmmm) REVERT: N 204 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7984 (mt-10) REVERT: O 306 LYS cc_start: 0.9072 (tttt) cc_final: 0.8864 (tttt) REVERT: O 307 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8486 (t80) REVERT: C 2 LYS cc_start: 0.9159 (tttt) cc_final: 0.8779 (ttmm) REVERT: P 102 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8932 (ttpt) REVERT: P 104 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8032 (mm-30) REVERT: P 106 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8560 (mmmm) REVERT: D 2 LYS cc_start: 0.9409 (tttt) cc_final: 0.9182 (ttmm) REVERT: D 4 GLU cc_start: 0.8739 (mp0) cc_final: 0.7451 (mp0) REVERT: S 106 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8511 (mmmm) REVERT: U 306 LYS cc_start: 0.8975 (tttt) cc_final: 0.8529 (ttmm) REVERT: E 4 GLU cc_start: 0.8354 (mp0) cc_final: 0.7515 (mp0) REVERT: E 6 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8668 (mmmt) REVERT: V 104 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8432 (mm-30) REVERT: W 205 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8722 (m-10) REVERT: X 307 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8548 (t80) REVERT: F 2 LYS cc_start: 0.9365 (tttt) cc_final: 0.8945 (tttp) REVERT: Y 104 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8000 (mm-30) REVERT: G 4 GLU cc_start: 0.8389 (mp0) cc_final: 0.7571 (mp0) REVERT: k 106 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8509 (mmmm) REVERT: m 306 LYS cc_start: 0.9214 (tttt) cc_final: 0.8687 (ttmm) REVERT: H 2 LYS cc_start: 0.9408 (tttt) cc_final: 0.9121 (tttp) REVERT: n 106 LYS cc_start: 0.8872 (tptm) cc_final: 0.8552 (tptm) REVERT: p 306 LYS cc_start: 0.9097 (mttt) cc_final: 0.8768 (mmmm) REVERT: s 302 LYS cc_start: 0.9317 (tttt) cc_final: 0.8630 (tptt) REVERT: s 306 LYS cc_start: 0.9184 (tttt) cc_final: 0.8827 (tptt) REVERT: b 4 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: y 303 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7802 (t80) REVERT: d 2 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8581 (ptpt) REVERT: 4 302 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8603 (tptp) REVERT: 7 302 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8245 (tptp) REVERT: f 2 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8688 (ttpt) REVERT: 8 102 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8755 (tptm) REVERT: AA 304 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8361 (tm-30) REVERT: BA 107 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8651 (t80) REVERT: FA 206 LYS cc_start: 0.8963 (tttt) cc_final: 0.8418 (pptt) REVERT: GA 302 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8567 (tptp) outliers start: 90 outliers final: 63 residues processed: 207 average time/residue: 0.3843 time to fit residues: 90.3726 Evaluate side-chains 212 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 137 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 206 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain t residue 106 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 305 PHE Chi-restraints excluded: chain y 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 z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 102 LYS Chi-restraints excluded: chain 2 residue 105 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 302 LYS Chi-restraints excluded: chain JA residue 305 PHE 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: 0.8548 moved from start: 0.8206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.429 6264 Z= 8.194 Angle : 4.903 33.927 8136 Z= 2.283 Chirality : 0.381 1.006 576 Planarity : 0.025 0.087 1080 Dihedral : 23.889 88.045 770 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 133.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.21 % Favored : 69.79 % Rotamer: Outliers : 24.07 % Allowed : 25.69 % Favored : 50.23 % Cbeta Deviations : 41.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.16 % 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: -7.07 (0.31), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.38 (0.24), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.187 0.025 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 138 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8296 (mp0) cc_final: 0.7357 (mp0) REVERT: J 104 GLU cc_start: 0.8159 (mm-30) cc_final: 0.6879 (mm-30) REVERT: J 107 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8133 (t80) REVERT: K 206 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8826 (ttmm) REVERT: L 304 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8181 (mm-30) REVERT: L 306 LYS cc_start: 0.9176 (tttt) cc_final: 0.8867 (mmmm) REVERT: B 2 LYS cc_start: 0.9213 (tttt) cc_final: 0.8844 (tttm) REVERT: B 6 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8716 (mtmt) REVERT: M 104 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8146 (mm-30) REVERT: M 106 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8816 (mmmm) REVERT: N 204 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8249 (tt0) REVERT: O 306 LYS cc_start: 0.9060 (tttt) cc_final: 0.8830 (tttt) REVERT: O 307 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8523 (t80) REVERT: C 2 LYS cc_start: 0.9142 (tttt) cc_final: 0.8918 (tttm) REVERT: C 4 GLU cc_start: 0.8181 (mp0) cc_final: 0.6986 (mp0) REVERT: P 102 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8996 (ttpt) REVERT: P 104 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8111 (mm-30) REVERT: P 106 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8468 (mmmm) REVERT: D 2 LYS cc_start: 0.9341 (tttt) cc_final: 0.9100 (ttmm) REVERT: D 4 GLU cc_start: 0.8815 (mp0) cc_final: 0.8106 (mp0) REVERT: S 106 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8436 (mmmm) REVERT: U 306 LYS cc_start: 0.8998 (tttt) cc_final: 0.8523 (ttmm) REVERT: E 6 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8614 (mtmt) REVERT: V 104 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8942 (mm-30) REVERT: W 205 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8707 (m-10) REVERT: X 307 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8662 (t80) REVERT: F 2 LYS cc_start: 0.9393 (tttt) cc_final: 0.9045 (tttp) REVERT: F 6 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8543 (mmmt) REVERT: Y 104 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8318 (mm-30) REVERT: Z 203 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: Z 206 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8824 (ttmm) REVERT: j 306 LYS cc_start: 0.9107 (mttt) cc_final: 0.8771 (mmmm) REVERT: j 307 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7940 (t80) REVERT: G 4 GLU cc_start: 0.8510 (mp0) cc_final: 0.8071 (mp0) REVERT: k 106 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8594 (mmmm) REVERT: m 306 LYS cc_start: 0.9188 (tttt) cc_final: 0.8782 (mmmm) REVERT: m 307 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8791 (t80) REVERT: H 2 LYS cc_start: 0.9398 (tttt) cc_final: 0.9135 (tttp) REVERT: n 106 LYS cc_start: 0.8867 (tptm) cc_final: 0.8521 (tptm) REVERT: o 207 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8479 (t80) REVERT: p 306 LYS cc_start: 0.9183 (mttt) cc_final: 0.8770 (mmmm) REVERT: I 6 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8578 (mtmt) REVERT: q 107 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: r 206 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8888 (ttmm) REVERT: s 302 LYS cc_start: 0.9259 (tttt) cc_final: 0.8556 (tptt) REVERT: s 306 LYS cc_start: 0.9220 (tttt) cc_final: 0.8843 (tptt) REVERT: v 305 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7648 (t80) REVERT: b 4 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: b 7 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9173 (t80) REVERT: y 302 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8437 (tptp) REVERT: y 303 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7843 (t80) REVERT: 0 204 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7721 (tm-30) REVERT: 1 302 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: 1 306 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8133 (tptp) REVERT: 4 302 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8492 (tptp) REVERT: 7 302 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (tptp) REVERT: AA 304 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8299 (tm-30) REVERT: BA 107 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8689 (t80) REVERT: DA 306 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8182 (ptmm) REVERT: GA 302 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (tptp) outliers start: 104 outliers final: 65 residues processed: 216 average time/residue: 0.3681 time to fit residues: 90.6914 Evaluate side-chains 228 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 138 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain r residue 206 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 305 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 102 LYS Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.439 6264 Z= 8.222 Angle : 4.935 43.983 8136 Z= 2.292 Chirality : 0.380 0.974 576 Planarity : 0.025 0.088 1080 Dihedral : 23.711 89.129 758 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 132.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.56 % Favored : 69.44 % Rotamer: Outliers : 27.31 % Allowed : 27.78 % Favored : 44.91 % Cbeta Deviations : 42.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.56 % 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: -7.30 (0.30), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.56 (0.23), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.187 0.025 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 138 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8347 (mp0) cc_final: 0.7401 (mp0) REVERT: A 6 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8682 (mtmt) REVERT: L 306 LYS cc_start: 0.9189 (tttt) cc_final: 0.8764 (mmmm) REVERT: L 307 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: B 6 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8711 (mtmt) REVERT: M 104 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8110 (mm-30) REVERT: M 106 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8858 (mmmm) REVERT: N 204 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8374 (tt0) REVERT: N 205 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9161 (m-10) REVERT: O 306 LYS cc_start: 0.9062 (tttt) cc_final: 0.8818 (tttt) REVERT: O 307 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8515 (t80) REVERT: C 2 LYS cc_start: 0.9127 (tttt) cc_final: 0.8909 (tttm) REVERT: C 4 GLU cc_start: 0.8171 (mp0) cc_final: 0.7491 (mp0) REVERT: P 102 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8962 (ttpt) REVERT: P 104 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: P 106 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8472 (mmmm) REVERT: D 2 LYS cc_start: 0.9380 (tttt) cc_final: 0.9142 (ttmm) REVERT: D 4 GLU cc_start: 0.8833 (mp0) cc_final: 0.8195 (mp0) REVERT: S 106 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8423 (mmmm) REVERT: U 306 LYS cc_start: 0.8951 (tttt) cc_final: 0.8489 (ttmm) REVERT: V 106 LYS cc_start: 0.9055 (tptm) cc_final: 0.8784 (tptm) REVERT: W 205 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8741 (m-10) REVERT: X 307 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8626 (t80) REVERT: F 2 LYS cc_start: 0.9370 (tttt) cc_final: 0.8993 (tttp) REVERT: F 6 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8603 (mmmt) REVERT: Y 104 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8379 (mm-30) REVERT: Z 202 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9005 (tttt) REVERT: Z 203 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: j 306 LYS cc_start: 0.9149 (mttt) cc_final: 0.8878 (mmmm) REVERT: j 307 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8036 (t80) REVERT: G 4 GLU cc_start: 0.8514 (mp0) cc_final: 0.8231 (mp0) REVERT: k 106 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8580 (mmmm) REVERT: m 306 LYS cc_start: 0.9192 (mttt) cc_final: 0.8773 (mmmm) REVERT: n 106 LYS cc_start: 0.8872 (tptm) cc_final: 0.8527 (tptm) REVERT: o 207 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8282 (t80) REVERT: p 303 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: p 306 LYS cc_start: 0.9220 (mttt) cc_final: 0.8837 (mmmm) REVERT: I 4 GLU cc_start: 0.8543 (mp0) cc_final: 0.7854 (mp0) REVERT: q 107 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: s 302 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8564 (tptt) REVERT: s 306 LYS cc_start: 0.9273 (tttt) cc_final: 0.8931 (tptt) REVERT: v 305 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7581 (t80) REVERT: v 306 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8240 (tptp) REVERT: b 4 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: b 7 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.9195 (t80) REVERT: y 302 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8301 (tptp) REVERT: y 303 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7769 (t80) REVERT: 1 306 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8144 (tptp) REVERT: d 2 LYS cc_start: 0.9053 (ptpt) cc_final: 0.8717 (ptpt) REVERT: 4 302 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8563 (tptp) REVERT: AA 304 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8381 (tm-30) REVERT: BA 107 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8631 (t80) REVERT: DA 306 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: JA 302 LYS cc_start: 0.9170 (tptp) cc_final: 0.8969 (tptp) outliers start: 118 outliers final: 73 residues processed: 221 average time/residue: 0.3600 time to fit residues: 91.0361 Evaluate side-chains 238 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 139 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain W residue 206 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.8513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.428 6264 Z= 8.230 Angle : 4.939 37.148 8136 Z= 2.297 Chirality : 0.381 0.962 576 Planarity : 0.025 0.086 1080 Dihedral : 23.624 89.419 758 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 136.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 32.29 % Favored : 67.36 % Rotamer: Outliers : 28.70 % Allowed : 28.01 % Favored : 43.29 % Cbeta Deviations : 41.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.25 (0.31), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.52 (0.24), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.184 0.025 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 138 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8387 (mp0) cc_final: 0.7516 (mp0) REVERT: A 6 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8717 (mtmt) REVERT: J 107 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8377 (t80) REVERT: L 306 LYS cc_start: 0.9218 (mttt) cc_final: 0.8910 (mmmm) REVERT: B 6 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8431 (mtmt) REVERT: M 104 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8097 (mm-30) REVERT: M 106 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8845 (mmmm) REVERT: N 205 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9114 (m-80) REVERT: O 306 LYS cc_start: 0.9053 (tttt) cc_final: 0.8819 (tttt) REVERT: O 307 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 2 LYS cc_start: 0.9126 (tttt) cc_final: 0.8851 (tttm) REVERT: C 4 GLU cc_start: 0.8195 (mp0) cc_final: 0.7568 (mp0) REVERT: P 102 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9007 (ttpt) REVERT: P 104 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: P 106 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8433 (mmmm) REVERT: D 2 LYS cc_start: 0.9406 (tttt) cc_final: 0.9152 (ttmm) REVERT: D 4 GLU cc_start: 0.8822 (mp0) cc_final: 0.8205 (mp0) REVERT: S 106 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8361 (mmmm) REVERT: U 306 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8479 (ttmm) REVERT: V 106 LYS cc_start: 0.9091 (tptm) cc_final: 0.8832 (tptm) REVERT: W 205 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: X 307 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8645 (t80) REVERT: F 2 LYS cc_start: 0.9373 (tttt) cc_final: 0.9065 (tttp) REVERT: F 6 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8550 (mmmt) REVERT: Y 104 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8409 (mm-30) REVERT: Z 202 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8832 (tttt) REVERT: Z 203 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: Z 204 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: j 306 LYS cc_start: 0.9122 (mttt) cc_final: 0.8816 (mmmm) REVERT: j 307 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8021 (t80) REVERT: G 4 GLU cc_start: 0.8545 (mp0) cc_final: 0.8230 (mp0) REVERT: k 106 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8576 (mmmm) REVERT: m 306 LYS cc_start: 0.9204 (mttt) cc_final: 0.8812 (mmmm) REVERT: H 2 LYS cc_start: 0.9413 (tttt) cc_final: 0.9153 (tttp) REVERT: n 106 LYS cc_start: 0.8881 (tptm) cc_final: 0.8525 (tptm) REVERT: o 207 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8366 (t80) REVERT: p 303 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: I 4 GLU cc_start: 0.8531 (mp0) cc_final: 0.7583 (mp0) REVERT: q 104 GLU cc_start: 0.8775 (tp30) cc_final: 0.8530 (tp30) REVERT: q 107 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: s 302 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8546 (tptt) REVERT: s 306 LYS cc_start: 0.9321 (tttt) cc_final: 0.8856 (tppt) REVERT: v 305 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7645 (t80) REVERT: v 306 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: b 4 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: b 7 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9171 (t80) REVERT: y 302 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8344 (tptp) REVERT: y 303 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7756 (t80) REVERT: 1 306 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8136 (tptp) REVERT: d 2 LYS cc_start: 0.9026 (ptpt) cc_final: 0.8701 (ptpt) REVERT: 4 302 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8603 (tptp) REVERT: 4 303 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7530 (t80) REVERT: e 7 PHE cc_start: 0.9517 (OUTLIER) cc_final: 0.9267 (t80) REVERT: AA 304 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8379 (tm-30) REVERT: BA 107 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8616 (t80) REVERT: DA 306 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8306 (tptp) REVERT: JA 302 LYS cc_start: 0.9197 (tptp) cc_final: 0.8967 (tptp) outliers start: 124 outliers final: 79 residues processed: 223 average time/residue: 0.3700 time to fit residues: 94.5420 Evaluate side-chains 248 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 138 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 104 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.8592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.428 6264 Z= 8.218 Angle : 4.953 38.491 8136 Z= 2.302 Chirality : 0.382 0.964 576 Planarity : 0.025 0.086 1080 Dihedral : 23.659 89.461 758 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 135.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.94 % Favored : 68.06 % Rotamer: Outliers : 28.94 % Allowed : 28.94 % Favored : 42.13 % Cbeta Deviations : 41.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % 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: -7.41 (0.30), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.23), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.185 0.024 PHE t 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 136 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8382 (mp0) cc_final: 0.7551 (mp0) REVERT: A 6 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (mtmt) REVERT: J 107 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8285 (t80) REVERT: L 306 LYS cc_start: 0.9202 (mttt) cc_final: 0.8929 (mmmm) REVERT: B 6 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8465 (mtmt) REVERT: M 106 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8840 (mmmm) REVERT: N 205 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: O 306 LYS cc_start: 0.9065 (tttt) cc_final: 0.8785 (tttt) REVERT: O 307 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8529 (t80) REVERT: C 2 LYS cc_start: 0.9132 (tttt) cc_final: 0.8763 (tttm) REVERT: C 4 GLU cc_start: 0.8188 (mp0) cc_final: 0.7610 (mp0) REVERT: P 102 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8957 (ttpt) REVERT: P 106 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8416 (mmmm) REVERT: D 2 LYS cc_start: 0.9402 (tttt) cc_final: 0.9142 (ttmm) REVERT: D 4 GLU cc_start: 0.8821 (mp0) cc_final: 0.8198 (mp0) REVERT: S 106 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8365 (mmmm) REVERT: U 306 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8470 (ttmm) REVERT: V 106 LYS cc_start: 0.9087 (tptm) cc_final: 0.8859 (tptm) REVERT: W 205 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8743 (m-10) REVERT: X 307 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8625 (t80) REVERT: F 6 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8561 (mmmt) REVERT: Y 104 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8381 (mm-30) REVERT: Z 202 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8846 (tttt) REVERT: Z 203 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: j 306 LYS cc_start: 0.9115 (mttt) cc_final: 0.8809 (mmmm) REVERT: j 307 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8019 (t80) REVERT: G 4 GLU cc_start: 0.8486 (mp0) cc_final: 0.8246 (mp0) REVERT: k 106 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8713 (mmmm) REVERT: m 306 LYS cc_start: 0.9194 (mttt) cc_final: 0.8802 (mmmm) REVERT: H 2 LYS cc_start: 0.9409 (tttt) cc_final: 0.9149 (tttp) REVERT: H 4 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6107 (pm20) REVERT: n 106 LYS cc_start: 0.8860 (tptm) cc_final: 0.8520 (tptm) REVERT: o 207 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (t80) REVERT: I 4 GLU cc_start: 0.8538 (mp0) cc_final: 0.7930 (mp0) REVERT: q 107 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8720 (m-80) REVERT: s 302 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8545 (tptt) REVERT: s 306 LYS cc_start: 0.9314 (tttt) cc_final: 0.8948 (tptt) REVERT: v 305 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7674 (t80) REVERT: v 306 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8231 (tptp) REVERT: b 4 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: b 7 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.9167 (t80) REVERT: y 302 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8263 (tptp) REVERT: y 303 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7635 (t80) REVERT: 1 306 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (tptp) REVERT: d 2 LYS cc_start: 0.9034 (ptpt) cc_final: 0.8697 (ptpt) REVERT: 4 303 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7778 (t80) REVERT: BA 107 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8611 (t80) REVERT: DA 306 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: GA 302 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8601 (tptp) outliers start: 125 outliers final: 83 residues processed: 221 average time/residue: 0.3599 time to fit residues: 91.1179 Evaluate side-chains 246 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 135 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.8653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.428 6264 Z= 8.220 Angle : 4.961 39.253 8136 Z= 2.301 Chirality : 0.381 0.964 576 Planarity : 0.025 0.084 1080 Dihedral : 23.685 89.314 758 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 136.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.29 % Favored : 67.71 % Rotamer: Outliers : 30.32 % Allowed : 29.17 % Favored : 40.51 % Cbeta Deviations : 41.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % 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: -7.38 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.62 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 135 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8330 (mp0) cc_final: 0.8109 (mp0) REVERT: A 6 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8723 (mtmt) REVERT: J 107 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8350 (t80) REVERT: K 204 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: L 304 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8055 (mp0) REVERT: L 306 LYS cc_start: 0.9181 (mttt) cc_final: 0.8926 (mmmm) REVERT: B 6 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8491 (mtmt) REVERT: M 106 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8830 (mmmm) REVERT: N 205 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.9120 (m-80) REVERT: O 303 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: O 306 LYS cc_start: 0.9066 (tttt) cc_final: 0.8783 (tttt) REVERT: O 307 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8528 (t80) REVERT: C 2 LYS cc_start: 0.9130 (tttt) cc_final: 0.8754 (tttm) REVERT: C 4 GLU cc_start: 0.8194 (mp0) cc_final: 0.7617 (mp0) REVERT: P 102 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8956 (ttpt) REVERT: P 106 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8416 (mmmm) REVERT: Q 207 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8056 (t80) REVERT: D 2 LYS cc_start: 0.9397 (tttt) cc_final: 0.9137 (ttmm) REVERT: D 4 GLU cc_start: 0.8820 (mp0) cc_final: 0.8204 (mp0) REVERT: S 106 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8376 (mmmm) REVERT: U 306 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: V 106 LYS cc_start: 0.9093 (tptm) cc_final: 0.8874 (tptm) REVERT: W 205 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8725 (m-10) REVERT: W 206 LYS cc_start: 0.8994 (ptmm) cc_final: 0.8664 (ptmm) REVERT: X 306 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8875 (mmmm) REVERT: X 307 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8606 (t80) REVERT: F 6 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8577 (mmmt) REVERT: Y 104 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) REVERT: Y 106 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8607 (tptm) REVERT: Z 202 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8851 (tttt) REVERT: Z 203 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: Z 206 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8840 (ttmm) REVERT: j 306 LYS cc_start: 0.9107 (mttt) cc_final: 0.8801 (mmmm) REVERT: j 307 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8021 (t80) REVERT: k 106 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8710 (mmmm) REVERT: m 304 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8196 (mp0) REVERT: m 306 LYS cc_start: 0.9194 (mttt) cc_final: 0.8800 (mmmm) REVERT: H 2 LYS cc_start: 0.9419 (tttt) cc_final: 0.9151 (tttp) REVERT: H 4 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: H 7 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8710 (t80) REVERT: n 106 LYS cc_start: 0.8857 (tptm) cc_final: 0.8534 (tptm) REVERT: o 207 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8347 (t80) REVERT: p 306 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8866 (mmmm) REVERT: I 4 GLU cc_start: 0.8493 (mp0) cc_final: 0.7867 (mp0) REVERT: I 6 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8870 (mtmt) REVERT: q 107 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: s 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8551 (tptt) REVERT: s 306 LYS cc_start: 0.9318 (tttt) cc_final: 0.8910 (tptt) REVERT: v 305 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7618 (t80) REVERT: v 306 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8226 (tptp) REVERT: b 4 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: b 7 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.9164 (t80) REVERT: y 302 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8106 (tptp) REVERT: y 303 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7595 (t80) REVERT: 1 306 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8157 (tptp) REVERT: d 2 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8689 (ptpt) REVERT: 4 303 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7716 (t80) REVERT: e 7 PHE cc_start: 0.9519 (OUTLIER) cc_final: 0.9227 (t80) REVERT: AA 307 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8476 (t80) REVERT: BA 107 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8598 (t80) REVERT: DA 306 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8309 (tptp) REVERT: GA 302 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8663 (tptp) outliers start: 131 outliers final: 86 residues processed: 225 average time/residue: 0.3478 time to fit residues: 89.9612 Evaluate side-chains 258 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 136 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain U residue 304 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE 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: 0.8563 moved from start: 0.8687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.150 0.426 6264 Z= 8.232 Angle : 4.964 39.584 8136 Z= 2.304 Chirality : 0.382 0.966 576 Planarity : 0.025 0.083 1080 Dihedral : 23.704 89.183 758 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 136.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.29 % Favored : 67.71 % Rotamer: Outliers : 29.86 % Allowed : 29.63 % Favored : 40.51 % Cbeta Deviations : 42.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.16 % 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: -7.44 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 134 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8730 (mtmt) REVERT: J 107 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8290 (t80) REVERT: L 306 LYS cc_start: 0.9189 (mttt) cc_final: 0.8924 (mmmm) REVERT: B 6 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8506 (mtmt) REVERT: M 106 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8831 (mmmm) REVERT: O 303 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: O 306 LYS cc_start: 0.9063 (tttt) cc_final: 0.8764 (tttt) REVERT: O 307 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8528 (t80) REVERT: C 2 LYS cc_start: 0.9125 (tttt) cc_final: 0.8750 (tttm) REVERT: C 4 GLU cc_start: 0.8195 (mp0) cc_final: 0.7621 (mp0) REVERT: P 102 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8955 (ttpt) REVERT: P 106 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8406 (mmmm) REVERT: Q 207 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8104 (t80) REVERT: D 2 LYS cc_start: 0.9396 (tttt) cc_final: 0.9135 (ttmm) REVERT: D 4 GLU cc_start: 0.8820 (mp0) cc_final: 0.8206 (mp0) REVERT: S 106 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8386 (mmmm) REVERT: U 306 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: V 106 LYS cc_start: 0.9108 (tptm) cc_final: 0.8881 (tptm) REVERT: W 205 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: W 206 LYS cc_start: 0.8985 (ptmm) cc_final: 0.8668 (ptmm) REVERT: X 306 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8886 (mmmm) REVERT: X 307 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8604 (t80) REVERT: F 6 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8603 (mmmt) REVERT: Y 104 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8379 (mm-30) REVERT: Y 106 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8614 (tptm) REVERT: Z 202 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8839 (tttt) REVERT: Z 203 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: j 306 LYS cc_start: 0.9116 (mttt) cc_final: 0.8817 (mmmm) REVERT: j 307 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8120 (t80) REVERT: k 106 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8692 (mmmm) REVERT: m 304 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8211 (mp0) REVERT: m 306 LYS cc_start: 0.9185 (mttt) cc_final: 0.8794 (mmmm) REVERT: H 2 LYS cc_start: 0.9416 (tttt) cc_final: 0.9148 (tttp) REVERT: H 4 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6130 (pm20) REVERT: H 7 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8703 (t80) REVERT: n 106 LYS cc_start: 0.8858 (tptm) cc_final: 0.8541 (tptm) REVERT: o 207 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8359 (t80) REVERT: p 303 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: p 306 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8865 (mmmm) REVERT: I 4 GLU cc_start: 0.8513 (mp0) cc_final: 0.7916 (mp0) REVERT: I 6 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8874 (mtmt) REVERT: q 104 GLU cc_start: 0.8402 (tp30) cc_final: 0.8181 (tp30) REVERT: q 107 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8715 (m-80) REVERT: s 302 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8550 (tptt) REVERT: s 306 LYS cc_start: 0.9310 (tttt) cc_final: 0.8922 (tptt) REVERT: v 305 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7613 (t80) REVERT: v 306 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8222 (tptp) REVERT: b 4 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: b 7 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9162 (t80) REVERT: y 302 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8113 (tptp) REVERT: y 303 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7596 (t80) REVERT: 1 306 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (tptp) REVERT: d 2 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8683 (ptpt) REVERT: 4 303 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7710 (t80) REVERT: BA 107 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8598 (t80) REVERT: DA 306 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: GA 302 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8654 (tptp) outliers start: 129 outliers final: 85 residues processed: 223 average time/residue: 0.3644 time to fit residues: 93.6451 Evaluate side-chains 252 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 134 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain U residue 304 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.8713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.426 6264 Z= 8.228 Angle : 4.974 39.372 8136 Z= 2.307 Chirality : 0.382 0.965 576 Planarity : 0.025 0.083 1080 Dihedral : 23.728 89.196 758 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 135.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.29 % Favored : 67.71 % Rotamer: Outliers : 29.17 % Allowed : 30.09 % Favored : 40.74 % Cbeta Deviations : 42.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.16 % 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: -7.48 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.70 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.024 PHE 7 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 135 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8727 (mtmt) REVERT: J 107 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8288 (t80) REVERT: L 306 LYS cc_start: 0.9175 (mttt) cc_final: 0.8909 (mmmm) REVERT: B 6 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8522 (mtmt) REVERT: M 106 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8817 (mmmm) REVERT: O 303 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: O 306 LYS cc_start: 0.9061 (tttt) cc_final: 0.8763 (tttt) REVERT: O 307 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8528 (t80) REVERT: C 2 LYS cc_start: 0.9123 (tttt) cc_final: 0.8750 (tttm) REVERT: C 4 GLU cc_start: 0.8198 (mp0) cc_final: 0.7629 (mp0) REVERT: P 102 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8956 (ttpt) REVERT: P 106 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8403 (mmmm) REVERT: Q 207 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8096 (t80) REVERT: D 2 LYS cc_start: 0.9394 (tttt) cc_final: 0.9135 (ttmm) REVERT: D 4 GLU cc_start: 0.8823 (mp0) cc_final: 0.8208 (mp0) REVERT: S 106 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8389 (mmmm) REVERT: U 306 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8470 (ttmm) REVERT: V 106 LYS cc_start: 0.9124 (tptm) cc_final: 0.8913 (tptm) REVERT: W 205 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: W 206 LYS cc_start: 0.9001 (ptmm) cc_final: 0.8690 (ptmm) REVERT: X 306 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8692 (mmmm) REVERT: X 307 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8590 (t80) REVERT: F 6 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8605 (mmmt) REVERT: Y 104 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8380 (mm-30) REVERT: Y 106 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8612 (tptm) REVERT: Z 202 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8853 (tttt) REVERT: Z 203 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: j 306 LYS cc_start: 0.9123 (mttt) cc_final: 0.8806 (mmmm) REVERT: j 307 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8118 (t80) REVERT: k 106 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8700 (mmmm) REVERT: m 304 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8226 (mp0) REVERT: m 306 LYS cc_start: 0.9190 (mttt) cc_final: 0.8797 (mmmm) REVERT: H 2 LYS cc_start: 0.9418 (tttt) cc_final: 0.9148 (tttp) REVERT: H 4 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: H 7 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8741 (t80) REVERT: n 106 LYS cc_start: 0.8860 (tptm) cc_final: 0.8546 (tptm) REVERT: o 207 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (t80) REVERT: p 306 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8836 (mmmm) REVERT: I 4 GLU cc_start: 0.8509 (mp0) cc_final: 0.7902 (mp0) REVERT: I 6 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8875 (mtmt) REVERT: q 107 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: s 302 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8549 (tptt) REVERT: s 306 LYS cc_start: 0.9309 (tttt) cc_final: 0.8909 (tptt) REVERT: v 305 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7614 (t80) REVERT: v 306 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8222 (tptp) REVERT: b 4 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: b 7 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9161 (t80) REVERT: y 303 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7947 (t80) REVERT: 1 306 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8161 (tptp) REVERT: d 2 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8682 (ptpt) REVERT: 4 303 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7713 (t80) REVERT: e 7 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.9276 (t80) REVERT: f 4 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: BA 107 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8596 (t80) REVERT: DA 306 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (tptp) REVERT: GA 302 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8673 (tptp) outliers start: 126 outliers final: 88 residues processed: 220 average time/residue: 0.3537 time to fit residues: 89.2392 Evaluate side-chains 256 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 135 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain U residue 304 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 206 LYS Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.8735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.150 0.434 6264 Z= 8.232 Angle : 4.976 39.238 8136 Z= 2.307 Chirality : 0.382 0.966 576 Planarity : 0.025 0.083 1080 Dihedral : 23.734 89.380 758 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 134.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.64 % Favored : 67.36 % Rotamer: Outliers : 28.94 % Allowed : 30.56 % Favored : 40.51 % Cbeta Deviations : 42.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.49 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.70 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.024 PHE 7 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 134 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8739 (mtmt) REVERT: J 107 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8293 (t80) REVERT: L 306 LYS cc_start: 0.9181 (mttt) cc_final: 0.8935 (mmmm) REVERT: B 6 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8537 (mtmt) REVERT: M 106 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8810 (mmmm) REVERT: N 205 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9103 (m-80) REVERT: O 303 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8578 (m-10) REVERT: O 306 LYS cc_start: 0.9063 (tttt) cc_final: 0.8771 (tttt) REVERT: O 307 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8530 (t80) REVERT: C 2 LYS cc_start: 0.9123 (tttt) cc_final: 0.8750 (tttm) REVERT: C 4 GLU cc_start: 0.8200 (mp0) cc_final: 0.7635 (mp0) REVERT: P 102 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8956 (ttpt) REVERT: P 106 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: Q 207 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8106 (t80) REVERT: D 2 LYS cc_start: 0.9394 (tttt) cc_final: 0.9136 (ttmm) REVERT: D 4 GLU cc_start: 0.8820 (mp0) cc_final: 0.8209 (mp0) REVERT: S 106 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8398 (mmmm) REVERT: U 306 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: V 106 LYS cc_start: 0.9109 (tptm) cc_final: 0.8900 (tptm) REVERT: W 204 GLU cc_start: 0.8610 (tt0) cc_final: 0.8366 (tt0) REVERT: W 205 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: W 206 LYS cc_start: 0.8986 (ptmm) cc_final: 0.8669 (ptmm) REVERT: X 306 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8695 (mmmm) REVERT: X 307 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8590 (t80) REVERT: F 6 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8610 (mmmt) REVERT: Y 104 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8381 (mm-30) REVERT: Y 106 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8616 (tptm) REVERT: Z 202 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9001 (tttt) REVERT: Z 203 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8703 (m-10) REVERT: j 306 LYS cc_start: 0.9128 (mttt) cc_final: 0.8806 (mmmm) REVERT: j 307 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8122 (t80) REVERT: k 106 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8707 (mmmm) REVERT: m 304 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8235 (mp0) REVERT: m 306 LYS cc_start: 0.9186 (mttt) cc_final: 0.8789 (mmmm) REVERT: H 2 LYS cc_start: 0.9418 (tttt) cc_final: 0.9142 (tttp) REVERT: H 4 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: H 7 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8736 (t80) REVERT: n 106 LYS cc_start: 0.8862 (tptm) cc_final: 0.8546 (tptm) REVERT: o 207 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8350 (t80) REVERT: p 303 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: p 306 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8850 (mmmm) REVERT: I 4 GLU cc_start: 0.8511 (mp0) cc_final: 0.7914 (mp0) REVERT: I 6 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8880 (mtmt) REVERT: q 107 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: s 302 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8549 (tptt) REVERT: s 306 LYS cc_start: 0.9309 (tttt) cc_final: 0.8920 (tptt) REVERT: v 305 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7617 (t80) REVERT: v 306 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8225 (tptp) REVERT: b 4 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: b 7 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9160 (t80) REVERT: y 303 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7948 (t80) REVERT: 1 306 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8170 (tptp) REVERT: d 2 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8682 (ptpt) REVERT: 4 303 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7698 (t80) REVERT: f 4 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: BA 107 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8592 (t80) REVERT: DA 306 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8316 (tptp) REVERT: GA 302 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (tptp) outliers start: 125 outliers final: 87 residues processed: 220 average time/residue: 0.3655 time to fit residues: 92.1681 Evaluate side-chains 256 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 135 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain U residue 304 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain V residue 104 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain u residue 206 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 306 LYS Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain y residue 306 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain 7 residue 306 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 206 LYS Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE 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 = 0.2968 r_free = 0.2968 target = 0.058279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.048534 restraints weight = 19478.613| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.13 r_work: 0.2539 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.8748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.426 6264 Z= 8.227 Angle : 4.980 39.284 8136 Z= 2.306 Chirality : 0.381 0.965 576 Planarity : 0.025 0.083 1080 Dihedral : 23.749 89.289 758 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 136.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.64 % Favored : 67.36 % Rotamer: Outliers : 28.47 % Allowed : 31.25 % Favored : 40.28 % Cbeta Deviations : 42.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.16 % 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: -7.49 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.71 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.024 PHE 7 303 =============================================================================== Job complete usr+sys time: 1521.28 seconds wall clock time: 28 minutes 6.06 seconds (1686.06 seconds total)