Starting phenix.real_space_refine on Mon Mar 11 14:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/03_2024/7lqi_23487_updated.pdb" } resolution = 3.5 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= -0.000 sd= 0.000 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 6000 2.51 5 N 1100 2.21 5 O 1300 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 "K PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "M PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 404": "OE1" <-> "OE2" Residue "N PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 204": "OE1" <-> "OE2" Residue "T PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 404": "OE1" <-> "OE2" Residue "U PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 204": "OE1" <-> "OE2" Residue "f PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 404": "OE1" <-> "OE2" Residue "g PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "m PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 404": "OE1" <-> "OE2" Residue "n PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "t PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 404": "OE1" <-> "OE2" Residue "u PHE 405": "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 "z PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 204": "OE1" <-> "OE2" Residue "0 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 404": "OE1" <-> "OE2" Residue "1 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 204": "OE1" <-> "OE2" Residue "7 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 404": "OE1" <-> "OE2" Residue "8 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 204": "OE1" <-> "OE2" Residue "EA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA GLU 404": "OE1" <-> "OE2" Residue "FA PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA GLU 204": "OE1" <-> "OE2" Residue "LA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA GLU 404": "OE1" <-> "OE2" Residue "MA PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 204": "OE1" <-> "OE2" Residue "SA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA GLU 404": "OE1" <-> "OE2" Residue "TA PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XA GLU 54": "OE1" <-> "OE2" Residue "XA PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YA GLU 104": "OE1" <-> "OE2" Residue "YA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZA GLU 154": "OE1" <-> "OE2" Residue "ZA PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "aA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "aA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bA GLU 254": "OE1" <-> "OE2" Residue "bA PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cA GLU 304": "OE1" <-> "OE2" Residue "cA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dA PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dA GLU 354": "OE1" <-> "OE2" Residue "dA PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eA PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eA GLU 404": "OE1" <-> "OE2" Residue "fA PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fA GLU 454": "OE1" <-> "OE2" Residue "fA PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 4": "OE1" <-> "OE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "mA GLU 54": "OE1" <-> "OE2" Residue "mA PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "nA PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "nA GLU 104": "OE1" <-> "OE2" Residue "nA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "oA GLU 154": "OE1" <-> "OE2" Residue "oA PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pA PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "qA GLU 254": "OE1" <-> "OE2" Residue "qA PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA GLU 304": "OE1" <-> "OE2" Residue "rA PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "sA PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "sA GLU 354": "OE1" <-> "OE2" Residue "sA PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "tA GLU 404": "OE1" <-> "OE2" Residue "uA PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "uA GLU 454": "OE1" <-> "OE2" Residue "uA PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 4": "OE1" <-> "OE2" Residue "c PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A GLU 54": "OE1" <-> "OE2" Residue "1A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A GLU 104": "OE1" <-> "OE2" Residue "2A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A GLU 154": "OE1" <-> "OE2" Residue "3A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A GLU 254": "OE1" <-> "OE2" Residue "5A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6A GLU 304": "OE1" <-> "OE2" Residue "6A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A GLU 354": "OE1" <-> "OE2" Residue "7A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A GLU 404": "OE1" <-> "OE2" Residue "9A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9A GLU 454": "OE1" <-> "OE2" Residue "9A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GB GLU 54": "OE1" <-> "OE2" Residue "GB PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HB GLU 104": "OE1" <-> "OE2" Residue "HB PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IB GLU 154": "OE1" <-> "OE2" Residue "IB PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KB GLU 254": "OE1" <-> "OE2" Residue "KB PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 304": "OE1" <-> "OE2" Residue "LB PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MB GLU 354": "OE1" <-> "OE2" Residue "MB PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB GLU 404": "OE1" <-> "OE2" Residue "OB PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OB GLU 454": "OE1" <-> "OE2" Residue "OB PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 4": "OE1" <-> "OE2" Residue "e PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VB GLU 54": "OE1" <-> "OE2" Residue "VB PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WB PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WB GLU 104": "OE1" <-> "OE2" Residue "WB PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XB GLU 154": "OE1" <-> "OE2" Residue "XB PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YB PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZB GLU 254": "OE1" <-> "OE2" Residue "ZB PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "aB PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "aB GLU 304": "OE1" <-> "OE2" Residue "aB PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bB PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bB GLU 354": "OE1" <-> "OE2" Residue "bB PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cB PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cB GLU 404": "OE1" <-> "OE2" Residue "dB PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "dB GLU 454": "OE1" <-> "OE2" Residue "dB PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8400 Number of models: 1 Model: "" Number of chains: 100 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: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "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: "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: "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: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "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: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "VB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.04, per 1000 atoms: 0.48 Number of scatterers: 8400 At special positions: 0 Unit cell: (98.28, 98.28, 64.8, 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 1300 8.00 N 1100 7.00 C 6000 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: 3.52 Conformation dependent library (CDL) restraints added in 600.1 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 994 1.25 - 1.33: 736 1.33 - 1.40: 2770 1.40 - 1.47: 900 1.47 - 1.54: 3300 Bond restraints: 8700 Sorted by residual: bond pdb=" N 5CRpA 201 " pdb=" CAL 5CRpA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRaA 201 " pdb=" CAL 5CRaA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRHB 101 " pdb=" CAL 5CRHB 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CR8A 401 " pdb=" CAL 5CR8A 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N 5CRnA 101 " pdb=" CAL 5CRnA 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 8695 not shown) Histogram of bond angle deviations from ideal: 106.38 - 109.98: 1011 109.98 - 113.58: 2399 113.58 - 117.19: 1357 117.19 - 120.79: 4275 120.79 - 124.40: 2258 Bond angle restraints: 11300 Sorted by residual: angle pdb=" CA 5CR U 401 " pdb=" N 5CR U 401 " pdb=" CAL 5CR U 401 " ideal model delta sigma weight residual 125.23 115.88 9.35 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CA 5CR u 401 " pdb=" N 5CR u 401 " pdb=" CAL 5CR u 401 " ideal model delta sigma weight residual 125.23 115.89 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" CA 5CR n 401 " pdb=" N 5CR n 401 " pdb=" CAL 5CR n 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRFA 401 " pdb=" N 5CRFA 401 " pdb=" CAL 5CRFA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRMA 401 " pdb=" N 5CRMA 401 " pdb=" CAL 5CRMA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.67e+00 ... (remaining 11295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3570 16.29 - 32.58: 425 32.58 - 48.87: 145 48.87 - 65.15: 125 65.15 - 81.44: 35 Dihedral angle restraints: 4300 sinusoidal: 2000 harmonic: 2300 Sorted by residual: dihedral pdb=" CA PHEaA 205 " pdb=" C PHEaA 205 " pdb=" N LYSaA 206 " pdb=" CA LYSaA 206 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEJB 205 " pdb=" C PHEJB 205 " pdb=" N LYSJB 206 " pdb=" CA LYSJB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEYB 205 " pdb=" C PHEYB 205 " pdb=" N LYSYB 206 " pdb=" CA LYSYB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.014: 229 0.014 - 0.029: 321 0.029 - 0.043: 198 0.043 - 0.057: 42 0.057 - 0.072: 10 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLU 1 404 " pdb=" N GLU 1 404 " pdb=" C GLU 1 404 " pdb=" CB GLU 1 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.28e-01 chirality pdb=" CA GLU n 404 " pdb=" N GLU n 404 " pdb=" C GLU n 404 " pdb=" CB GLU n 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.25e-01 chirality pdb=" CA GLU N 404 " pdb=" N GLU N 404 " pdb=" C GLU N 404 " pdb=" CB GLU N 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.21e-01 ... (remaining 797 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEpA 205 " -0.007 2.00e-02 2.50e+03 7.22e-03 9.11e-01 pdb=" CG PHEpA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEpA 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEpA 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEpA 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEpA 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEpA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEJB 205 " -0.007 2.00e-02 2.50e+03 7.08e-03 8.78e-01 pdb=" CG PHEJB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEJB 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEJB 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEJB 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEJB 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEJB 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE4A 205 " -0.007 2.00e-02 2.50e+03 7.05e-03 8.71e-01 pdb=" CG PHE4A 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE4A 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE4A 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE4A 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE4A 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE4A 205 " -0.002 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2545 2.77 - 3.31: 6602 3.31 - 3.84: 13737 3.84 - 4.37: 17712 4.37 - 4.90: 28943 Nonbonded interactions: 69539 Sorted by model distance: nonbonded pdb=" OE1 GMAcB 408 " pdb=" N2 GMAcB 408 " model vdw 2.242 2.520 nonbonded pdb=" OE1 GMAeA 408 " pdb=" N2 GMAeA 408 " model vdw 2.242 2.520 nonbonded pdb=" OE1 GMAtA 408 " pdb=" N2 GMAtA 408 " model vdw 2.243 2.520 nonbonded pdb=" OE1 GMANB 408 " pdb=" N2 GMANB 408 " model vdw 2.243 2.520 nonbonded pdb=" OE1 GMA8A 408 " pdb=" N2 GMA8A 408 " model vdw 2.243 2.520 ... (remaining 69534 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 '1A' selection = chain '2A' selection = chain '3A' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9A' selection = chain 'A' selection = chain 'B' 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 'GB' selection = chain 'H' selection = chain 'HB' selection = chain 'I' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NB' selection = chain 'OB' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'VB' selection = chain 'WB' selection = chain 'XA' selection = chain 'XB' selection = chain 'Y' selection = chain 'YA' selection = chain 'YB' selection = chain 'Z' selection = chain 'ZA' selection = chain 'ZB' selection = chain 'a' selection = chain 'aA' selection = chain 'aB' selection = chain 'b' selection = chain 'bA' selection = chain 'bB' selection = chain 'c' selection = chain 'cA' selection = chain 'cB' selection = chain 'd' selection = chain 'dA' selection = chain 'dB' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'oA' selection = chain 'pA' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.910 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.310 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.112 8700 Z= 0.771 Angle : 1.399 9.345 11300 Z= 0.568 Chirality : 0.027 0.072 800 Planarity : 0.002 0.007 1500 Dihedral : 20.423 81.443 2700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 8.33 % Favored : 86.67 % 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: -3.42 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEpA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 368 time to evaluate : 0.908 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: M 302 LYS cc_start: 0.8276 (tttt) cc_final: 0.7660 (tttm) REVERT: N 404 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6945 (mm-30) REVERT: B 2 LYS cc_start: 0.8999 (tttt) cc_final: 0.8790 (ttmm) REVERT: B 4 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: S 202 LYS cc_start: 0.9090 (tttt) cc_final: 0.8886 (ttmt) REVERT: U 402 LYS cc_start: 0.9254 (tttt) cc_final: 0.9045 (ttmm) REVERT: U 404 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6851 (mt-10) REVERT: C 2 LYS cc_start: 0.8944 (tttt) cc_final: 0.8666 (tttm) REVERT: C 4 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 6 LYS cc_start: 0.8693 (tttt) cc_final: 0.8425 (tttp) REVERT: g 406 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8330 (tttp) REVERT: l 204 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: m 302 LYS cc_start: 0.9180 (tttt) cc_final: 0.8905 (ttmt) REVERT: E 4 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: t 302 LYS cc_start: 0.9052 (tttt) cc_final: 0.8815 (ttmm) REVERT: u 402 LYS cc_start: 0.9187 (tttt) cc_final: 0.8774 (ttmm) REVERT: F 2 LYS cc_start: 0.9203 (tttt) cc_final: 0.8897 (tttm) REVERT: y 106 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8723 (tttm) REVERT: 0 304 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7420 (mt-10) REVERT: 1 406 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8652 (ttpt) REVERT: 5 104 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8142 (tm-30) REVERT: 6 204 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: 8 402 LYS cc_start: 0.9116 (tttt) cc_final: 0.8904 (tttp) REVERT: 8 404 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7144 (mt-10) REVERT: H 6 LYS cc_start: 0.8646 (tttt) cc_final: 0.8276 (tptt) REVERT: I 4 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: XA 53 PHE cc_start: 0.7733 (t80) cc_final: 0.7514 (t80) REVERT: XA 56 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8355 (tmtt) REVERT: YA 105 PHE cc_start: 0.8199 (t80) cc_final: 0.7996 (t80) REVERT: ZA 156 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8462 (tmtt) REVERT: aA 206 LYS cc_start: 0.9027 (tttm) cc_final: 0.8764 (tttp) REVERT: bA 257 PHE cc_start: 0.7440 (t80) cc_final: 0.7230 (t80) REVERT: cA 302 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8056 (tmtt) REVERT: dA 352 LYS cc_start: 0.8915 (tmtt) cc_final: 0.8684 (tmtt) REVERT: eA 406 LYS cc_start: 0.9333 (tttp) cc_final: 0.9115 (tttp) REVERT: fA 456 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8472 (tmtt) REVERT: mA 56 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8438 (tptp) REVERT: oA 154 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8011 (tm-30) REVERT: oA 156 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8418 (tptp) REVERT: qA 254 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8044 (tm-30) REVERT: rA 302 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8484 (tmtt) REVERT: sA 354 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8060 (tm-30) REVERT: sA 356 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8441 (tmtt) REVERT: tA 406 LYS cc_start: 0.9404 (tttp) cc_final: 0.9192 (tttm) REVERT: uA 456 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8334 (tmtt) REVERT: 3A 152 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8615 (tmtt) REVERT: 5A 256 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8288 (tmtt) REVERT: 7A 352 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8611 (tmtt) REVERT: 7A 356 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8294 (tmtt) REVERT: GB 52 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8658 (tmtt) REVERT: GB 56 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8650 (tmtt) REVERT: HB 107 PHE cc_start: 0.9122 (t80) cc_final: 0.8172 (t80) REVERT: JB 207 PHE cc_start: 0.9068 (t80) cc_final: 0.8360 (t80) REVERT: KB 256 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8484 (tmtt) REVERT: LB 302 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8360 (ttmm) REVERT: LB 305 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80) REVERT: MB 353 PHE cc_start: 0.7755 (t80) cc_final: 0.7514 (t80) REVERT: MB 356 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8472 (tmtt) REVERT: OB 452 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8586 (tmtt) REVERT: OB 456 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8582 (tmtt) REVERT: ZB 256 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8675 (tmtt) outliers start: 30 outliers final: 4 residues processed: 373 average time/residue: 0.3953 time to fit residues: 173.6346 Evaluate side-chains 340 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain I residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 0.8525 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.232 8700 Z= 2.321 Angle : 2.753 17.454 11300 Z= 1.313 Chirality : 0.134 0.325 800 Planarity : 0.011 0.036 1500 Dihedral : 25.493 88.556 1030 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 122.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.75 % Favored : 72.25 % Rotamer: Outliers : 12.33 % Allowed : 23.33 % Favored : 64.33 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.74 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.083 0.011 PHEtA 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 337 time to evaluate : 0.914 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: 0.8756 (mp0) cc_final: 0.8276 (mp0) REVERT: A 6 LYS cc_start: 0.9176 (tttt) cc_final: 0.8711 (tttm) REVERT: A 7 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8150 (m-10) REVERT: K 104 GLU cc_start: 0.8687 (mp0) cc_final: 0.8236 (mp0) REVERT: K 107 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: L 207 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: M 306 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8652 (tttt) REVERT: M 307 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: B 4 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 6 LYS cc_start: 0.8954 (tttt) cc_final: 0.8606 (tttm) REVERT: n 404 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7929 (mt-10) REVERT: E 6 LYS cc_start: 0.9062 (tttt) cc_final: 0.8724 (tttp) REVERT: r 104 GLU cc_start: 0.8744 (mp0) cc_final: 0.8510 (mp0) REVERT: u 404 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7997 (mm-30) REVERT: u 406 LYS cc_start: 0.8921 (mptt) cc_final: 0.8561 (ttmt) REVERT: F 7 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: y 107 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: z 207 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: 0 307 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: G 6 LYS cc_start: 0.9386 (tttt) cc_final: 0.8956 (tttm) REVERT: 6 207 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: 7 307 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: H 4 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7619 (tm-30) REVERT: H 6 LYS cc_start: 0.9301 (tttt) cc_final: 0.8882 (ttmt) REVERT: I 6 LYS cc_start: 0.9086 (tttt) cc_final: 0.8781 (tttm) REVERT: KA 204 GLU cc_start: 0.8555 (mp0) cc_final: 0.8340 (pm20) REVERT: LA 304 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8391 (pm20) REVERT: MA 404 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8099 (pm20) REVERT: J 4 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7787 (tm-30) REVERT: RA 204 GLU cc_start: 0.9014 (pm20) cc_final: 0.8301 (pm20) REVERT: TA 404 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7864 (tm-30) REVERT: XA 54 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7810 (tm-30) REVERT: YA 106 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9165 (tttm) REVERT: ZA 156 LYS cc_start: 0.9366 (tmtt) cc_final: 0.8802 (tmtt) REVERT: aA 203 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8476 (t80) REVERT: bA 256 LYS cc_start: 0.9298 (tmtt) cc_final: 0.9041 (tttm) REVERT: cA 303 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.7618 (t80) REVERT: cA 304 GLU cc_start: 0.8529 (tp30) cc_final: 0.8043 (tp30) REVERT: dA 355 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7215 (t80) REVERT: dA 356 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8904 (tttm) REVERT: eA 406 LYS cc_start: 0.9484 (tttp) cc_final: 0.9104 (tttm) REVERT: mA 56 LYS cc_start: 0.9340 (tmtt) cc_final: 0.9137 (tttp) REVERT: oA 156 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9124 (tttp) REVERT: pA 204 GLU cc_start: 0.8660 (tp30) cc_final: 0.8307 (tm-30) REVERT: rA 302 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8655 (ttmm) REVERT: uA 456 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9155 (tttp) REVERT: c 4 GLU cc_start: 0.8484 (tp30) cc_final: 0.8108 (tm-30) REVERT: c 5 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8526 (t80) REVERT: 1A 52 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8592 (ttmm) REVERT: 3A 152 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8593 (ttmm) REVERT: 4A 202 LYS cc_start: 0.9011 (tptp) cc_final: 0.8803 (tptp) REVERT: 5A 256 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9114 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9275 (tmtt) cc_final: 0.9001 (tttm) REVERT: d 5 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8732 (t80) REVERT: GB 52 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8589 (ttmm) REVERT: IB 156 LYS cc_start: 0.9408 (tmtt) cc_final: 0.9200 (tmtt) REVERT: JB 205 PHE cc_start: 0.9071 (t80) cc_final: 0.8737 (t80) REVERT: KB 256 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9129 (tmtt) REVERT: LB 302 LYS cc_start: 0.9185 (tmtt) cc_final: 0.8799 (ttmm) REVERT: LB 304 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: LB 305 PHE cc_start: 0.9118 (t80) cc_final: 0.8864 (t80) REVERT: LB 306 LYS cc_start: 0.9341 (tttm) cc_final: 0.9093 (tttm) REVERT: MB 353 PHE cc_start: 0.8611 (t80) cc_final: 0.8334 (t80) REVERT: MB 356 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9084 (tmtt) REVERT: OB 452 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8525 (ttmm) REVERT: e 4 GLU cc_start: 0.8416 (tp30) cc_final: 0.7996 (tm-30) REVERT: VB 55 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7688 (t80) REVERT: WB 104 GLU cc_start: 0.8416 (tp30) cc_final: 0.7962 (tm-30) REVERT: YB 204 GLU cc_start: 0.8542 (tp30) cc_final: 0.8156 (tm-30) REVERT: ZB 256 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9162 (tttp) REVERT: aB 302 LYS cc_start: 0.9157 (tmtt) cc_final: 0.8680 (tmtt) REVERT: cB 402 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8748 (ttmm) outliers start: 74 outliers final: 37 residues processed: 362 average time/residue: 0.3904 time to fit residues: 168.6643 Evaluate side-chains 385 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 329 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain 7 residue 307 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 202 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 405 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8537 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.167 8700 Z= 2.317 Angle : 2.747 16.589 11300 Z= 1.323 Chirality : 0.136 0.335 800 Planarity : 0.011 0.037 1500 Dihedral : 25.462 89.659 1012 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 127.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.00 % Favored : 64.00 % Rotamer: Outliers : 16.17 % Allowed : 28.50 % Favored : 55.33 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.86 % 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: -6.34 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.83 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.082 0.010 PHE c 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 332 time to evaluate : 0.970 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: A 6 LYS cc_start: 0.9084 (tttt) cc_final: 0.8649 (tttm) REVERT: A 7 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: K 104 GLU cc_start: 0.8695 (mp0) cc_final: 0.8355 (mp0) REVERT: K 107 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8283 (m-10) REVERT: L 207 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: M 306 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8664 (tttt) REVERT: M 307 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: B 4 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: C 6 LYS cc_start: 0.9077 (tttt) cc_final: 0.8712 (tttm) REVERT: g 404 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8521 (mp0) REVERT: D 4 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7778 (tm-30) REVERT: E 6 LYS cc_start: 0.9057 (tttt) cc_final: 0.8766 (tttp) REVERT: r 104 GLU cc_start: 0.8706 (mp0) cc_final: 0.8351 (mp0) REVERT: t 304 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: u 404 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8040 (mm-30) REVERT: u 406 LYS cc_start: 0.8947 (mptt) cc_final: 0.8590 (ttmt) REVERT: F 7 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8164 (m-10) REVERT: y 107 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: z 206 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: z 207 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: 0 307 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: 1 404 GLU cc_start: 0.8863 (mp0) cc_final: 0.8505 (mp0) REVERT: G 7 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: 6 206 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8793 (ttpt) REVERT: 6 207 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: H 4 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: H 6 LYS cc_start: 0.9305 (tttt) cc_final: 0.8839 (ttmt) REVERT: I 6 LYS cc_start: 0.9046 (tttt) cc_final: 0.8758 (tttm) REVERT: KA 204 GLU cc_start: 0.8701 (mp0) cc_final: 0.8426 (pm20) REVERT: LA 304 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8348 (pm20) REVERT: MA 404 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8373 (pm20) REVERT: J 4 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7749 (tm-30) REVERT: QA 104 GLU cc_start: 0.8840 (pm20) cc_final: 0.7074 (mm-30) REVERT: TA 404 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7905 (tm-30) REVERT: a 3 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8592 (t80) REVERT: XA 53 PHE cc_start: 0.8856 (t80) cc_final: 0.8581 (t80) REVERT: XA 54 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8407 (tm-30) REVERT: YA 106 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8859 (tttm) REVERT: bA 252 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8526 (ttmm) REVERT: bA 254 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8102 (tm-30) REVERT: bA 256 LYS cc_start: 0.9316 (tmtt) cc_final: 0.9005 (tttp) REVERT: cA 302 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8941 (tmtt) REVERT: cA 303 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.7700 (t80) REVERT: cA 304 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: eA 403 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8692 (t80) REVERT: eA 406 LYS cc_start: 0.9499 (tttp) cc_final: 0.8824 (tttm) REVERT: fA 452 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8691 (ttmm) REVERT: nA 104 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: oA 152 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8630 (tmtt) REVERT: oA 156 LYS cc_start: 0.9352 (tmtt) cc_final: 0.9140 (tttp) REVERT: pA 204 GLU cc_start: 0.8617 (tp30) cc_final: 0.8226 (tm-30) REVERT: rA 305 PHE cc_start: 0.9084 (t80) cc_final: 0.8759 (t80) REVERT: sA 352 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8641 (tmtt) REVERT: tA 404 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: uA 452 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8701 (tmtt) REVERT: uA 456 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9123 (tttp) REVERT: c 4 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: c 5 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8421 (t80) REVERT: 1A 52 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8560 (ttmm) REVERT: 1A 54 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7031 (tm-30) REVERT: 2A 105 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8598 (t80) REVERT: 3A 152 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8593 (ttmm) REVERT: 3A 156 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8995 (tmtt) REVERT: 4A 202 LYS cc_start: 0.8994 (tptp) cc_final: 0.8782 (tptp) REVERT: 6A 304 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: 7A 355 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7853 (t80) REVERT: 7A 356 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9011 (tttm) REVERT: 8A 404 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8032 (tm-30) REVERT: 8A 405 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8635 (t80) REVERT: 9A 452 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8628 (ttmm) REVERT: d 4 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: d 5 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8516 (t80) REVERT: GB 52 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8633 (ttmm) REVERT: HB 105 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8594 (t80) REVERT: IB 156 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9118 (tmtt) REVERT: JB 202 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8882 (pptt) REVERT: KB 252 LYS cc_start: 0.9008 (tmtt) cc_final: 0.8741 (ttmm) REVERT: KB 253 PHE cc_start: 0.8759 (t80) cc_final: 0.8465 (t80) REVERT: KB 256 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9073 (tmtt) REVERT: LB 302 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8847 (ttmm) REVERT: LB 304 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: LB 305 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8735 (t80) REVERT: LB 306 LYS cc_start: 0.9301 (tttm) cc_final: 0.9024 (tttm) REVERT: MB 356 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9108 (tmtt) REVERT: NB 405 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8512 (t80) REVERT: OB 452 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8550 (ttmm) REVERT: e 4 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: VB 52 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8598 (pptt) REVERT: XB 152 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8659 (pptt) REVERT: YB 204 GLU cc_start: 0.8506 (tp30) cc_final: 0.7982 (tm-30) REVERT: ZB 256 LYS cc_start: 0.9316 (tmtt) cc_final: 0.9098 (tttp) REVERT: aB 302 LYS cc_start: 0.9224 (tmtt) cc_final: 0.9010 (tmtt) REVERT: cB 402 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8701 (ttmm) outliers start: 97 outliers final: 39 residues processed: 354 average time/residue: 0.3755 time to fit residues: 158.4771 Evaluate side-chains 406 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 331 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8541 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.148 8700 Z= 2.319 Angle : 2.723 16.820 11300 Z= 1.313 Chirality : 0.137 0.340 800 Planarity : 0.011 0.036 1500 Dihedral : 25.249 89.720 1009 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 125.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 39.50 % Favored : 60.50 % Rotamer: Outliers : 17.50 % Allowed : 34.17 % Favored : 48.33 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -6.42 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.89 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.080 0.010 PHE c 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 328 time to evaluate : 0.842 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: A 6 LYS cc_start: 0.9076 (tttt) cc_final: 0.8647 (tttm) REVERT: A 7 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: K 107 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: L 207 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: M 306 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8640 (tttt) REVERT: M 307 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: U 404 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: C 6 LYS cc_start: 0.9081 (tttt) cc_final: 0.8843 (ttmt) REVERT: Y 106 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8801 (ttmt) REVERT: g 404 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: D 4 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: E 6 LYS cc_start: 0.9081 (tttt) cc_final: 0.8785 (tttp) REVERT: r 104 GLU cc_start: 0.8725 (mp0) cc_final: 0.8377 (mp0) REVERT: u 404 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8012 (mm-30) REVERT: u 406 LYS cc_start: 0.9052 (mptt) cc_final: 0.8537 (ttmt) REVERT: F 7 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: y 107 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8185 (m-10) REVERT: z 206 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8838 (ttpt) REVERT: z 207 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: 0 307 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: 1 404 GLU cc_start: 0.8841 (mp0) cc_final: 0.8626 (mp0) REVERT: 6 206 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8802 (ttpt) REVERT: 6 207 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: H 4 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: H 6 LYS cc_start: 0.9288 (tttt) cc_final: 0.8822 (ttmt) REVERT: I 6 LYS cc_start: 0.9055 (tttt) cc_final: 0.8789 (tttm) REVERT: JA 104 GLU cc_start: 0.4561 (OUTLIER) cc_final: 0.3962 (pm20) REVERT: KA 204 GLU cc_start: 0.8646 (mp0) cc_final: 0.8342 (pm20) REVERT: LA 304 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8353 (pm20) REVERT: MA 404 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8272 (pm20) REVERT: J 4 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: QA 104 GLU cc_start: 0.8747 (pm20) cc_final: 0.6868 (mm-30) REVERT: TA 404 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7888 (tm-30) REVERT: a 3 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8648 (t80) REVERT: bA 252 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8539 (ttmm) REVERT: bA 254 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8181 (tm-30) REVERT: bA 255 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7616 (t80) REVERT: bA 256 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8977 (tttp) REVERT: cA 303 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7827 (t80) REVERT: cA 304 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: dA 355 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.6760 (t80) REVERT: eA 403 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8549 (t80) REVERT: eA 406 LYS cc_start: 0.9503 (tttp) cc_final: 0.8798 (tttp) REVERT: fA 452 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8676 (ttmm) REVERT: fA 454 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7122 (tm-30) REVERT: nA 104 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: oA 152 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8772 (tmtt) REVERT: oA 156 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9138 (tttp) REVERT: pA 204 GLU cc_start: 0.8521 (tp30) cc_final: 0.8242 (tm-30) REVERT: qA 256 LYS cc_start: 0.9308 (tmtt) cc_final: 0.9104 (tmtt) REVERT: sA 352 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8656 (tmtt) REVERT: tA 404 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: uA 452 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8795 (tmtt) REVERT: uA 456 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9069 (tttp) REVERT: 1A 52 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8729 (ttmm) REVERT: 1A 54 GLU cc_start: 0.8627 (tm-30) cc_final: 0.7248 (tm-30) REVERT: 2A 105 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8751 (t80) REVERT: 3A 152 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8627 (ttmm) REVERT: 3A 156 LYS cc_start: 0.9348 (tmtt) cc_final: 0.8972 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9504 (tttm) cc_final: 0.9259 (tttm) REVERT: 7A 355 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7807 (t80) REVERT: 7A 356 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9055 (tttm) REVERT: 8A 404 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7388 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8660 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7960 (tm-30) REVERT: GB 52 LYS cc_start: 0.9105 (tmtt) cc_final: 0.8741 (ttmm) REVERT: KB 252 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8719 (ttmm) REVERT: KB 256 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9059 (tttm) REVERT: LB 302 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8860 (ttmm) REVERT: LB 304 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: LB 305 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8807 (t80) REVERT: MB 352 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8648 (ttmm) REVERT: MB 356 LYS cc_start: 0.9364 (tmtt) cc_final: 0.8962 (tmtt) REVERT: NB 405 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8489 (t80) REVERT: OB 452 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8591 (ttmm) REVERT: OB 454 GLU cc_start: 0.8641 (tm-30) cc_final: 0.6717 (tm-30) REVERT: e 4 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: VB 52 LYS cc_start: 0.8946 (tmtt) cc_final: 0.8536 (pptt) REVERT: XB 152 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8653 (pptt) REVERT: XB 157 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7418 (t80) REVERT: YB 204 GLU cc_start: 0.8522 (tp30) cc_final: 0.8002 (tm-30) REVERT: ZB 256 LYS cc_start: 0.9319 (tmtt) cc_final: 0.9114 (tttp) REVERT: cB 402 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8749 (ttmm) REVERT: dB 452 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8617 (pptt) REVERT: dB 456 LYS cc_start: 0.9396 (tmtt) cc_final: 0.8985 (tptp) outliers start: 105 outliers final: 48 residues processed: 355 average time/residue: 0.3705 time to fit residues: 157.6321 Evaluate side-chains 410 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 327 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 404 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8541 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.146 8700 Z= 2.322 Angle : 2.716 16.737 11300 Z= 1.311 Chirality : 0.138 0.337 800 Planarity : 0.011 0.034 1500 Dihedral : 25.168 89.995 1006 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 122.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % Rotamer: Outliers : 19.33 % Allowed : 31.50 % Favored : 49.17 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.29 % 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: -6.51 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.077 0.010 PHEpA 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 326 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9082 (tttt) cc_final: 0.8587 (tttm) REVERT: A 7 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8161 (m-10) REVERT: K 107 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: L 204 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: L 207 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: M 306 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8658 (tttt) REVERT: M 307 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8050 (m-10) REVERT: N 404 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8356 (mp0) REVERT: B 6 LYS cc_start: 0.9033 (tttp) cc_final: 0.8831 (ttmt) REVERT: C 6 LYS cc_start: 0.9112 (tttt) cc_final: 0.8856 (ttmt) REVERT: Y 106 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8832 (ttmt) REVERT: D 4 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: E 6 LYS cc_start: 0.9096 (tttt) cc_final: 0.8803 (tttp) REVERT: r 104 GLU cc_start: 0.8711 (mp0) cc_final: 0.8373 (mp0) REVERT: t 304 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: u 404 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: u 406 LYS cc_start: 0.8984 (mptt) cc_final: 0.8540 (ttmt) REVERT: F 7 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: y 107 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: z 206 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8828 (ttpt) REVERT: z 207 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: 0 307 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: 6 206 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8793 (ttpt) REVERT: 6 207 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: H 4 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: H 6 LYS cc_start: 0.9286 (tttt) cc_final: 0.8826 (ttmt) REVERT: I 6 LYS cc_start: 0.9058 (tttt) cc_final: 0.8802 (tttm) REVERT: JA 104 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.3950 (pm20) REVERT: KA 204 GLU cc_start: 0.8602 (mp0) cc_final: 0.8377 (pm20) REVERT: LA 304 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8264 (pm20) REVERT: MA 404 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: J 4 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: QA 104 GLU cc_start: 0.8747 (pm20) cc_final: 0.6796 (tp30) REVERT: SA 304 GLU cc_start: 0.8935 (pm20) cc_final: 0.8439 (pm20) REVERT: TA 404 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7885 (tm-30) REVERT: a 3 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8633 (t80) REVERT: YA 103 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8565 (t80) REVERT: YA 104 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7961 (tm-30) REVERT: aA 202 LYS cc_start: 0.9268 (tmtt) cc_final: 0.8853 (tptt) REVERT: aA 203 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8329 (t80) REVERT: bA 252 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8525 (ttmm) REVERT: bA 254 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7810 (tm-30) REVERT: bA 255 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7626 (t80) REVERT: bA 256 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8953 (tttp) REVERT: cA 303 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8021 (t80) REVERT: cA 304 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: dA 355 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.6703 (t80) REVERT: eA 403 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8556 (t80) REVERT: eA 404 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7783 (tm-30) REVERT: eA 406 LYS cc_start: 0.9504 (tttp) cc_final: 0.8747 (tttp) REVERT: fA 452 LYS cc_start: 0.9093 (tmtt) cc_final: 0.8620 (ttmm) REVERT: fA 453 PHE cc_start: 0.8909 (t80) cc_final: 0.8303 (t80) REVERT: fA 454 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7308 (tm-30) REVERT: nA 104 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: oA 156 LYS cc_start: 0.9350 (tmtt) cc_final: 0.9099 (tttp) REVERT: pA 204 GLU cc_start: 0.8593 (tp30) cc_final: 0.8270 (tm-30) REVERT: sA 357 PHE cc_start: 0.8179 (t80) cc_final: 0.7962 (t80) REVERT: tA 404 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: uA 452 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8757 (tmtt) REVERT: uA 456 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9057 (tttp) REVERT: c 5 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8632 (t80) REVERT: 1A 52 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8803 (ttmm) REVERT: 3A 152 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8737 (ttmm) REVERT: 3A 156 LYS cc_start: 0.9372 (tmtt) cc_final: 0.8948 (tmtt) REVERT: 4A 204 GLU cc_start: 0.8723 (tm-30) cc_final: 0.7878 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9501 (tttm) cc_final: 0.9270 (tttm) REVERT: 6A 304 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: 7A 355 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7820 (t80) REVERT: 7A 356 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9024 (tttm) REVERT: 8A 404 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7566 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8724 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8042 (tm-30) REVERT: GB 52 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8706 (ttmm) REVERT: KB 252 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8767 (ttmm) REVERT: KB 256 LYS cc_start: 0.9356 (tmtt) cc_final: 0.8691 (tmtt) REVERT: LB 302 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8910 (ttmm) REVERT: LB 304 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: LB 305 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8754 (t80) REVERT: MB 352 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8629 (ttmm) REVERT: MB 356 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8920 (tmtt) REVERT: NB 405 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8492 (t80) REVERT: OB 452 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8630 (ttmm) REVERT: OB 454 GLU cc_start: 0.8613 (tm-30) cc_final: 0.6968 (tm-30) REVERT: e 4 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: VB 52 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8531 (pptt) REVERT: XB 152 LYS cc_start: 0.9025 (tmtt) cc_final: 0.8678 (pptt) REVERT: XB 157 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7397 (t80) REVERT: YB 204 GLU cc_start: 0.8534 (tp30) cc_final: 0.8054 (tm-30) REVERT: bB 352 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8681 (ttmm) REVERT: dB 452 LYS cc_start: 0.9034 (tmtt) cc_final: 0.8620 (pptt) outliers start: 116 outliers final: 49 residues processed: 353 average time/residue: 0.3777 time to fit residues: 158.8111 Evaluate side-chains 416 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 326 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8543 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.144 8700 Z= 2.321 Angle : 2.710 16.746 11300 Z= 1.308 Chirality : 0.138 0.341 800 Planarity : 0.011 0.034 1500 Dihedral : 25.088 89.902 1006 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 121.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.25 % Favored : 59.75 % Rotamer: Outliers : 19.17 % Allowed : 33.33 % Favored : 47.50 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.43 % 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: -6.60 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.02 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.079 0.010 PHEpA 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 326 time to evaluate : 0.898 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: 0.8767 (mp0) cc_final: 0.8417 (mp0) REVERT: A 6 LYS cc_start: 0.9062 (tttt) cc_final: 0.8565 (tttm) REVERT: A 7 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: K 107 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: L 207 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: M 306 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8681 (tttt) REVERT: M 307 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: N 404 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8327 (mp0) REVERT: C 6 LYS cc_start: 0.9138 (tttt) cc_final: 0.8771 (tttp) REVERT: Y 106 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8854 (ttmt) REVERT: D 4 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: E 6 LYS cc_start: 0.9081 (tttt) cc_final: 0.8784 (tttp) REVERT: r 104 GLU cc_start: 0.8704 (mp0) cc_final: 0.8372 (mp0) REVERT: t 304 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: u 404 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: u 406 LYS cc_start: 0.9010 (mptt) cc_final: 0.8545 (ttmt) REVERT: F 7 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8161 (m-10) REVERT: y 106 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9004 (ttpt) REVERT: y 107 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8095 (m-10) REVERT: z 206 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8826 (ttpt) REVERT: z 207 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: 0 307 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: 6 206 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8798 (ttpt) REVERT: 6 207 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: H 4 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: H 6 LYS cc_start: 0.9283 (tttt) cc_final: 0.8819 (ttmt) REVERT: JA 104 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.3989 (pm20) REVERT: LA 304 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8411 (pm20) REVERT: MA 404 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: J 4 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: QA 104 GLU cc_start: 0.8691 (pm20) cc_final: 0.6786 (tp30) REVERT: TA 404 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7784 (tm-30) REVERT: a 3 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8656 (t80) REVERT: YA 103 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8441 (t80) REVERT: YA 104 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7971 (tm-30) REVERT: aA 202 LYS cc_start: 0.9219 (tmtt) cc_final: 0.8766 (tptp) REVERT: aA 203 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8375 (t80) REVERT: bA 252 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8533 (ttmm) REVERT: bA 254 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7795 (tm-30) REVERT: bA 255 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7621 (t80) REVERT: bA 256 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8971 (tttp) REVERT: cA 303 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8165 (t80) REVERT: cA 304 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: dA 355 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.6765 (t80) REVERT: eA 403 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8478 (t80) REVERT: eA 404 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7844 (tm-30) REVERT: eA 406 LYS cc_start: 0.9456 (tttp) cc_final: 0.8740 (tttp) REVERT: fA 452 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8620 (ttmm) REVERT: fA 453 PHE cc_start: 0.8896 (t80) cc_final: 0.8280 (t80) REVERT: fA 454 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7606 (tm-30) REVERT: nA 104 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: oA 156 LYS cc_start: 0.9318 (tmtt) cc_final: 0.9049 (tttp) REVERT: pA 204 GLU cc_start: 0.8573 (tp30) cc_final: 0.8281 (tm-30) REVERT: sA 357 PHE cc_start: 0.8272 (t80) cc_final: 0.8060 (t80) REVERT: tA 404 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: uA 452 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8797 (tmtt) REVERT: uA 456 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9064 (tttp) REVERT: c 5 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8586 (t80) REVERT: 1A 52 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8837 (ttmm) REVERT: 2A 105 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8836 (t80) REVERT: 3A 152 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8766 (ttmm) REVERT: 3A 156 LYS cc_start: 0.9359 (tmtt) cc_final: 0.8924 (tmtt) REVERT: 4A 204 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7891 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9502 (tttm) cc_final: 0.9276 (tttm) REVERT: 6A 304 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: 7A 355 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7824 (t80) REVERT: 7A 356 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9034 (tttm) REVERT: 8A 404 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7712 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9034 (tmtt) cc_final: 0.8793 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8107 (tm-30) REVERT: d 5 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8593 (t80) REVERT: GB 52 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8820 (ttmm) REVERT: HB 104 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8357 (tm-30) REVERT: JB 202 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8849 (pptt) REVERT: KB 252 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8787 (ttmm) REVERT: KB 256 LYS cc_start: 0.9290 (tmtt) cc_final: 0.8646 (tmtt) REVERT: LB 302 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8897 (ttmm) REVERT: LB 304 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: LB 305 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8769 (t80) REVERT: MB 352 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8650 (ttmm) REVERT: MB 354 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7984 (tm-30) REVERT: MB 356 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8899 (tmtt) REVERT: NB 405 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8487 (t80) REVERT: OB 452 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8706 (ttmm) REVERT: OB 454 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7991 (tm-30) REVERT: e 4 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: VB 52 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8488 (pptt) REVERT: XB 152 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8671 (pptt) REVERT: XB 157 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7361 (t80) REVERT: YB 204 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: dB 452 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8627 (pptt) outliers start: 115 outliers final: 52 residues processed: 359 average time/residue: 0.3705 time to fit residues: 158.7371 Evaluate side-chains 422 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 325 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 106 LYS Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 202 LYS Chi-restraints excluded: chain JB residue 203 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8536 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.179 8700 Z= 2.320 Angle : 2.714 16.724 11300 Z= 1.313 Chirality : 0.139 0.341 800 Planarity : 0.011 0.034 1500 Dihedral : 25.053 89.991 1006 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 121.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 41.25 % Favored : 58.75 % Rotamer: Outliers : 21.17 % Allowed : 34.17 % Favored : 44.67 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -6.68 (0.31), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.09 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.079 0.010 PHEpA 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 327 time to evaluate : 0.930 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: 0.8766 (mp0) cc_final: 0.8414 (mp0) REVERT: A 6 LYS cc_start: 0.9071 (tttt) cc_final: 0.8622 (tttm) REVERT: A 7 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: K 104 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: K 107 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: L 204 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: M 306 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8684 (tttt) REVERT: M 307 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8050 (m-10) REVERT: N 404 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8312 (mp0) REVERT: U 404 GLU cc_start: 0.8811 (mp0) cc_final: 0.8203 (mp0) REVERT: C 6 LYS cc_start: 0.9148 (tttt) cc_final: 0.8778 (tttm) REVERT: Y 106 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8849 (ttmt) REVERT: D 4 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: k 104 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: E 6 LYS cc_start: 0.9055 (tttt) cc_final: 0.8761 (tttp) REVERT: r 104 GLU cc_start: 0.8714 (mp0) cc_final: 0.8366 (mp0) REVERT: t 304 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: u 404 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: u 406 LYS cc_start: 0.8997 (mptt) cc_final: 0.8544 (ttmt) REVERT: F 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: y 106 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9065 (ttpt) REVERT: y 107 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: z 206 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8826 (ttpt) REVERT: z 207 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: 0 307 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: G 6 LYS cc_start: 0.9265 (tttt) cc_final: 0.8834 (tttm) REVERT: 6 206 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8824 (ttpt) REVERT: 6 207 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.7964 (m-10) REVERT: H 4 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: H 6 LYS cc_start: 0.9284 (tttt) cc_final: 0.8815 (ttmt) REVERT: JA 104 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.3940 (pm20) REVERT: LA 304 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8288 (pm20) REVERT: MA 404 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: J 4 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: QA 104 GLU cc_start: 0.8700 (pm20) cc_final: 0.6848 (tp30) REVERT: SA 304 GLU cc_start: 0.8936 (pm20) cc_final: 0.8450 (pm20) REVERT: TA 404 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7813 (tm-30) REVERT: a 3 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8668 (t80) REVERT: YA 103 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8463 (t80) REVERT: YA 104 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8002 (tm-30) REVERT: aA 202 LYS cc_start: 0.9223 (tmtt) cc_final: 0.8752 (tptp) REVERT: aA 203 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8348 (t80) REVERT: aA 204 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: bA 252 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8511 (ttmm) REVERT: bA 254 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7806 (tm-30) REVERT: bA 255 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7626 (t80) REVERT: bA 256 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8976 (tttp) REVERT: cA 303 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8051 (t80) REVERT: cA 304 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (tp30) REVERT: eA 403 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8442 (t80) REVERT: eA 404 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7923 (tm-30) REVERT: eA 406 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.8702 (tttp) REVERT: fA 452 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8610 (ttmm) REVERT: fA 453 PHE cc_start: 0.8904 (t80) cc_final: 0.8274 (t80) REVERT: fA 454 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7626 (tm-30) REVERT: nA 104 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: oA 156 LYS cc_start: 0.9320 (tmtt) cc_final: 0.9048 (tttp) REVERT: pA 204 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: sA 357 PHE cc_start: 0.8325 (t80) cc_final: 0.8009 (t80) REVERT: tA 404 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: uA 452 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8802 (tmtt) REVERT: uA 456 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9033 (tttp) REVERT: c 5 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8567 (t80) REVERT: 1A 52 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8852 (ttmm) REVERT: 2A 105 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8876 (t80) REVERT: 3A 152 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8805 (ttmm) REVERT: 3A 155 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8118 (t80) REVERT: 3A 156 LYS cc_start: 0.9339 (tmtt) cc_final: 0.8893 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (tptp) REVERT: 4A 204 GLU cc_start: 0.8788 (tm-30) cc_final: 0.7854 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9492 (tttm) cc_final: 0.9280 (tttm) REVERT: 6A 304 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: 7A 355 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7820 (t80) REVERT: 7A 356 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9031 (tttm) REVERT: 8A 404 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7762 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8784 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8091 (tm-30) REVERT: GB 52 LYS cc_start: 0.9183 (tmtt) cc_final: 0.8805 (ttmm) REVERT: HB 104 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8375 (tm-30) REVERT: IB 156 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9153 (tmtt) REVERT: JB 202 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8843 (pptt) REVERT: KB 252 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8744 (ttmm) REVERT: KB 256 LYS cc_start: 0.9316 (tmtt) cc_final: 0.9002 (tttm) REVERT: LB 302 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8900 (ttmm) REVERT: LB 304 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: LB 305 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8756 (t80) REVERT: MB 352 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8670 (ttmm) REVERT: MB 354 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8002 (tm-30) REVERT: MB 356 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8894 (tmtt) REVERT: NB 405 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8477 (t80) REVERT: OB 452 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8750 (ttmm) REVERT: OB 454 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8216 (tm-30) REVERT: e 4 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: VB 52 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8485 (pptt) REVERT: VB 56 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9046 (tptp) REVERT: XB 152 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8680 (pptt) REVERT: XB 157 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7375 (t80) REVERT: YB 204 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: dB 452 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8546 (pptt) outliers start: 127 outliers final: 66 residues processed: 357 average time/residue: 0.3696 time to fit residues: 157.6068 Evaluate side-chains 443 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 327 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 106 LYS Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain CA residue 106 LYS Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain XA residue 54 GLU Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 204 GLU Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 406 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 202 LYS Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 202 LYS Chi-restraints excluded: chain JB residue 203 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8536 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.163 8700 Z= 2.319 Angle : 2.716 16.766 11300 Z= 1.314 Chirality : 0.139 0.340 800 Planarity : 0.011 0.034 1500 Dihedral : 25.007 89.983 1006 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 121.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 41.50 % Favored : 58.50 % Rotamer: Outliers : 22.17 % Allowed : 35.33 % Favored : 42.50 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.86 % 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: -6.73 (0.31), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.12 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.079 0.010 PHEpA 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 326 time to evaluate : 0.938 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: A 4 GLU cc_start: 0.8762 (mp0) cc_final: 0.8406 (mp0) REVERT: A 6 LYS cc_start: 0.9054 (tttt) cc_final: 0.8594 (tttm) REVERT: A 7 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: K 104 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: K 107 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: L 204 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: M 306 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8680 (tttt) REVERT: M 307 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: N 404 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8320 (mp0) REVERT: U 404 GLU cc_start: 0.8761 (mp0) cc_final: 0.8155 (mp0) REVERT: C 6 LYS cc_start: 0.9159 (tttt) cc_final: 0.8790 (tttm) REVERT: Y 106 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8858 (ttmt) REVERT: D 4 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: k 104 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: E 6 LYS cc_start: 0.9045 (tttt) cc_final: 0.8745 (tttp) REVERT: r 104 GLU cc_start: 0.8727 (mp0) cc_final: 0.8382 (mp0) REVERT: t 304 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: u 404 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: u 406 LYS cc_start: 0.9002 (mptt) cc_final: 0.8561 (ttmt) REVERT: F 2 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9082 (tttp) REVERT: F 7 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8150 (m-10) REVERT: y 106 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9062 (ttpt) REVERT: y 107 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: z 206 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8831 (ttpt) REVERT: z 207 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: 0 307 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: 6 206 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: 6 207 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: H 4 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: H 6 LYS cc_start: 0.9283 (tttt) cc_final: 0.8818 (ttmt) REVERT: EA 302 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8787 (ttmm) REVERT: JA 104 GLU cc_start: 0.4524 (OUTLIER) cc_final: 0.3931 (pm20) REVERT: LA 304 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8303 (pm20) REVERT: MA 404 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: J 4 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: QA 104 GLU cc_start: 0.8671 (pm20) cc_final: 0.6796 (tp30) REVERT: TA 404 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7855 (tm-30) REVERT: a 3 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8681 (t80) REVERT: YA 103 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8451 (t80) REVERT: ZA 154 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7978 (tm-30) REVERT: aA 202 LYS cc_start: 0.9218 (tmtt) cc_final: 0.8748 (tptp) REVERT: aA 203 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8333 (t80) REVERT: aA 204 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: bA 252 LYS cc_start: 0.8824 (tmtt) cc_final: 0.8512 (ttmm) REVERT: bA 254 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7858 (tm-30) REVERT: bA 255 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7630 (t80) REVERT: bA 256 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8975 (tttp) REVERT: cA 303 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8156 (t80) REVERT: cA 304 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: eA 403 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8431 (t80) REVERT: eA 404 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7982 (tm-30) REVERT: eA 406 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.8686 (tttp) REVERT: fA 452 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8595 (ttmm) REVERT: fA 453 PHE cc_start: 0.8903 (t80) cc_final: 0.8268 (t80) REVERT: fA 454 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7652 (tm-30) REVERT: nA 104 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: oA 156 LYS cc_start: 0.9315 (tmtt) cc_final: 0.9054 (tttp) REVERT: pA 204 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: rA 304 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8615 (tp30) REVERT: sA 357 PHE cc_start: 0.8345 (t80) cc_final: 0.8087 (t80) REVERT: tA 404 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: uA 452 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8810 (tmtt) REVERT: uA 456 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9041 (tttp) REVERT: c 5 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8637 (t80) REVERT: 1A 52 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8857 (ttmm) REVERT: 2A 105 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8786 (t80) REVERT: 3A 155 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8091 (t80) REVERT: 3A 156 LYS cc_start: 0.9345 (tmtt) cc_final: 0.8865 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8813 (tptp) REVERT: 4A 204 GLU cc_start: 0.8794 (tm-30) cc_final: 0.7831 (tm-30) REVERT: 4A 205 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8380 (t80) REVERT: 4A 206 LYS cc_start: 0.9491 (tttm) cc_final: 0.9168 (tttm) REVERT: 6A 302 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8927 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: 7A 355 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7828 (t80) REVERT: 7A 356 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9037 (tttm) REVERT: 8A 404 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7779 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8778 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8129 (tm-30) REVERT: d 5 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8687 (t80) REVERT: GB 52 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8853 (ttmm) REVERT: GB 53 PHE cc_start: 0.8915 (t80) cc_final: 0.8258 (m-80) REVERT: HB 104 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8389 (tm-30) REVERT: IB 156 LYS cc_start: 0.9416 (tmtt) cc_final: 0.9133 (tmtt) REVERT: JB 202 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8835 (pptt) REVERT: JB 204 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8663 (tm-30) REVERT: KB 252 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8785 (ttmm) REVERT: KB 254 GLU cc_start: 0.8631 (tm-30) cc_final: 0.6933 (tm-30) REVERT: KB 256 LYS cc_start: 0.9328 (tmtt) cc_final: 0.9021 (tttm) REVERT: LB 302 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8898 (ttmm) REVERT: LB 304 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: LB 305 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8764 (t80) REVERT: MB 352 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8660 (ttmm) REVERT: MB 354 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8073 (tm-30) REVERT: MB 356 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.8920 (tmtt) REVERT: NB 405 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8488 (t80) REVERT: OB 452 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8735 (ttmm) REVERT: OB 454 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8326 (tm-30) REVERT: e 4 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: VB 52 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8489 (pptt) REVERT: XB 152 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8684 (pptt) REVERT: YB 204 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: ZB 252 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8610 (pptt) REVERT: bB 357 PHE cc_start: 0.8404 (t80) cc_final: 0.8128 (t80) REVERT: dB 452 LYS cc_start: 0.9107 (tmtt) cc_final: 0.8541 (pptt) outliers start: 133 outliers final: 70 residues processed: 361 average time/residue: 0.3700 time to fit residues: 159.4958 Evaluate side-chains 450 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 326 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 106 LYS Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain CA residue 106 LYS Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain XA residue 54 GLU Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 204 GLU Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 406 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 302 LYS Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 202 LYS Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 202 LYS Chi-restraints excluded: chain JB residue 203 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8536 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.162 8700 Z= 2.318 Angle : 2.717 16.745 11300 Z= 1.314 Chirality : 0.139 0.340 800 Planarity : 0.011 0.036 1500 Dihedral : 24.991 89.911 1006 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 121.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 42.25 % Favored : 57.75 % Rotamer: Outliers : 21.83 % Allowed : 35.33 % Favored : 42.83 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.86 % 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: -6.77 (0.31), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.15 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.080 0.010 PHEfA 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 327 time to evaluate : 0.885 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: A 4 GLU cc_start: 0.8763 (mp0) cc_final: 0.8406 (mp0) REVERT: A 6 LYS cc_start: 0.9060 (tttt) cc_final: 0.8598 (tttm) REVERT: A 7 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8140 (m-10) REVERT: K 104 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: K 107 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8231 (m-10) REVERT: L 204 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: M 306 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8687 (tttt) REVERT: M 307 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8050 (m-10) REVERT: N 404 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8317 (mp0) REVERT: U 404 GLU cc_start: 0.8790 (mp0) cc_final: 0.8249 (mp0) REVERT: C 6 LYS cc_start: 0.9162 (tttt) cc_final: 0.8790 (tttm) REVERT: Y 106 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8857 (ttmt) REVERT: D 4 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: k 104 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: E 6 LYS cc_start: 0.9051 (tttt) cc_final: 0.8751 (tttp) REVERT: r 104 GLU cc_start: 0.8725 (mp0) cc_final: 0.8377 (mp0) REVERT: t 304 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: u 404 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: u 406 LYS cc_start: 0.9005 (mptt) cc_final: 0.8563 (ttmt) REVERT: F 2 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9083 (tttp) REVERT: F 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: y 106 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9060 (ttpt) REVERT: y 107 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: z 206 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: z 207 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: 0 307 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: 6 206 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8836 (ttpt) REVERT: 6 207 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: H 6 LYS cc_start: 0.9282 (tttt) cc_final: 0.8817 (ttmt) REVERT: EA 302 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8790 (ttmm) REVERT: JA 104 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.3922 (pm20) REVERT: LA 304 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8302 (pm20) REVERT: MA 404 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: J 4 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: QA 104 GLU cc_start: 0.8672 (pm20) cc_final: 0.6769 (tp30) REVERT: SA 304 GLU cc_start: 0.8916 (pm20) cc_final: 0.8481 (pm20) REVERT: TA 404 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7853 (tm-30) REVERT: a 3 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8707 (t80) REVERT: YA 103 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8455 (t80) REVERT: ZA 154 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8001 (tm-30) REVERT: aA 202 LYS cc_start: 0.9210 (tmtt) cc_final: 0.8735 (tptp) REVERT: aA 203 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8336 (t80) REVERT: aA 204 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: bA 252 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8511 (ttmm) REVERT: bA 254 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7856 (tm-30) REVERT: bA 255 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7632 (t80) REVERT: bA 256 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8975 (tttp) REVERT: cA 303 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8156 (t80) REVERT: cA 304 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8401 (tp30) REVERT: eA 403 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8449 (t80) REVERT: eA 404 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8048 (tm-30) REVERT: eA 406 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8682 (tttp) REVERT: fA 452 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8634 (ttmm) REVERT: fA 453 PHE cc_start: 0.8921 (t80) cc_final: 0.8269 (t80) REVERT: fA 454 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7684 (tm-30) REVERT: nA 104 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: oA 156 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9055 (tttp) REVERT: pA 204 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: rA 304 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (tp30) REVERT: tA 404 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: uA 452 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8785 (tmtt) REVERT: uA 456 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9041 (tttp) REVERT: c 5 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8594 (t80) REVERT: 1A 52 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8844 (ttmm) REVERT: 2A 105 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8789 (t80) REVERT: 3A 155 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8090 (t80) REVERT: 3A 156 LYS cc_start: 0.9337 (tmtt) cc_final: 0.8849 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (tptp) REVERT: 4A 204 GLU cc_start: 0.8750 (tm-30) cc_final: 0.7804 (tm-30) REVERT: 4A 205 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8376 (t80) REVERT: 4A 206 LYS cc_start: 0.9488 (tttm) cc_final: 0.9166 (tttm) REVERT: 6A 302 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8923 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: 7A 355 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7901 (t80) REVERT: 7A 356 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9025 (tttm) REVERT: 8A 404 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7805 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8770 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8136 (tm-30) REVERT: d 5 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8616 (t80) REVERT: GB 52 LYS cc_start: 0.9239 (tmtt) cc_final: 0.8876 (ttmm) REVERT: GB 53 PHE cc_start: 0.8910 (t80) cc_final: 0.8253 (m-80) REVERT: HB 104 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8392 (tm-30) REVERT: JB 202 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8845 (pptt) REVERT: JB 204 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8687 (tm-30) REVERT: KB 252 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8802 (ttmm) REVERT: KB 256 LYS cc_start: 0.9340 (tmtt) cc_final: 0.9076 (tttm) REVERT: LB 302 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8899 (ttmm) REVERT: LB 304 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: LB 305 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8761 (t80) REVERT: MB 352 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8660 (ttmm) REVERT: MB 354 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8068 (tm-30) REVERT: MB 355 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7856 (t80) REVERT: MB 356 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8897 (tmtt) REVERT: NB 405 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8481 (t80) REVERT: OB 452 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8734 (ttmm) REVERT: OB 454 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8232 (tm-30) REVERT: e 4 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: VB 52 LYS cc_start: 0.8911 (tmtt) cc_final: 0.8485 (pptt) REVERT: VB 56 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9117 (tptp) REVERT: XB 152 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8686 (pptt) REVERT: YB 204 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: ZB 252 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8611 (pptt) REVERT: bB 357 PHE cc_start: 0.8406 (t80) cc_final: 0.8135 (t80) REVERT: dB 452 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8532 (pptt) outliers start: 131 outliers final: 69 residues processed: 362 average time/residue: 0.3668 time to fit residues: 158.6122 Evaluate side-chains 451 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 327 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 106 LYS Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain CA residue 106 LYS Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 204 GLU Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 406 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 202 LYS Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 202 LYS Chi-restraints excluded: chain JB residue 203 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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: 0.8536 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.163 8700 Z= 2.317 Angle : 2.716 16.733 11300 Z= 1.314 Chirality : 0.139 0.341 800 Planarity : 0.011 0.037 1500 Dihedral : 24.976 89.844 1006 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 121.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.25 % Favored : 56.75 % Rotamer: Outliers : 21.83 % Allowed : 35.33 % Favored : 42.83 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.86 % 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: -6.75 (0.31), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.14 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.084 0.010 PHEfA 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 327 time to evaluate : 0.926 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: A 4 GLU cc_start: 0.8760 (mp0) cc_final: 0.8404 (mp0) REVERT: A 6 LYS cc_start: 0.9060 (tttt) cc_final: 0.8599 (tttm) REVERT: A 7 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: K 104 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: K 107 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8229 (m-10) REVERT: L 204 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: M 306 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8684 (tttt) REVERT: M 307 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: N 404 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8317 (mp0) REVERT: U 404 GLU cc_start: 0.8793 (mp0) cc_final: 0.8248 (mp0) REVERT: C 6 LYS cc_start: 0.9164 (tttt) cc_final: 0.8797 (tttm) REVERT: D 4 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: k 104 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: E 6 LYS cc_start: 0.9048 (tttt) cc_final: 0.8753 (tttp) REVERT: r 104 GLU cc_start: 0.8723 (mp0) cc_final: 0.8371 (mp0) REVERT: u 404 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: u 406 LYS cc_start: 0.9006 (mptt) cc_final: 0.8567 (ttmt) REVERT: F 2 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9082 (tttp) REVERT: F 7 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: y 106 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9062 (ttpt) REVERT: y 107 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: z 206 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8831 (ttpt) REVERT: z 207 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: 0 307 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: 6 206 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8838 (ttpt) REVERT: 6 207 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: H 4 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: H 6 LYS cc_start: 0.9282 (tttt) cc_final: 0.8817 (ttmt) REVERT: EA 302 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8794 (ttmm) REVERT: JA 104 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.3917 (pm20) REVERT: LA 304 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8313 (pm20) REVERT: MA 404 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: J 4 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: QA 104 GLU cc_start: 0.8670 (pm20) cc_final: 0.6764 (tp30) REVERT: SA 304 GLU cc_start: 0.8917 (pm20) cc_final: 0.8440 (pm20) REVERT: TA 404 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7857 (tm-30) REVERT: a 3 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8710 (t80) REVERT: YA 103 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8456 (t80) REVERT: ZA 154 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8012 (tm-30) REVERT: aA 202 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8738 (tptp) REVERT: aA 203 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8334 (t80) REVERT: aA 204 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: bA 252 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8511 (ttmm) REVERT: bA 254 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7838 (tm-30) REVERT: bA 255 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7629 (t80) REVERT: bA 256 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8973 (tttp) REVERT: cA 303 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8158 (t80) REVERT: cA 304 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: eA 403 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8433 (t80) REVERT: eA 404 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8042 (tm-30) REVERT: eA 406 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8697 (tttp) REVERT: fA 452 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8587 (ttmm) REVERT: fA 453 PHE cc_start: 0.8916 (t80) cc_final: 0.8290 (t80) REVERT: fA 454 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7659 (tm-30) REVERT: nA 104 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: oA 156 LYS cc_start: 0.9312 (tmtt) cc_final: 0.9052 (tttp) REVERT: pA 204 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: rA 304 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8585 (tp30) REVERT: tA 404 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: uA 452 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8794 (tmtt) REVERT: uA 456 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9014 (tttp) REVERT: c 5 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8551 (t80) REVERT: 1A 52 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8815 (ttmm) REVERT: 2A 105 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8797 (t80) REVERT: 3A 155 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8087 (t80) REVERT: 3A 156 LYS cc_start: 0.9337 (tmtt) cc_final: 0.8850 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8814 (tptp) REVERT: 4A 204 GLU cc_start: 0.8751 (tm-30) cc_final: 0.7780 (tm-30) REVERT: 4A 205 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8368 (t80) REVERT: 4A 206 LYS cc_start: 0.9483 (tttm) cc_final: 0.9165 (tttm) REVERT: 6A 304 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: 7A 355 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7900 (t80) REVERT: 7A 356 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9022 (tttm) REVERT: 8A 404 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7789 (tm-30) REVERT: 9A 452 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8783 (ttmm) REVERT: 9A 454 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8140 (tm-30) REVERT: d 5 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8605 (t80) REVERT: GB 52 LYS cc_start: 0.9245 (tmtt) cc_final: 0.8859 (ttmm) REVERT: GB 53 PHE cc_start: 0.8916 (t80) cc_final: 0.8276 (m-80) REVERT: HB 104 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8394 (tm-30) REVERT: IB 156 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9222 (tmtt) REVERT: JB 202 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8845 (pptt) REVERT: KB 252 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8785 (ttmm) REVERT: KB 256 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9080 (tttm) REVERT: LB 302 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8901 (ttmm) REVERT: LB 304 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (tp30) REVERT: LB 305 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8766 (t80) REVERT: MB 352 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8667 (ttmm) REVERT: MB 354 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8048 (tm-30) REVERT: MB 356 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8917 (tmtt) REVERT: NB 405 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8484 (t80) REVERT: OB 452 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8728 (ttmm) REVERT: OB 454 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8241 (tm-30) REVERT: e 4 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: VB 52 LYS cc_start: 0.8912 (tmtt) cc_final: 0.8483 (pptt) REVERT: VB 56 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9116 (tptp) REVERT: XB 152 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8686 (pptt) REVERT: YB 204 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: ZB 252 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8614 (pptt) REVERT: bB 357 PHE cc_start: 0.8402 (t80) cc_final: 0.8125 (t80) REVERT: dB 452 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8531 (pptt) outliers start: 131 outliers final: 69 residues processed: 362 average time/residue: 0.3811 time to fit residues: 165.7968 Evaluate side-chains 449 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 327 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain m residue 304 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 106 LYS Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain CA residue 106 LYS Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain XA residue 54 GLU Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 204 GLU Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain aA residue 206 LYS Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain bA residue 256 LYS Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 402 LYS Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 406 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 104 GLU Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 202 LYS Chi-restraints excluded: chain pA residue 204 GLU Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 302 LYS Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain rA residue 306 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 404 GLU Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain tA residue 406 LYS Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 202 LYS Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 202 LYS Chi-restraints excluded: chain JB residue 203 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 356 LYS Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain cB residue 406 LYS Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070273 restraints weight = 23418.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072097 restraints weight = 9606.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073271 restraints weight = 5127.451| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.159 8700 Z= 2.317 Angle : 2.723 16.747 11300 Z= 1.318 Chirality : 0.139 0.341 800 Planarity : 0.011 0.042 1500 Dihedral : 24.974 89.817 1006 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 121.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.00 % Favored : 57.00 % Rotamer: Outliers : 22.17 % Allowed : 35.17 % Favored : 42.67 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.86 % 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: -6.80 (0.31), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.18 (0.23), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.010 PHEfA 457 =============================================================================== Job complete usr+sys time: 2264.48 seconds wall clock time: 41 minutes 47.18 seconds (2507.18 seconds total)