Starting phenix.real_space_refine on Fri Jul 19 16:29:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/07_2024/7lqi_23487.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/07_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_23487/07_2024/7lqi_23487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/07_2024/7lqi_23487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/07_2024/7lqi_23487.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/07_2024/7lqi_23487.cif" } 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-5388/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: 4.53, per 1000 atoms: 0.54 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: 3.76 Conformation dependent library (CDL) restraints added in 826.8 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... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'I' and resid 6 through 7 removed outlier: 6.912A pdb=" N LYS G 6 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS E 6 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 6 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 6 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'JA' and resid 102 through 104 removed outlier: 5.642A pdb=" N LYS K 102 " --> pdb=" O PHE Y 103 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE Y 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU K 104 " --> pdb=" O PHE Y 105 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE Y 107 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS K 106 " --> pdb=" O PHE Y 107 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE K 103 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE R 103 " --> pdb=" O GLU k 104 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE k 103 " --> pdb=" O GLU y 104 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE y 103 " --> pdb=" O GLUCA 104 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYSCA 106 " --> pdb=" O PHE y 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLUQA 104 " --> pdb=" O PHECA 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYSQA 106 " --> pdb=" O PHECA 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE z 203 " --> pdb=" O GLUDA 204 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYSDA 206 " --> pdb=" O PHE z 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LA' and resid 302 through 307 removed outlier: 6.205A pdb=" N LYS 7 302 " --> pdb=" O PHELA 303 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHELA 305 " --> pdb=" O LYS 7 302 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU 7 304 " --> pdb=" O PHELA 305 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHELA 307 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS 7 306 " --> pdb=" O PHELA 307 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS t 302 " --> pdb=" O PHE 7 303 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE 7 305 " --> pdb=" O LYS t 302 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU t 304 " --> pdb=" O PHE 7 305 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE 7 307 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS t 306 " --> pdb=" O PHE 7 307 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS M 302 " --> pdb=" O PHE f 303 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE f 305 " --> pdb=" O LYS M 302 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU M 304 " --> pdb=" O PHE f 305 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE f 307 " --> pdb=" O GLU M 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS M 306 " --> pdb=" O PHE f 307 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE M 303 " --> pdb=" O GLU T 304 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS T 306 " --> pdb=" O PHE M 303 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE M 305 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE 0 303 " --> pdb=" O GLUEA 304 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYSEA 306 " --> pdb=" O PHE 0 303 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE 0 305 " --> pdb=" O LYSEA 306 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHEEA 303 " --> pdb=" O GLUSA 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'MA' and resid 402 through 403 removed outlier: 6.357A pdb=" N LYS 8 402 " --> pdb=" O PHEMA 403 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS u 402 " --> pdb=" O PHE 8 403 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS g 402 " --> pdb=" O PHE u 403 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS N 402 " --> pdb=" O PHE g 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'MA' and resid 406 through 407 removed outlier: 6.747A pdb=" N LYS 8 406 " --> pdb=" O PHEMA 407 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS u 406 " --> pdb=" O PHE 8 407 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS g 406 " --> pdb=" O PHE u 407 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS N 406 " --> pdb=" O PHE g 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.791A pdb=" N LYS C 2 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS E 2 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS G 2 " --> pdb=" O PHE I 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'd' and resid 5 through 6 removed outlier: 3.743A pdb=" N LYS b 6 " --> pdb=" O GLUGB 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS a 6 " --> pdb=" O GLUmA 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS c 6 " --> pdb=" O GLUXA 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSXA 56 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE1A 55 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS e 6 " --> pdb=" O GLU1A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'HB' and resid 105 through 106 removed outlier: 3.686A pdb=" N LYSnA 106 " --> pdb=" O GLUIB 154 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSYA 106 " --> pdb=" O GLUoA 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS2A 106 " --> pdb=" O GLUZA 154 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSWB 106 " --> pdb=" O GLU3A 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'JB' and resid 205 through 206 removed outlier: 3.810A pdb=" N PHEKB 253 " --> pdb=" O PHEJB 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSpA 206 " --> pdb=" O GLUKB 254 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSKB 256 " --> pdb=" O GLUpA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEqA 255 " --> pdb=" O PHEpA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEqA 253 " --> pdb=" O PHEpA 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSqA 256 " --> pdb=" O GLUaA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEbA 255 " --> pdb=" O PHEaA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEbA 253 " --> pdb=" O PHEaA 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSbA 256 " --> pdb=" O GLU4A 204 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE5A 255 " --> pdb=" O PHE4A 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE5A 253 " --> pdb=" O PHE4A 205 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSYB 206 " --> pdb=" O GLU5A 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS5A 256 " --> pdb=" O GLUYB 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHEZB 253 " --> pdb=" O PHEYB 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LB' and resid 305 through 306 removed outlier: 3.555A pdb=" N PHEMB 353 " --> pdb=" O PHELB 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYSrA 306 " --> pdb=" O GLUMB 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSMB 356 " --> pdb=" O GLUrA 304 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHEsA 355 " --> pdb=" O PHErA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEsA 353 " --> pdb=" O PHErA 305 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYScA 306 " --> pdb=" O GLUsA 354 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHEdA 355 " --> pdb=" O PHEcA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEdA 353 " --> pdb=" O PHEcA 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS6A 306 " --> pdb=" O GLUdA 354 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE7A 355 " --> pdb=" O PHE6A 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE7A 353 " --> pdb=" O PHE6A 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU7A 354 " --> pdb=" O LYSaB 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSaB 306 " --> pdb=" O GLU7A 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEbB 353 " --> pdb=" O PHEaB 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'NB' and resid 405 through 406 removed outlier: 3.651A pdb=" N LYStA 406 " --> pdb=" O GLUOB 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSeA 406 " --> pdb=" O GLUuA 454 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS8A 406 " --> pdb=" O GLUfA 454 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYScB 406 " --> pdb=" O GLU9A 454 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 4.01 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: 6509 3.31 - 3.84: 13602 3.84 - 4.37: 17423 4.37 - 4.90: 28904 Nonbonded interactions: 68983 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 68978 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 25.520 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.110 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- 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= 0.861 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 : 0.898 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: 0.3889 time to fit residues: 170.9869 Evaluate side-chains 340 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.210 8700 Z= 2.775 Angle : 2.725 17.454 11300 Z= 1.298 Chirality : 0.136 0.330 800 Planarity : 0.011 0.038 1500 Dihedral : 25.452 89.477 1030 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 126.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 15.33 % Allowed : 25.33 % Favored : 59.33 % 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: -4.74 (0.34), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.085 0.011 PHE c 3 *********************** 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 418 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 326 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8763 (mp0) cc_final: 0.8450 (mp0) REVERT: A 6 LYS cc_start: 0.9165 (tttt) cc_final: 0.8776 (tttm) REVERT: A 7 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: K 104 GLU cc_start: 0.8727 (mp0) cc_final: 0.8323 (mp0) REVERT: K 107 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: L 207 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: M 306 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8673 (tttt) REVERT: M 307 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: C 6 LYS cc_start: 0.8962 (tttt) cc_final: 0.8629 (tttm) REVERT: n 404 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7849 (mt-10) REVERT: E 6 LYS cc_start: 0.9062 (tttt) cc_final: 0.8725 (tttp) REVERT: t 307 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9240 (m-10) REVERT: u 404 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8131 (mm-30) REVERT: u 406 LYS cc_start: 0.8916 (mptt) cc_final: 0.8553 (ttmt) REVERT: F 7 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: y 107 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: z 207 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: 0 304 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8359 (mt-10) REVERT: 0 307 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: G 6 LYS cc_start: 0.9385 (tttt) cc_final: 0.8965 (tttm) REVERT: 6 207 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: 7 307 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: H 4 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7621 (tm-30) REVERT: H 6 LYS cc_start: 0.9336 (tttt) cc_final: 0.8929 (ttmt) REVERT: I 6 LYS cc_start: 0.9087 (tttt) cc_final: 0.8774 (tttm) REVERT: LA 304 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8360 (pm20) REVERT: MA 404 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7934 (pm20) REVERT: J 4 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7775 (tm-30) REVERT: TA 404 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7885 (tm-30) REVERT: XA 55 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7686 (t80) REVERT: XA 56 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8943 (tttm) REVERT: ZA 155 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7835 (t80) REVERT: ZA 156 LYS cc_start: 0.9392 (tmtt) cc_final: 0.9076 (tmtt) REVERT: aA 203 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.6773 (t80) REVERT: aA 204 GLU cc_start: 0.8429 (tp30) cc_final: 0.8029 (tm-30) REVERT: aA 206 LYS cc_start: 0.9044 (tttm) cc_final: 0.8838 (tttp) REVERT: bA 255 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7735 (t80) REVERT: bA 256 LYS cc_start: 0.9178 (tmtt) cc_final: 0.8840 (tmtt) REVERT: cA 302 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8802 (tmtt) REVERT: cA 303 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.6206 (t80) REVERT: cA 304 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: dA 355 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7589 (t80) REVERT: dA 356 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8688 (tttm) REVERT: eA 406 LYS cc_start: 0.9381 (tttp) cc_final: 0.9144 (tttp) REVERT: fA 455 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8089 (t80) REVERT: fA 456 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9141 (tttm) REVERT: b 2 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8974 (ttmm) REVERT: mA 55 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7279 (t80) REVERT: mA 56 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9139 (tttp) REVERT: oA 156 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9083 (tmtt) REVERT: pA 204 GLU cc_start: 0.8553 (tp30) cc_final: 0.8334 (tm-30) REVERT: qA 255 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6777 (t80) REVERT: rA 302 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8911 (tmtt) REVERT: sA 355 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.6639 (t80) REVERT: uA 455 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7209 (t80) REVERT: uA 456 LYS cc_start: 0.9402 (tmtt) cc_final: 0.9112 (tttp) REVERT: 1A 56 LYS cc_start: 0.9323 (tmtt) cc_final: 0.9067 (tmtt) REVERT: 3A 153 PHE cc_start: 0.8418 (t80) cc_final: 0.8190 (t80) REVERT: 3A 156 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9078 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9005 (tptp) cc_final: 0.8749 (tptp) REVERT: 4A 204 GLU cc_start: 0.8655 (tp30) cc_final: 0.8408 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9072 (tttm) cc_final: 0.8798 (tttm) REVERT: 5A 256 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8921 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: 6A 305 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8376 (t80) REVERT: 7A 356 LYS cc_start: 0.9224 (tmtt) cc_final: 0.8577 (tmtt) REVERT: d 5 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8263 (t80) REVERT: GB 56 LYS cc_start: 0.9343 (tmtt) cc_final: 0.9004 (tmtt) REVERT: HB 105 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8366 (t80) REVERT: JB 204 GLU cc_start: 0.8648 (tp30) cc_final: 0.8286 (pm20) REVERT: LB 302 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8799 (ttmm) REVERT: LB 304 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: LB 305 PHE cc_start: 0.8792 (t80) cc_final: 0.8468 (t80) REVERT: LB 306 LYS cc_start: 0.9304 (tttm) cc_final: 0.9073 (tttm) REVERT: MB 352 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8723 (tmtt) REVERT: MB 353 PHE cc_start: 0.8451 (t80) cc_final: 0.8212 (t80) REVERT: OB 456 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9183 (tttm) REVERT: e 4 GLU cc_start: 0.8611 (tp30) cc_final: 0.8090 (tm-30) REVERT: VB 55 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7684 (t80) REVERT: YB 204 GLU cc_start: 0.8613 (tp30) cc_final: 0.8248 (tm-30) REVERT: ZB 256 LYS cc_start: 0.9363 (tmtt) cc_final: 0.9149 (tttp) REVERT: aB 302 LYS cc_start: 0.9174 (tmtt) cc_final: 0.8655 (tmtt) REVERT: cB 402 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8727 (ttmm) outliers start: 92 outliers final: 42 residues processed: 354 average time/residue: 0.3739 time to fit residues: 157.4743 Evaluate side-chains 388 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 317 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain t residue 307 PHE 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 XA residue 55 PHE Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 202 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain bA residue 255 PHE 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 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain sA residue 355 PHE 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 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 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 6A residue 305 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 HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 304 GLU Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain ZB residue 255 PHE 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: 0.8506 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.180 8700 Z= 2.762 Angle : 2.729 16.954 11300 Z= 1.311 Chirality : 0.136 0.336 800 Planarity : 0.011 0.040 1500 Dihedral : 25.370 88.383 1012 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 129.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.75 % Favored : 76.25 % Rotamer: Outliers : 17.67 % Allowed : 31.67 % Favored : 50.67 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.57 % 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: -5.22 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.093 0.011 PHEaA 203 *********************** 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 426 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 320 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8714 (mp0) cc_final: 0.8437 (mp0) REVERT: A 6 LYS cc_start: 0.9093 (tttt) cc_final: 0.8661 (tttm) REVERT: A 7 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: K 107 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: L 204 GLU cc_start: 0.8679 (mp0) cc_final: 0.8473 (mp0) REVERT: L 207 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: M 306 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8595 (tttt) REVERT: M 307 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: C 6 LYS cc_start: 0.9033 (tttt) cc_final: 0.8684 (tttm) REVERT: g 404 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8329 (mp0) REVERT: D 4 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7685 (tm-30) REVERT: E 6 LYS cc_start: 0.9049 (tttt) cc_final: 0.8756 (tttp) REVERT: u 404 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8364 (mm-30) REVERT: u 406 LYS cc_start: 0.8948 (mptt) cc_final: 0.8577 (ttmt) REVERT: F 7 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8254 (m-10) REVERT: y 107 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8047 (m-10) REVERT: z 206 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8860 (ttpt) REVERT: z 207 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: 0 307 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: 1 404 GLU cc_start: 0.8850 (mp0) cc_final: 0.8601 (mp0) REVERT: G 7 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.7871 (m-10) REVERT: 6 206 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8805 (ttpt) REVERT: 6 207 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: H 4 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: H 6 LYS cc_start: 0.9309 (tttt) cc_final: 0.8859 (ttmt) REVERT: I 6 LYS cc_start: 0.9051 (tttt) cc_final: 0.8763 (tttm) REVERT: LA 304 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8356 (pm20) REVERT: MA 404 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8183 (pm20) REVERT: J 4 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7757 (tm-30) REVERT: J 6 LYS cc_start: 0.9255 (tttp) cc_final: 0.9045 (tttm) REVERT: QA 104 GLU cc_start: 0.8740 (pm20) cc_final: 0.6969 (mm-30) REVERT: TA 404 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7907 (tm-30) REVERT: a 3 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7374 (t80) REVERT: a 4 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: XA 56 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8921 (tttp) REVERT: YA 104 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: aA 204 GLU cc_start: 0.8395 (tp30) cc_final: 0.8095 (tm-30) REVERT: aA 206 LYS cc_start: 0.9028 (tttm) cc_final: 0.8422 (tttp) REVERT: bA 255 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7720 (t80) REVERT: bA 256 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8766 (tmtt) REVERT: cA 303 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.6945 (t80) REVERT: cA 304 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: dA 355 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7714 (t80) REVERT: dA 356 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8849 (tttt) REVERT: eA 403 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.7470 (t80) REVERT: eA 406 LYS cc_start: 0.9392 (tttp) cc_final: 0.9171 (tttp) REVERT: fA 456 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9163 (tttp) REVERT: b 4 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: mA 55 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7011 (t80) REVERT: mA 56 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9122 (tttp) REVERT: oA 156 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9142 (tttp) REVERT: sA 355 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.6946 (t80) REVERT: sA 356 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8741 (tmtt) REVERT: uA 455 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.6861 (t80) REVERT: uA 456 LYS cc_start: 0.9405 (tmtt) cc_final: 0.9076 (tttp) REVERT: 1A 56 LYS cc_start: 0.9387 (tmtt) cc_final: 0.9061 (tmtt) REVERT: 3A 156 LYS cc_start: 0.9336 (tmtt) cc_final: 0.8944 (tmtt) REVERT: 4A 202 LYS cc_start: 0.9006 (tptp) cc_final: 0.8770 (tptp) REVERT: 4A 206 LYS cc_start: 0.9074 (tttm) cc_final: 0.8818 (tttm) REVERT: 6A 304 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: 6A 305 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8310 (t80) REVERT: 7A 356 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8779 (tmtt) REVERT: d 4 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: GB 53 PHE cc_start: 0.8790 (t80) cc_final: 0.8159 (t80) REVERT: GB 56 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9113 (tmtt) REVERT: HB 105 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8291 (t80) REVERT: JB 204 GLU cc_start: 0.8651 (tp30) cc_final: 0.8202 (pm20) REVERT: KB 256 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8813 (tmtt) REVERT: LB 302 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8833 (ttmm) REVERT: LB 304 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: LB 305 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8419 (t80) REVERT: LB 306 LYS cc_start: 0.9367 (tttm) cc_final: 0.9106 (tttm) REVERT: MB 352 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8796 (tmtt) REVERT: OB 456 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9143 (tttm) REVERT: e 4 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: VB 55 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7744 (t80) REVERT: XB 155 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7781 (t80) REVERT: XB 157 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7570 (t80) REVERT: YB 204 GLU cc_start: 0.8544 (tp30) cc_final: 0.8106 (tm-30) REVERT: ZB 256 LYS cc_start: 0.9305 (tmtt) cc_final: 0.9093 (tttp) REVERT: aB 302 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8950 (tmtt) REVERT: aB 304 GLU cc_start: 0.8545 (tp30) cc_final: 0.8220 (tm-30) REVERT: bB 352 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8563 (pptt) REVERT: cB 402 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8790 (ttmm) outliers start: 106 outliers final: 53 residues processed: 347 average time/residue: 0.3789 time to fit residues: 155.8867 Evaluate side-chains 409 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 318 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain l residue 204 GLU 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 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 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 KA residue 206 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain bA residue 255 PHE 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 eA residue 405 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 303 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE 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 5 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 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 6A residue 304 GLU Chi-restraints excluded: chain 6A residue 305 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 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 IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 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 NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 456 LYS 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 105 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 ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 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: 0.8513 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.168 8700 Z= 2.766 Angle : 2.724 17.343 11300 Z= 1.308 Chirality : 0.137 0.339 800 Planarity : 0.011 0.037 1500 Dihedral : 25.147 89.784 1012 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 129.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.50 % Favored : 75.50 % Rotamer: Outliers : 19.67 % Allowed : 33.17 % Favored : 47.17 % 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: -5.38 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.011 PHEaA 203 *********************** 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 446 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 328 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8717 (mp0) cc_final: 0.8452 (mp0) REVERT: A 6 LYS cc_start: 0.9092 (tttt) cc_final: 0.8668 (tttm) REVERT: A 7 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8168 (m-10) REVERT: K 107 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: L 207 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: M 306 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8635 (tttt) REVERT: M 307 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: U 404 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: C 6 LYS cc_start: 0.9089 (tttt) cc_final: 0.8733 (tttp) REVERT: Y 106 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8845 (ttmt) REVERT: D 4 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: E 6 LYS cc_start: 0.9084 (tttt) cc_final: 0.8790 (tttp) REVERT: u 406 LYS cc_start: 0.9037 (mptt) cc_final: 0.8518 (ttmt) REVERT: F 7 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: y 107 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: z 206 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8868 (ttpt) REVERT: z 207 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: 0 307 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: 1 404 GLU cc_start: 0.8782 (mp0) cc_final: 0.8574 (mp0) REVERT: 6 206 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8833 (ttpt) REVERT: 6 207 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.7983 (m-10) REVERT: H 4 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: H 6 LYS cc_start: 0.9296 (tttt) cc_final: 0.8837 (ttmt) REVERT: I 6 LYS cc_start: 0.9056 (tttt) cc_final: 0.8787 (tttm) REVERT: JA 104 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.3754 (pm20) REVERT: LA 304 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8354 (pm20) REVERT: MA 404 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: J 4 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: QA 104 GLU cc_start: 0.8689 (pm20) cc_final: 0.8395 (pm20) REVERT: TA 404 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7909 (tm-30) REVERT: a 4 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: XA 56 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8956 (tttp) REVERT: YA 104 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: ZA 155 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7943 (t80) REVERT: aA 203 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8478 (t80) REVERT: bA 255 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7758 (t80) REVERT: cA 303 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.7248 (t80) REVERT: cA 304 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: dA 355 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7716 (t80) REVERT: eA 403 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.7195 (t80) REVERT: eA 406 LYS cc_start: 0.9392 (tttp) cc_final: 0.9175 (tttp) REVERT: fA 456 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9158 (tttm) REVERT: b 4 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: mA 55 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7266 (t80) REVERT: mA 56 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9072 (tttp) REVERT: oA 156 LYS cc_start: 0.9352 (tmtt) cc_final: 0.9108 (tttp) REVERT: qA 256 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8817 (tmtt) REVERT: rA 304 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: sA 355 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.6898 (t80) REVERT: uA 455 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.6879 (t80) REVERT: uA 456 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9063 (tttp) REVERT: 1A 56 LYS cc_start: 0.9412 (tmtt) cc_final: 0.9083 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8406 (t80) REVERT: 3A 156 LYS cc_start: 0.9357 (tmtt) cc_final: 0.8987 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9121 (tttm) cc_final: 0.8893 (tttm) REVERT: 5A 256 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8518 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: 7A 356 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9058 (tttm) REVERT: d 4 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: GB 52 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8865 (tmtt) REVERT: GB 56 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9094 (tmtt) REVERT: HB 105 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8350 (t80) REVERT: IB 156 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9145 (tmtt) REVERT: JB 204 GLU cc_start: 0.8710 (tp30) cc_final: 0.8166 (pm20) REVERT: JB 205 PHE cc_start: 0.8904 (t80) cc_final: 0.8672 (t80) REVERT: LB 302 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8848 (ttmm) REVERT: LB 304 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: LB 305 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8358 (t80) REVERT: OB 456 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9123 (tttm) REVERT: e 4 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: XB 152 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8410 (pptt) REVERT: XB 157 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7737 (t80) REVERT: ZB 256 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9089 (tttp) REVERT: aB 305 PHE cc_start: 0.8829 (t80) cc_final: 0.8548 (t80) REVERT: bB 352 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8419 (pptt) REVERT: cB 402 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8741 (ttmm) outliers start: 118 outliers final: 59 residues processed: 358 average time/residue: 0.3596 time to fit residues: 153.5581 Evaluate side-chains 429 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 327 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain l residue 204 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 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 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE 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 eA residue 405 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 2A residue 103 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 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 NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 456 LYS 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 105 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 bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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: 0.8514 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.154 8700 Z= 2.763 Angle : 2.716 19.367 11300 Z= 1.303 Chirality : 0.137 0.340 800 Planarity : 0.011 0.036 1500 Dihedral : 25.066 89.800 1012 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 128.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.75 % Favored : 75.25 % Rotamer: Outliers : 21.00 % Allowed : 32.00 % Favored : 47.00 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.14 % 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: -5.47 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.083 0.010 PHEaA 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 453 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 327 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8737 (mp0) cc_final: 0.8475 (mp0) REVERT: A 6 LYS cc_start: 0.9079 (tttt) cc_final: 0.8659 (tttm) REVERT: A 7 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: K 107 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 207 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: M 306 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8644 (tttt) REVERT: M 307 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: N 404 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8359 (mp0) REVERT: U 404 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: C 6 LYS cc_start: 0.9134 (tttt) cc_final: 0.8878 (ttmt) REVERT: Y 106 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8859 (ttmt) REVERT: g 404 GLU cc_start: 0.8897 (mp0) cc_final: 0.8642 (mp0) REVERT: D 4 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: E 6 LYS cc_start: 0.9088 (tttt) cc_final: 0.8795 (tttp) REVERT: u 406 LYS cc_start: 0.8814 (mptt) cc_final: 0.8538 (ttmt) REVERT: F 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: y 106 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9127 (ttpt) REVERT: y 107 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: z 206 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8862 (ttpt) REVERT: z 207 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8137 (m-10) REVERT: 0 307 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: 1 404 GLU cc_start: 0.8789 (mp0) cc_final: 0.8568 (mp0) REVERT: 6 206 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8827 (ttpt) REVERT: 6 207 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: H 6 LYS cc_start: 0.9287 (tttt) cc_final: 0.8818 (ttmt) REVERT: JA 104 GLU cc_start: 0.4490 (OUTLIER) cc_final: 0.3688 (pm20) REVERT: LA 304 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8382 (pm20) REVERT: MA 404 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: J 4 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: QA 104 GLU cc_start: 0.8666 (pm20) cc_final: 0.6748 (tp30) REVERT: RA 204 GLU cc_start: 0.9022 (pm20) cc_final: 0.6954 (mm-30) REVERT: SA 304 GLU cc_start: 0.8964 (pm20) cc_final: 0.8474 (pm20) REVERT: TA 404 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7833 (tm-30) REVERT: a 3 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7653 (t80) REVERT: a 4 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8180 (tp30) REVERT: XA 56 LYS cc_start: 0.9264 (tmtt) cc_final: 0.9001 (tttp) REVERT: YA 104 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: aA 203 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8460 (t80) REVERT: bA 255 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7747 (t80) REVERT: cA 302 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9113 (tttm) REVERT: cA 304 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: dA 355 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7648 (t80) REVERT: eA 403 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.7201 (t80) REVERT: eA 406 LYS cc_start: 0.9386 (tttp) cc_final: 0.9141 (tttp) REVERT: fA 456 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9148 (tttp) REVERT: b 4 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: mA 55 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.6990 (t80) REVERT: mA 56 LYS cc_start: 0.9327 (tmtt) cc_final: 0.9043 (tttp) REVERT: oA 156 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9098 (tttp) REVERT: qA 256 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8679 (tmtt) REVERT: sA 355 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7036 (t80) REVERT: uA 455 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.6903 (t80) REVERT: uA 456 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9061 (tttp) REVERT: 1A 56 LYS cc_start: 0.9406 (tmtt) cc_final: 0.9041 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8357 (t80) REVERT: 3A 156 LYS cc_start: 0.9338 (tmtt) cc_final: 0.8920 (tmtt) REVERT: 5A 256 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8807 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: 7A 356 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9029 (tttm) REVERT: d 4 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: HB 105 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8341 (t80) REVERT: KB 256 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8761 (tmtt) REVERT: LB 302 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8894 (ttmm) REVERT: LB 304 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: LB 305 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8310 (t80) REVERT: MB 353 PHE cc_start: 0.8542 (t80) cc_final: 0.8331 (t80) REVERT: e 4 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: XB 152 LYS cc_start: 0.8998 (tmtt) cc_final: 0.8414 (pptt) REVERT: XB 157 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7643 (t80) REVERT: YB 205 PHE cc_start: 0.8970 (t80) cc_final: 0.8619 (t80) REVERT: ZB 256 LYS cc_start: 0.9271 (tmtt) cc_final: 0.9047 (tttp) REVERT: bB 352 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8503 (pptt) REVERT: cB 402 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8738 (ttmm) REVERT: dB 452 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8428 (pptt) outliers start: 126 outliers final: 70 residues processed: 363 average time/residue: 0.3666 time to fit residues: 159.0427 Evaluate side-chains 439 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 328 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 304 GLU 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 Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain l residue 204 GLU 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 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 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 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 52 LYS Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 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 bA residue 255 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 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 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 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 VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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: 0.8517 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.765 Angle : 2.714 20.121 11300 Z= 1.301 Chirality : 0.138 0.342 800 Planarity : 0.011 0.036 1500 Dihedral : 25.000 89.509 1012 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 129.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 21.67 % Allowed : 33.17 % Favored : 45.17 % 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: -5.53 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.085 0.011 PHEaA 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 456 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 326 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8739 (mp0) cc_final: 0.8469 (mp0) REVERT: A 6 LYS cc_start: 0.9075 (tttt) cc_final: 0.8590 (tttm) REVERT: A 7 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: K 107 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: L 207 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: M 306 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8649 (tttt) REVERT: M 307 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8028 (m-10) REVERT: N 404 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8362 (mp0) REVERT: B 6 LYS cc_start: 0.9044 (tttp) cc_final: 0.8807 (ttmt) REVERT: U 404 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: C 6 LYS cc_start: 0.9142 (tttt) cc_final: 0.8770 (tttm) REVERT: Y 106 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8862 (ttmt) REVERT: g 404 GLU cc_start: 0.8858 (mp0) cc_final: 0.8613 (mp0) REVERT: D 4 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: k 104 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: m 304 GLU cc_start: 0.8716 (mp0) cc_final: 0.8472 (mp0) REVERT: E 6 LYS cc_start: 0.9073 (tttt) cc_final: 0.8775 (tttp) REVERT: r 104 GLU cc_start: 0.8687 (mp0) cc_final: 0.8479 (mp0) REVERT: u 406 LYS cc_start: 0.8911 (mptt) cc_final: 0.8588 (ttmt) REVERT: F 7 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: y 107 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: z 206 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8859 (ttpt) REVERT: z 207 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: 0 307 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: 6 206 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8827 (ttpt) REVERT: 6 207 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: H 6 LYS cc_start: 0.9287 (tttt) cc_final: 0.8821 (ttmt) REVERT: JA 104 GLU cc_start: 0.4508 (OUTLIER) cc_final: 0.3803 (pm20) REVERT: KA 204 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.3552 (pm20) REVERT: LA 304 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8425 (pm20) REVERT: MA 404 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: J 4 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: QA 104 GLU cc_start: 0.8650 (pm20) cc_final: 0.6693 (tp30) REVERT: RA 204 GLU cc_start: 0.9015 (pm20) cc_final: 0.6953 (mm-30) REVERT: TA 404 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7908 (tm-30) REVERT: a 3 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7567 (t80) REVERT: a 4 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: XA 56 LYS cc_start: 0.9274 (tmtt) cc_final: 0.9015 (tttp) REVERT: YA 103 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8191 (t80) REVERT: YA 104 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: aA 203 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8493 (t80) REVERT: bA 255 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7743 (t80) REVERT: cA 302 LYS cc_start: 0.9322 (tmtt) cc_final: 0.9110 (tttm) REVERT: cA 303 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7036 (t80) REVERT: cA 304 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: dA 355 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7673 (t80) REVERT: eA 403 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.7178 (t80) REVERT: eA 406 LYS cc_start: 0.9400 (tttp) cc_final: 0.9168 (tttp) REVERT: fA 456 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9165 (tttp) REVERT: b 4 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: mA 55 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.6932 (t80) REVERT: mA 56 LYS cc_start: 0.9327 (tmtt) cc_final: 0.9032 (tttp) REVERT: oA 156 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9075 (tttp) REVERT: qA 256 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8700 (tmtt) REVERT: sA 355 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6866 (t80) REVERT: sA 356 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8647 (tttm) REVERT: uA 455 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.6914 (t80) REVERT: uA 456 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9062 (tttp) REVERT: 1A 56 LYS cc_start: 0.9416 (tmtt) cc_final: 0.9073 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8403 (t80) REVERT: 5A 256 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8875 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: 7A 355 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7831 (t80) REVERT: 7A 356 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9026 (tttm) REVERT: 9A 456 LYS cc_start: 0.9282 (tttm) cc_final: 0.9052 (tttm) REVERT: d 4 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: HB 105 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8343 (t80) REVERT: JB 205 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8251 (t80) REVERT: LB 302 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8894 (ttmm) REVERT: LB 304 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: LB 305 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8299 (t80) REVERT: MB 352 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8780 (tmtt) REVERT: MB 356 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8806 (tmtt) REVERT: e 4 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: VB 52 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8380 (pptt) REVERT: XB 152 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8435 (pptt) REVERT: XB 157 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7461 (t80) REVERT: YB 205 PHE cc_start: 0.8981 (t80) cc_final: 0.8647 (t80) REVERT: ZB 252 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8449 (pptt) REVERT: ZB 256 LYS cc_start: 0.9272 (tmtt) cc_final: 0.9048 (tttp) REVERT: bB 352 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8492 (pptt) REVERT: cB 402 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8712 (ttmm) REVERT: dB 452 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8381 (pptt) outliers start: 130 outliers final: 73 residues processed: 363 average time/residue: 0.3611 time to fit residues: 157.4179 Evaluate side-chains 444 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 325 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 R residue 104 GLU 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 Z residue 204 GLU Chi-restraints excluded: chain f residue 304 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 l residue 204 GLU 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 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 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 204 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 a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 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 bA residue 255 PHE 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 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 452 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 52 LYS Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 252 LYS Chi-restraints excluded: chain KB residue 255 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 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 VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE 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: 0.8515 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.151 8700 Z= 2.762 Angle : 2.714 20.280 11300 Z= 1.303 Chirality : 0.138 0.339 800 Planarity : 0.011 0.037 1500 Dihedral : 24.967 89.570 1012 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 130.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.75 % Favored : 74.25 % Rotamer: Outliers : 22.67 % Allowed : 32.17 % Favored : 45.17 % 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: -5.56 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.011 PHEaA 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 459 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 323 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8738 (mp0) cc_final: 0.8468 (mp0) REVERT: A 6 LYS cc_start: 0.9078 (tttt) cc_final: 0.8594 (tttm) REVERT: A 7 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: K 107 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: L 207 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8985 (m-80) REVERT: M 306 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8653 (tttt) REVERT: M 307 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: B 6 LYS cc_start: 0.9046 (tttp) cc_final: 0.8808 (ttmt) REVERT: U 404 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: C 6 LYS cc_start: 0.9148 (tttt) cc_final: 0.8776 (tttp) REVERT: Y 106 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8872 (ttmt) REVERT: g 404 GLU cc_start: 0.8835 (mp0) cc_final: 0.8555 (mp0) REVERT: D 4 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: k 104 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: m 304 GLU cc_start: 0.8699 (mp0) cc_final: 0.8466 (mp0) REVERT: E 6 LYS cc_start: 0.9052 (tttt) cc_final: 0.8755 (tttp) REVERT: r 104 GLU cc_start: 0.8697 (mp0) cc_final: 0.8487 (mp0) REVERT: u 406 LYS cc_start: 0.8917 (mptt) cc_final: 0.8609 (ttmt) REVERT: F 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: y 106 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9088 (ttpt) REVERT: y 107 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: z 206 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8865 (ttpt) REVERT: z 207 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: 0 307 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: G 6 LYS cc_start: 0.9267 (tttt) cc_final: 0.8841 (tttm) REVERT: 6 206 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: 6 207 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: H 4 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: H 6 LYS cc_start: 0.9281 (tttt) cc_final: 0.8815 (ttmt) REVERT: EA 302 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8761 (ttmm) REVERT: JA 104 GLU cc_start: 0.4513 (OUTLIER) cc_final: 0.3799 (pm20) REVERT: KA 204 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.3653 (pm20) REVERT: LA 304 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8328 (pm20) REVERT: MA 404 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: J 4 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: QA 104 GLU cc_start: 0.8644 (pm20) cc_final: 0.6694 (tp30) REVERT: RA 204 GLU cc_start: 0.8999 (pm20) cc_final: 0.6923 (mm-30) REVERT: SA 304 GLU cc_start: 0.8947 (pm20) cc_final: 0.8446 (pm20) REVERT: TA 404 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7909 (tm-30) REVERT: a 3 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7653 (t80) REVERT: a 4 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: XA 56 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9074 (tttm) REVERT: YA 103 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8097 (t80) REVERT: YA 104 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: aA 202 LYS cc_start: 0.9152 (tmtt) cc_final: 0.8873 (tptp) REVERT: aA 203 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8501 (t80) REVERT: bA 255 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (t80) REVERT: cA 304 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: dA 355 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7695 (t80) REVERT: eA 403 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7276 (t80) REVERT: eA 404 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8420 (tm-30) REVERT: eA 406 LYS cc_start: 0.9399 (tttp) cc_final: 0.9182 (tttp) REVERT: fA 456 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9171 (tttp) REVERT: b 4 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: mA 55 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.6935 (t80) REVERT: mA 56 LYS cc_start: 0.9327 (tmtt) cc_final: 0.9031 (tttp) REVERT: oA 156 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9089 (tttp) REVERT: qA 252 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8740 (tmtt) REVERT: rA 305 PHE cc_start: 0.8934 (t80) cc_final: 0.8628 (t80) REVERT: sA 355 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7056 (t80) REVERT: sA 356 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8784 (tmtt) REVERT: uA 455 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.6927 (t80) REVERT: uA 456 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9066 (tttp) REVERT: c 5 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8311 (t80) REVERT: 1A 56 LYS cc_start: 0.9421 (tmtt) cc_final: 0.9058 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8389 (t80) REVERT: 3A 156 LYS cc_start: 0.9377 (tmtt) cc_final: 0.9110 (tmtt) REVERT: 5A 256 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8881 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: 7A 355 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7867 (t80) REVERT: 7A 356 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9009 (tttm) REVERT: 9A 456 LYS cc_start: 0.9262 (tttm) cc_final: 0.9021 (tttm) REVERT: d 4 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: HB 105 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8376 (t80) REVERT: JB 205 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8157 (t80) REVERT: KB 256 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8824 (tmtt) REVERT: LB 302 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8891 (ttmm) REVERT: LB 304 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: LB 305 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8266 (t80) REVERT: e 4 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: VB 52 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8390 (pptt) REVERT: XB 152 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8476 (pptt) REVERT: XB 157 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7492 (t80) REVERT: YB 205 PHE cc_start: 0.8986 (t80) cc_final: 0.8668 (t80) REVERT: ZB 252 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8476 (pptt) REVERT: ZB 256 LYS cc_start: 0.9294 (tmtt) cc_final: 0.9076 (tttp) REVERT: bB 352 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8492 (pptt) REVERT: dB 452 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8424 (pptt) outliers start: 136 outliers final: 76 residues processed: 362 average time/residue: 0.3547 time to fit residues: 153.7719 Evaluate side-chains 449 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 324 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 304 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 U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 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 l residue 204 GLU 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 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 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 204 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 a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 52 LYS Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 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 bA residue 255 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 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 452 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 52 LYS Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 252 LYS Chi-restraints excluded: chain KB residue 255 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 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 VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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: 0.8515 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.151 8700 Z= 2.764 Angle : 2.717 20.387 11300 Z= 1.305 Chirality : 0.138 0.339 800 Planarity : 0.011 0.037 1500 Dihedral : 24.950 89.493 1012 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 130.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.25 % Favored : 73.75 % Rotamer: Outliers : 23.17 % Allowed : 32.67 % Favored : 44.17 % Cbeta Deviations : 0.25 % 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: -5.58 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.011 PHEaA 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 462 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 323 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8738 (mp0) cc_final: 0.8364 (mp0) REVERT: A 6 LYS cc_start: 0.9075 (tttt) cc_final: 0.8580 (tttm) REVERT: A 7 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8028 (m-10) REVERT: K 104 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: K 107 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: L 207 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: M 306 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8670 (tttt) REVERT: M 307 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8025 (m-10) REVERT: B 4 GLU cc_start: 0.8789 (mp0) cc_final: 0.8114 (mp0) REVERT: B 6 LYS cc_start: 0.9048 (tttp) cc_final: 0.8807 (ttmt) REVERT: U 404 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: C 6 LYS cc_start: 0.9158 (tttt) cc_final: 0.8785 (tttm) REVERT: Y 106 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8870 (ttmt) REVERT: D 4 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: k 104 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: m 304 GLU cc_start: 0.8703 (mp0) cc_final: 0.8473 (mp0) REVERT: E 6 LYS cc_start: 0.9046 (tttt) cc_final: 0.8742 (tttp) REVERT: r 104 GLU cc_start: 0.8704 (mp0) cc_final: 0.8489 (mp0) REVERT: u 406 LYS cc_start: 0.8933 (mptt) cc_final: 0.8611 (ttmt) REVERT: F 7 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: y 106 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9113 (ttpt) REVERT: y 107 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: z 206 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8859 (ttpt) REVERT: z 207 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: 0 307 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8622 (m-80) REVERT: G 6 LYS cc_start: 0.9270 (tttt) cc_final: 0.8905 (tttm) REVERT: 6 206 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: 6 207 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.7926 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: H 6 LYS cc_start: 0.9281 (tttt) cc_final: 0.8813 (ttmt) REVERT: EA 302 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8753 (ttmm) REVERT: JA 104 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.3855 (pm20) REVERT: KA 204 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.3686 (pm20) REVERT: LA 304 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8318 (pm20) REVERT: MA 404 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: J 4 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: QA 104 GLU cc_start: 0.8618 (pm20) cc_final: 0.6681 (tp30) REVERT: RA 204 GLU cc_start: 0.9007 (pm20) cc_final: 0.6954 (mm-30) REVERT: TA 404 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: a 3 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7651 (t80) REVERT: a 4 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: XA 56 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9089 (tttm) REVERT: YA 103 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8093 (t80) REVERT: YA 104 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: aA 202 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8869 (tptp) REVERT: aA 203 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8493 (t80) REVERT: bA 255 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7765 (t80) REVERT: dA 355 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7661 (t80) REVERT: eA 403 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7167 (t80) REVERT: eA 406 LYS cc_start: 0.9404 (tttp) cc_final: 0.9192 (tttp) REVERT: fA 456 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9158 (tttp) REVERT: b 4 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: mA 55 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6923 (t80) REVERT: mA 56 LYS cc_start: 0.9310 (tttt) cc_final: 0.8980 (tttp) REVERT: oA 156 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9089 (tttp) REVERT: qA 252 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8771 (tmtt) REVERT: qA 256 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8877 (tttp) REVERT: rA 305 PHE cc_start: 0.8924 (t80) cc_final: 0.8652 (t80) REVERT: sA 355 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7102 (t80) REVERT: sA 356 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8715 (tmtt) REVERT: uA 455 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.6890 (t80) REVERT: uA 456 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9074 (tttp) REVERT: c 5 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8323 (t80) REVERT: 1A 56 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9145 (tmtt) REVERT: 3A 156 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9041 (tmtt) REVERT: 5A 256 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8879 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: 7A 355 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7811 (t80) REVERT: 7A 356 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9023 (tttm) REVERT: 9A 456 LYS cc_start: 0.9274 (tttm) cc_final: 0.9032 (tttm) REVERT: d 4 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: HB 105 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8404 (t80) REVERT: JB 205 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8213 (t80) REVERT: KB 256 LYS cc_start: 0.9135 (tmtt) cc_final: 0.8795 (tmtt) REVERT: LB 302 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8890 (ttmm) REVERT: LB 304 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: LB 305 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8275 (t80) REVERT: e 4 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: VB 52 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8394 (pptt) REVERT: XB 152 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8472 (pptt) REVERT: XB 157 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7488 (t80) REVERT: YB 204 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: YB 205 PHE cc_start: 0.8987 (t80) cc_final: 0.8605 (t80) REVERT: ZB 252 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8487 (pptt) REVERT: ZB 256 LYS cc_start: 0.9288 (tmtt) cc_final: 0.9074 (tttp) REVERT: bB 352 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8507 (pptt) REVERT: dB 452 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8414 (pptt) outliers start: 139 outliers final: 81 residues processed: 364 average time/residue: 0.3792 time to fit residues: 166.0394 Evaluate side-chains 454 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 323 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 207 PHE Chi-restraints excluded: chain M residue 304 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 U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 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 l residue 204 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 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 204 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 TA residue 404 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 52 LYS Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 452 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 52 LYS Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 252 LYS Chi-restraints excluded: chain KB residue 255 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 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 VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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: 0.8515 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.151 8700 Z= 2.764 Angle : 2.717 20.396 11300 Z= 1.305 Chirality : 0.138 0.339 800 Planarity : 0.011 0.039 1500 Dihedral : 24.928 89.482 1012 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 131.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.25 % Favored : 73.75 % Rotamer: Outliers : 22.83 % Allowed : 32.83 % Favored : 44.33 % Cbeta Deviations : 0.25 % 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: -5.57 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.011 PHEcA 303 *********************** 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 460 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 323 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8739 (mp0) cc_final: 0.8373 (mp0) REVERT: A 6 LYS cc_start: 0.9076 (tttt) cc_final: 0.8647 (tttm) REVERT: A 7 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8028 (m-10) REVERT: K 104 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: K 107 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: L 207 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8783 (m-80) REVERT: M 306 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8685 (tttt) REVERT: M 307 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: B 4 GLU cc_start: 0.8730 (mp0) cc_final: 0.8068 (mp0) REVERT: U 404 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: C 6 LYS cc_start: 0.9160 (tttt) cc_final: 0.8789 (tttm) REVERT: Y 106 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8883 (ttmt) REVERT: D 4 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: k 104 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: E 6 LYS cc_start: 0.9047 (tttt) cc_final: 0.8745 (tttp) REVERT: r 104 GLU cc_start: 0.8707 (mp0) cc_final: 0.8488 (mp0) REVERT: u 406 LYS cc_start: 0.8928 (mptt) cc_final: 0.8642 (ttmt) REVERT: F 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: y 106 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9100 (ttpt) REVERT: y 107 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8085 (m-10) REVERT: z 206 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: z 207 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: 0 307 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: G 6 LYS cc_start: 0.9270 (tttt) cc_final: 0.8900 (tttm) REVERT: 6 206 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: 6 207 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: H 6 LYS cc_start: 0.9281 (tttt) cc_final: 0.8804 (ttmt) REVERT: EA 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8759 (ttmm) REVERT: JA 104 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.3860 (pm20) REVERT: KA 204 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.3669 (pm20) REVERT: LA 304 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8318 (pm20) REVERT: MA 404 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: J 4 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: QA 104 GLU cc_start: 0.8617 (pm20) cc_final: 0.6697 (tp30) REVERT: RA 204 GLU cc_start: 0.8996 (pm20) cc_final: 0.6953 (mm-30) REVERT: SA 304 GLU cc_start: 0.8918 (pm20) cc_final: 0.8489 (pm20) REVERT: TA 404 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: a 3 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8564 (t80) REVERT: a 4 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: XA 56 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9082 (tttm) REVERT: YA 103 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8095 (t80) REVERT: YA 104 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: aA 202 LYS cc_start: 0.9158 (tmtt) cc_final: 0.8871 (tptp) REVERT: aA 203 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8464 (t80) REVERT: bA 255 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (t80) REVERT: dA 355 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7706 (t80) REVERT: eA 403 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8520 (t80) REVERT: eA 406 LYS cc_start: 0.9395 (tttp) cc_final: 0.9190 (tttp) REVERT: fA 456 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9155 (tttp) REVERT: b 4 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: mA 56 LYS cc_start: 0.9309 (tttt) cc_final: 0.9086 (tttp) REVERT: oA 156 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9090 (tttp) REVERT: qA 252 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8798 (tmtt) REVERT: qA 256 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8870 (tttp) REVERT: rA 305 PHE cc_start: 0.8917 (t80) cc_final: 0.8654 (t80) REVERT: sA 355 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7164 (t80) REVERT: sA 356 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8631 (tttm) REVERT: uA 456 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9142 (tttp) REVERT: c 5 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8335 (t80) REVERT: 1A 56 LYS cc_start: 0.9434 (tmtt) cc_final: 0.9089 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8403 (t80) REVERT: 3A 156 LYS cc_start: 0.9377 (tmtt) cc_final: 0.9033 (tmtt) REVERT: 5A 256 LYS cc_start: 0.9236 (tmtt) cc_final: 0.8893 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: 7A 355 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7824 (t80) REVERT: 7A 356 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9020 (tttm) REVERT: 9A 456 LYS cc_start: 0.9272 (tttm) cc_final: 0.9030 (tttm) REVERT: d 4 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: HB 105 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8358 (t80) REVERT: JB 205 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8253 (t80) REVERT: KB 256 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8829 (tmtt) REVERT: LB 302 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8887 (ttmm) REVERT: LB 304 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: LB 305 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8275 (t80) REVERT: e 4 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: VB 52 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8392 (pptt) REVERT: VB 56 LYS cc_start: 0.9454 (tmtt) cc_final: 0.9151 (tptp) REVERT: XB 152 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8476 (pptt) REVERT: XB 157 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7490 (t80) REVERT: YB 205 PHE cc_start: 0.8990 (t80) cc_final: 0.8680 (t80) REVERT: ZB 252 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8484 (pptt) REVERT: ZB 256 LYS cc_start: 0.9292 (tmtt) cc_final: 0.9084 (tttp) REVERT: bB 352 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8510 (pptt) REVERT: dB 452 LYS cc_start: 0.9089 (tmtt) cc_final: 0.8399 (pptt) outliers start: 137 outliers final: 83 residues processed: 364 average time/residue: 0.3509 time to fit residues: 152.4566 Evaluate side-chains 454 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 323 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 207 PHE Chi-restraints excluded: chain M residue 304 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 U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 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 l residue 204 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 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 204 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 TA residue 404 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 52 LYS Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 452 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 52 LYS Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 252 LYS Chi-restraints excluded: chain KB residue 255 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 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 WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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: 0.8516 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.151 8700 Z= 2.763 Angle : 2.717 20.747 11300 Z= 1.304 Chirality : 0.138 0.339 800 Planarity : 0.011 0.042 1500 Dihedral : 24.922 89.466 1012 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 132.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.75 % Favored : 73.25 % Rotamer: Outliers : 22.83 % Allowed : 32.67 % Favored : 44.50 % 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: -5.57 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.011 PHEcA 303 ********************** 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 460 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 323 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8740 (mp0) cc_final: 0.8373 (mp0) REVERT: A 6 LYS cc_start: 0.9078 (tttt) cc_final: 0.8649 (tttm) REVERT: A 7 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8028 (m-10) REVERT: K 104 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: K 107 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: L 207 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: M 306 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8679 (tttt) REVERT: M 307 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: B 4 GLU cc_start: 0.8724 (mp0) cc_final: 0.8073 (mp0) REVERT: U 404 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: C 6 LYS cc_start: 0.9158 (tttt) cc_final: 0.8782 (tttm) REVERT: Y 106 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8882 (ttmt) REVERT: D 4 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: k 104 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: E 6 LYS cc_start: 0.9045 (tttt) cc_final: 0.8743 (tttp) REVERT: r 104 GLU cc_start: 0.8718 (mp0) cc_final: 0.8503 (mp0) REVERT: u 406 LYS cc_start: 0.8925 (mptt) cc_final: 0.8629 (ttmt) REVERT: F 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8182 (m-10) REVERT: y 106 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9100 (ttpt) REVERT: y 107 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8092 (m-10) REVERT: z 206 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8862 (ttpt) REVERT: z 207 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: 0 307 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: G 6 LYS cc_start: 0.9271 (tttt) cc_final: 0.8900 (tttm) REVERT: 6 206 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8831 (ttpt) REVERT: 6 207 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: H 4 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: H 6 LYS cc_start: 0.9280 (tttt) cc_final: 0.8804 (ttmt) REVERT: EA 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: JA 104 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.3861 (pm20) REVERT: KA 204 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.3676 (pm20) REVERT: LA 304 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8319 (pm20) REVERT: MA 404 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: J 4 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: QA 104 GLU cc_start: 0.8615 (pm20) cc_final: 0.6698 (tp30) REVERT: RA 204 GLU cc_start: 0.8995 (pm20) cc_final: 0.6952 (mm-30) REVERT: SA 304 GLU cc_start: 0.8920 (pm20) cc_final: 0.8476 (pm20) REVERT: TA 404 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: a 3 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8565 (t80) REVERT: a 4 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: XA 56 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9080 (tttm) REVERT: YA 103 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.7986 (t80) REVERT: YA 104 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: aA 202 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8871 (tptp) REVERT: aA 203 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8456 (t80) REVERT: bA 255 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7805 (t80) REVERT: cA 303 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7947 (t80) REVERT: dA 355 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7657 (t80) REVERT: eA 403 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8424 (t80) REVERT: eA 406 LYS cc_start: 0.9397 (tttp) cc_final: 0.9191 (tttp) REVERT: fA 456 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9152 (tttp) REVERT: b 4 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: mA 56 LYS cc_start: 0.9310 (tttt) cc_final: 0.9084 (tttp) REVERT: oA 156 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9092 (tttp) REVERT: qA 252 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8798 (tmtt) REVERT: qA 256 LYS cc_start: 0.9157 (tmtt) cc_final: 0.8865 (tttp) REVERT: rA 305 PHE cc_start: 0.8920 (t80) cc_final: 0.8648 (t80) REVERT: sA 355 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7209 (t80) REVERT: sA 356 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8594 (tttm) REVERT: uA 456 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9139 (tttp) REVERT: c 5 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8319 (t80) REVERT: 1A 56 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9084 (tmtt) REVERT: 2A 105 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8400 (t80) REVERT: 3A 156 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9016 (tmtt) REVERT: 5A 256 LYS cc_start: 0.9235 (tmtt) cc_final: 0.8890 (tmtt) REVERT: 6A 304 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: 7A 355 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7823 (t80) REVERT: 7A 356 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9034 (tttm) REVERT: 9A 456 LYS cc_start: 0.9270 (tttm) cc_final: 0.9024 (tttm) REVERT: d 4 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: HB 105 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8351 (t80) REVERT: JB 205 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8184 (t80) REVERT: KB 256 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8829 (tmtt) REVERT: LB 302 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8890 (ttmm) REVERT: LB 304 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: LB 305 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8277 (t80) REVERT: e 4 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: VB 52 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8384 (pptt) REVERT: XB 152 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8473 (pptt) REVERT: XB 157 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7490 (t80) REVERT: YB 205 PHE cc_start: 0.8988 (t80) cc_final: 0.8679 (t80) REVERT: ZB 252 LYS cc_start: 0.9158 (tmtt) cc_final: 0.8489 (pptt) REVERT: ZB 256 LYS cc_start: 0.9278 (tmtt) cc_final: 0.9062 (tttp) REVERT: bB 352 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8488 (pptt) REVERT: dB 452 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8369 (pptt) outliers start: 137 outliers final: 83 residues processed: 364 average time/residue: 0.3554 time to fit residues: 154.5725 Evaluate side-chains 455 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 323 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 207 PHE Chi-restraints excluded: chain M residue 304 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 U residue 404 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain f residue 306 LYS 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 l residue 204 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 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 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 204 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 TA residue 404 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 52 LYS Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 306 LYS Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 452 LYS Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE 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 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE 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 52 LYS Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 152 LYS 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 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 52 LYS Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 252 LYS Chi-restraints excluded: chain KB residue 255 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 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 WB residue 105 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 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE 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 = 0.3392 r_free = 0.3392 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071077 restraints weight = 23460.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.072863 restraints weight = 9153.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.074023 restraints weight = 4733.818| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.150 8700 Z= 2.763 Angle : 2.717 20.562 11300 Z= 1.304 Chirality : 0.138 0.340 800 Planarity : 0.011 0.044 1500 Dihedral : 24.913 89.619 1012 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 131.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.75 % Favored : 73.25 % Rotamer: Outliers : 23.17 % Allowed : 32.67 % Favored : 44.17 % 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: -5.57 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.102 0.011 PHEcA 303 =============================================================================== Job complete usr+sys time: 2240.20 seconds wall clock time: 40 minutes 53.74 seconds (2453.74 seconds total)