Starting phenix.real_space_refine on Sun Jul 5 15:34:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vrj_32100/07_2026/7vrj_32100.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 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: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 5 7.16 5 P 28 5.49 5 Mg 37 5.21 5 S 102 5.16 5 C 18284 2.51 5 N 3570 2.21 5 O 4277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26309 Number of models: 1 Model: "" Number of chains: 77 Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2450 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 285} Chain: "L" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2212 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2539 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1987 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Conformer: "B" Number of residues, atoms: 259, 1987 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} bond proxies already assigned to first conformer: 2037 Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 401 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "S" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 419 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 416 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 455 Classifications: {'peptide': 56} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Y" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 342 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "4" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "C" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 233 Unusual residues: {' MG': 1, 'DGA': 1, 'HEC': 4, 'PGV': 1, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 584 Unusual residues: {'BCL': 3, 'BPH': 1, 'CDL': 1, 'PGV': 4, 'UQ8': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 4, 'UQ8:plan-6': 2, 'UQ8:plan-7': 2, 'UQ8:plan-8': 2, 'UQ8:plan-9': 2} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 520 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'MQ8': 2, 'PGV': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 3, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'CDL': 2, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 160 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'BCL': 1, 'LDA': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.23 Number of scatterers: 26309 At special positions: 0 Unit cell: (140.822, 136.752, 140.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 6 19.99 S 102 16.00 P 28 15.00 Mg 37 11.99 O 4277 8.00 N 3570 7.00 C 18284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4826 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 9 sheets defined 65.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.639A pdb=" N GLN C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.516A pdb=" N ASP C 74 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 121 through 141 removed outlier: 3.926A pdb=" N VAL C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.551A pdb=" N VAL C 192 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.773A pdb=" N PHE C 205 " --> pdb=" O PRO C 201 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 246 removed outlier: 4.110A pdb=" N ALA C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 265 through 286 removed outlier: 4.305A pdb=" N THR C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.309A pdb=" N ASP C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 removed outlier: 3.559A pdb=" N LYS C 298 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.850A pdb=" N TYR C 333 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.727A pdb=" N ARG L 10 " --> pdb=" O ARG L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 56 Processing helix chain 'L' and resid 75 through 79 removed outlier: 3.600A pdb=" N GLY L 79 " --> pdb=" O LEU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 87 Processing helix chain 'L' and resid 88 through 117 removed outlier: 3.708A pdb=" N GLN L 92 " --> pdb=" O GLY L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 138 removed outlier: 3.839A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA L 129 " --> pdb=" O ALA L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 145 Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 156 through 168 removed outlier: 3.573A pdb=" N ASP L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 170 No H-bonds generated for 'chain 'L' and resid 169 through 170' Processing helix chain 'L' and resid 171 through 174 removed outlier: 3.631A pdb=" N TYR L 174 " --> pdb=" O HIS L 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 171 through 174' Processing helix chain 'L' and resid 175 through 204 Processing helix chain 'L' and resid 213 through 225 removed outlier: 3.959A pdb=" N GLU L 217 " --> pdb=" O THR L 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE L 221 " --> pdb=" O GLU L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 255 removed outlier: 4.059A pdb=" N HIS L 235 " --> pdb=" O ALA L 231 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL L 246 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 268 through 273 Processing helix chain 'M' and resid 38 through 42 removed outlier: 3.640A pdb=" N ILE M 42 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 77 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.800A pdb=" N GLY M 102 " --> pdb=" O PRO M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 110 Processing helix chain 'M' and resid 111 through 139 removed outlier: 3.826A pdb=" N LEU M 139 " --> pdb=" O ARG M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 161 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 169 through 173 removed outlier: 3.891A pdb=" N GLU M 172 " --> pdb=" O SER M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 192 removed outlier: 3.615A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 198 through 225 Processing helix chain 'M' and resid 226 through 229 Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'M' and resid 241 through 256 removed outlier: 3.612A pdb=" N TRP M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.527A pdb=" N ALA M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR M 275 " --> pdb=" O CYS M 271 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA M 279 " --> pdb=" O THR M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 300 Processing helix chain 'H' and resid 10 through 35 removed outlier: 3.508A pdb=" N LEU H 14 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 49 removed outlier: 3.671A pdb=" N GLU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.538A pdb=" N SER H 109 " --> pdb=" O PRO H 106 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY H 110 " --> pdb=" O MET H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.664A pdb=" N ALA H 114 " --> pdb=" O PHE H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 215 through 221 removed outlier: 3.601A pdb=" N PHE H 219 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 removed outlier: 3.803A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.776A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'B' and resid 11 through 44 removed outlier: 3.893A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 4.285A pdb=" N TRP D 6 " --> pdb=" O PRO D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 38 removed outlier: 3.637A pdb=" N VAL D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 42 removed outlier: 3.842A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN E 24 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.733A pdb=" N LYS F 7 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 11 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 39 removed outlier: 3.874A pdb=" N VAL F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 39 " --> pdb=" O ILE F 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 44 removed outlier: 3.730A pdb=" N GLU G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 34 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 11 Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 13 through 44 removed outlier: 4.089A pdb=" N GLU J 17 " --> pdb=" O GLN J 13 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE J 18 " --> pdb=" O GLU J 14 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS J 19 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN J 24 " --> pdb=" O GLY J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 11 removed outlier: 3.563A pdb=" N TRP K 9 " --> pdb=" O HIS K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 39 Processing helix chain 'N' and resid 11 through 44 removed outlier: 3.691A pdb=" N HIS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL N 23 " --> pdb=" O HIS N 19 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN N 24 " --> pdb=" O GLY N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 13 through 39 Processing helix chain 'P' and resid 11 through 44 removed outlier: 3.673A pdb=" N GLU P 17 " --> pdb=" O GLN P 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 11 Processing helix chain 'Q' and resid 13 through 39 Processing helix chain 'R' and resid 12 through 44 removed outlier: 4.227A pdb=" N PHE R 18 " --> pdb=" O GLU R 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 11 removed outlier: 3.509A pdb=" N LYS S 7 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 38 removed outlier: 3.844A pdb=" N ILE S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA S 20 " --> pdb=" O ARG S 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 44 removed outlier: 3.624A pdb=" N GLY T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 11 removed outlier: 3.559A pdb=" N LEU U 5 " --> pdb=" O SER U 2 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP U 6 " --> pdb=" O PRO U 3 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 Processing helix chain 'V' and resid 11 through 44 removed outlier: 3.677A pdb=" N PHE V 18 " --> pdb=" O GLU V 14 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.705A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 38 removed outlier: 3.715A pdb=" N ILE W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE W 24 " --> pdb=" O ALA W 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 42 removed outlier: 4.010A pdb=" N GLU X 17 " --> pdb=" O ASP X 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 11 removed outlier: 4.362A pdb=" N TRP Y 6 " --> pdb=" O PRO Y 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Y 7 " --> pdb=" O ASP Y 4 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 39 removed outlier: 3.619A pdb=" N VAL Y 17 " --> pdb=" O ASP Y 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Y 20 " --> pdb=" O ARG Y 16 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR Y 26 " --> pdb=" O PHE Y 22 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR Y 39 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.870A pdb=" N LYS Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU Z 17 " --> pdb=" O ASP Z 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN Z 24 " --> pdb=" O GLY Z 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE Z 35 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 12 removed outlier: 3.966A pdb=" N ILE 1 11 " --> pdb=" O LYS 1 7 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 38 removed outlier: 3.625A pdb=" N THR 1 17 " --> pdb=" O ASP 1 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL 1 19 " --> pdb=" O ARG 1 15 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 44 removed outlier: 4.016A pdb=" N PHE 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 11 removed outlier: 3.638A pdb=" N ALA 3 11 " --> pdb=" O ILE 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 39 removed outlier: 3.747A pdb=" N ILE 3 19 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 47 Processing helix chain '4' and resid 11 through 44 removed outlier: 3.875A pdb=" N GLN 4 16 " --> pdb=" O GLU 4 12 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY 4 20 " --> pdb=" O GLN 4 16 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE 4 21 " --> pdb=" O GLU 4 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR 4 27 " --> pdb=" O VAL 4 23 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 11 removed outlier: 4.152A pdb=" N TRP 5 9 " --> pdb=" O HIS 5 6 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 38 removed outlier: 3.591A pdb=" N GLY 5 23 " --> pdb=" O VAL 5 19 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 15 removed outlier: 3.952A pdb=" N ALA 6 15 " --> pdb=" O GLU 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 16 through 44 removed outlier: 3.637A pdb=" N ILE 6 21 " --> pdb=" O GLU 6 17 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN 6 24 " --> pdb=" O GLY 6 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 6 32 " --> pdb=" O ALA 6 28 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 38 removed outlier: 4.042A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 7 20 " --> pdb=" O ARG 7 16 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 16 removed outlier: 3.833A pdb=" N GLN 8 16 " --> pdb=" O GLU 8 12 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 12 through 16' Processing helix chain '8' and resid 18 through 44 removed outlier: 3.983A pdb=" N GLN 8 24 " --> pdb=" O GLY 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 11 Processing helix chain '9' and resid 13 through 38 removed outlier: 3.850A pdb=" N VAL 9 19 " --> pdb=" O ARG 9 15 " (cutoff:3.500A) Processing helix chain '0' and resid 11 through 44 removed outlier: 3.627A pdb=" N ILE 0 21 " --> pdb=" O GLU 0 17 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE 0 32 " --> pdb=" O ALA 0 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 0 33 " --> pdb=" O PHE 0 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 69 removed outlier: 4.315A pdb=" N GLY H 74 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 133 through 135 removed outlier: 3.840A pdb=" N THR H 166 " --> pdb=" O ASP H 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR H 181 " --> pdb=" O ILE H 170 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL H 172 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS H 191 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.675A pdb=" N VAL H 156 " --> pdb=" O ALA H 164 " (cutoff:3.500A) 1227 hydrogen bonds defined for protein. 3429 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: 4.71 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9228 1.38 - 1.56: 17639 1.56 - 1.74: 56 1.74 - 1.93: 192 1.93 - 2.11: 156 Bond restraints: 27271 Sorted by residual: bond pdb=" CB7 CDL S 101 " pdb=" OB8 CDL S 101 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" CA7 CDL M 408 " pdb=" OA8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" CA7 CDL H 301 " pdb=" OA8 CDL H 301 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CB7 CDL I 101 " pdb=" OB8 CDL I 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 410 " pdb=" OA8 CDL M 410 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 27266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.08: 36051 5.08 - 10.17: 1299 10.17 - 15.25: 84 15.25 - 20.33: 19 20.33 - 25.42: 7 Bond angle restraints: 37460 Sorted by residual: angle pdb=" C39 CRT S 104 " pdb=" C38 CRT S 104 " pdb=" O2 CRT S 104 " ideal model delta sigma weight residual 111.76 86.34 25.42 3.00e+00 1.11e-01 7.18e+01 angle pdb=" C39 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.76 87.71 24.05 3.00e+00 1.11e-01 6.43e+01 angle pdb=" C1D BCL M 402 " pdb=" C2D BCL M 402 " pdb=" CMD BCL M 402 " ideal model delta sigma weight residual 125.57 139.92 -14.34 1.83e+00 2.99e-01 6.16e+01 angle pdb=" C40 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.40 87.87 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C3 CRT P 102 " pdb=" C1 CRT P 102 " pdb=" C4 CRT P 102 " ideal model delta sigma weight residual 108.82 85.50 23.32 3.00e+00 1.11e-01 6.04e+01 ... (remaining 37455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 13647 35.99 - 71.97: 529 71.97 - 107.96: 49 107.96 - 143.94: 7 143.94 - 179.93: 8 Dihedral angle restraints: 14240 sinusoidal: 6793 harmonic: 7447 Sorted by residual: dihedral pdb=" C1 BCL 0 102 " pdb=" CGA BCL 0 102 " pdb=" O2A BCL 0 102 " pdb=" CBA BCL 0 102 " ideal model delta sinusoidal sigma weight residual -180.00 -78.88 -101.12 1 6.00e+00 2.78e-02 3.18e+02 dihedral pdb=" C1 BCL Q 101 " pdb=" C2 BCL Q 101 " pdb=" C3 BCL Q 101 " pdb=" C5 BCL Q 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL F 101 " pdb=" C2 BCL F 101 " pdb=" C3 BCL F 101 " pdb=" C5 BCL F 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.13 -179.87 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 14237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2951 0.057 - 0.114: 608 0.114 - 0.172: 143 0.172 - 0.229: 55 0.229 - 0.286: 12 Chirality restraints: 3769 Sorted by residual: chirality pdb=" C05 PGV 5 101 " pdb=" C04 PGV 5 101 " pdb=" C06 PGV 5 101 " pdb=" O05 PGV 5 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C05 PGV C 508 " pdb=" C04 PGV C 508 " pdb=" C06 PGV C 508 " pdb=" O05 PGV C 508 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C05 PGV M 411 " pdb=" C04 PGV M 411 " pdb=" C06 PGV M 411 " pdb=" O05 PGV M 411 " both_signs ideal model delta sigma weight residual False 2.29 2.56 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3766 not shown) Planarity restraints: 4433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 103 " 0.386 3.00e-02 1.11e+03 3.15e-01 5.52e+02 pdb=" CBA BCL K 103 " 0.161 3.00e-02 1.11e+03 pdb=" CGA BCL K 103 " -0.087 3.00e-02 1.11e+03 pdb=" O1A BCL K 103 " 0.094 3.00e-02 1.11e+03 pdb=" O2A BCL K 103 " -0.553 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 102 " -0.369 3.00e-02 1.11e+03 3.08e-01 5.29e+02 pdb=" CBA BCL T 102 " -0.095 3.00e-02 1.11e+03 pdb=" CGA BCL T 102 " 0.075 3.00e-02 1.11e+03 pdb=" O1A BCL T 102 " -0.159 3.00e-02 1.11e+03 pdb=" O2A BCL T 102 " 0.548 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 509 " -0.371 3.00e-02 1.11e+03 3.07e-01 5.23e+02 pdb=" CBA BCL L 509 " -0.132 3.00e-02 1.11e+03 pdb=" CGA BCL L 509 " 0.079 3.00e-02 1.11e+03 pdb=" O1A BCL L 509 " -0.120 3.00e-02 1.11e+03 pdb=" O2A BCL L 509 " 0.544 3.00e-02 1.11e+03 ... (remaining 4430 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 259 2.63 - 3.20: 21005 3.20 - 3.77: 39342 3.77 - 4.33: 57576 4.33 - 4.90: 93053 Nonbonded interactions: 211235 Sorted by model distance: nonbonded pdb="MG MG C 505 " pdb=" O HOH C 606 " model vdw 2.064 2.170 nonbonded pdb="MG MG C 505 " pdb=" O HOH M 507 " model vdw 2.065 2.170 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.068 2.260 nonbonded pdb="MG MG C 505 " pdb=" O HOH C 602 " model vdw 2.071 2.170 nonbonded pdb=" O ILE W 49 " pdb="CA CA W 102 " model vdw 2.129 2.510 ... (remaining 211230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '2' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '4' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '6' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '8' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'B' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'E' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'G' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'J' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'N' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'P' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'R' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'T' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'V' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'X' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'Z' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) } ncs_group { reference = (chain '1' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain '5' and resid 5 through 47) selection = (chain '7' and resid 5 through 47) selection = (chain '9' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'I' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'K' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'O' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'Q' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) } ncs_group { reference = (chain 'D' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'F' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'S' and resid 2 through 50) selection = (chain 'U' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'W' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 25.540 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.021 0.488 27319 Z= 1.269 Angle : 1.881 25.416 37460 Z= 0.826 Chirality : 0.056 0.286 3769 Planarity : 0.020 0.315 4433 Dihedral : 18.014 179.926 9414 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.43 % Allowed : 4.80 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2517 helix: 2.09 (0.14), residues: 1470 sheet: 0.29 (0.74), residues: 52 loop : -0.80 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 44 TYR 0.013 0.002 TYR H 234 PHE 0.018 0.002 PHE 1 26 TRP 0.013 0.001 TRP U 9 HIS 0.008 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.01920 / 0.88 (27271) covalent geometry : angle 1.88142 / 0.83 (37460) hydrogen bonds : bond 0.16065 / 10.85 ( 1225) hydrogen bonds : angle 4.74246 / 3.39 ( 3429) Misc. bond : bond 0.22432 / 15.29 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 0.818 Fit side-chains REVERT: M 58 LEU cc_start: 0.8062 (mm) cc_final: 0.7839 (mp) REVERT: M 141 MET cc_start: 0.8111 (mtp) cc_final: 0.7772 (mtm) REVERT: M 215 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.7945 (t80) REVERT: H 124 ASP cc_start: 0.7354 (t0) cc_final: 0.6996 (t70) REVERT: H 190 LYS cc_start: 0.7162 (mppt) cc_final: 0.6902 (mmtm) REVERT: F 16 ARG cc_start: 0.6877 (mtt-85) cc_final: 0.6669 (mtt-85) REVERT: I 7 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7508 (ttmt) REVERT: P 13 GLN cc_start: 0.6962 (tp-100) cc_final: 0.6665 (pp30) REVERT: P 14 GLU cc_start: 0.6644 (tt0) cc_final: 0.6248 (mt-10) REVERT: U 27 ILE cc_start: 0.8385 (mt) cc_final: 0.8153 (mp) REVERT: W 40 THR cc_start: 0.8618 (t) cc_final: 0.8392 (m) REVERT: X 26 MET cc_start: 0.7286 (ttp) cc_final: 0.7071 (ttm) REVERT: Z 26 MET cc_start: 0.6769 (mtp) cc_final: 0.6496 (mtp) REVERT: Z 28 MET cc_start: 0.6018 (tpp) cc_final: 0.5804 (tmt) REVERT: 2 8 THR cc_start: 0.5524 (p) cc_final: 0.5055 (m) REVERT: 3 6 TYR cc_start: 0.6744 (p90) cc_final: 0.6413 (p90) REVERT: 7 22 PHE cc_start: 0.7300 (m-10) cc_final: 0.6687 (m-80) outliers start: 31 outliers final: 19 residues processed: 399 average time/residue: 0.5403 time to fit residues: 254.8018 Evaluate side-chains 327 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 8 residue 21 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN C 78 ASN C 186 ASN L 206 GLN L 216 HIS M 4 GLN M 258 ASN B 16 GLN G 24 GLN J 16 GLN J 24 GLN K 10 GLN P 13 GLN P 16 GLN Z 24 GLN 2 13 GLN ** 2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 5 43 ASN 7 6 HIS 7 10 GLN 8 16 GLN 0 16 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103931 restraints weight = 34227.007| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.59 r_work: 0.2902 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.219 27319 Z= 0.226 Angle : 0.876 24.361 37460 Z= 0.343 Chirality : 0.046 0.176 3769 Planarity : 0.005 0.062 4433 Dihedral : 19.480 179.630 4838 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 3.92 % Allowed : 9.28 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2517 helix: 2.05 (0.13), residues: 1477 sheet: -0.33 (0.89), residues: 32 loop : -0.76 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 64 TYR 0.017 0.002 TYR M 192 PHE 0.037 0.002 PHE 1 26 TRP 0.016 0.002 TRP U 9 HIS 0.010 0.002 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (27271) covalent geometry : angle 0.87611 / 0.34 (37460) hydrogen bonds : bond 0.08283 / 5.52 ( 1225) hydrogen bonds : angle 3.95211 / 2.76 ( 3429) Misc. bond : bond 0.03457 / 1.67 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 314 time to evaluate : 0.621 Fit side-chains REVERT: L 206 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7246 (mp-120) REVERT: M 215 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8001 (t80) REVERT: M 262 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: H 136 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: H 190 LYS cc_start: 0.7239 (mppt) cc_final: 0.6841 (mmpt) REVERT: B 17 GLU cc_start: 0.7408 (tp30) cc_final: 0.7139 (tp30) REVERT: K 31 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8388 (tp) REVERT: N 26 MET cc_start: 0.7321 (ttp) cc_final: 0.7074 (ttm) REVERT: P 7 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.4610 (mpt) REVERT: P 13 GLN cc_start: 0.7407 (tp40) cc_final: 0.6666 (pp30) REVERT: P 14 GLU cc_start: 0.6895 (tt0) cc_final: 0.6293 (mt-10) REVERT: S 16 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6566 (mtt180) REVERT: T 17 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6877 (tp30) REVERT: U 19 ILE cc_start: 0.8002 (pt) cc_final: 0.7702 (mp) REVERT: V 17 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7160 (tm-30) REVERT: W 4 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7268 (t0) REVERT: W 7 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: X 26 MET cc_start: 0.7766 (ttp) cc_final: 0.7503 (ttm) REVERT: X 28 MET cc_start: 0.6967 (tmt) cc_final: 0.6709 (pp-130) REVERT: Y 49 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8170 (mm) REVERT: Z 26 MET cc_start: 0.7541 (mtp) cc_final: 0.7218 (mtp) REVERT: Z 28 MET cc_start: 0.7134 (tpp) cc_final: 0.6452 (tmt) REVERT: 2 8 THR cc_start: 0.5232 (p) cc_final: 0.4901 (m) REVERT: 5 21 LEU cc_start: 0.8418 (tp) cc_final: 0.8179 (tp) REVERT: 7 10 GLN cc_start: 0.2258 (OUTLIER) cc_final: 0.1123 (mm-40) REVERT: 7 22 PHE cc_start: 0.7398 (m-10) cc_final: 0.6855 (m-80) REVERT: 8 19 HIS cc_start: 0.6432 (OUTLIER) cc_final: 0.6002 (t-90) outliers start: 85 outliers final: 51 residues processed: 360 average time/residue: 0.5328 time to fit residues: 227.3876 Evaluate side-chains 367 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 9 residue 8 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 130 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 ASN B 16 GLN J 24 GLN K 10 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 7 6 HIS 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105719 restraints weight = 34229.620| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.47 r_work: 0.2986 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 27319 Z= 0.122 Angle : 0.674 17.894 37460 Z= 0.262 Chirality : 0.038 0.159 3769 Planarity : 0.004 0.056 4433 Dihedral : 18.059 180.000 4833 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 11.49 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2517 helix: 2.39 (0.13), residues: 1497 sheet: -0.26 (0.80), residues: 42 loop : -0.75 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 16 TYR 0.015 0.001 TYR M 192 PHE 0.024 0.001 PHE 1 26 TRP 0.011 0.001 TRP U 9 HIS 0.008 0.001 HIS L 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27271) covalent geometry : angle 0.67380 / 0.26 (37460) hydrogen bonds : bond 0.05805 / 3.86 ( 1225) hydrogen bonds : angle 3.55609 / 2.48 ( 3429) Misc. bond : bond 0.01959 / 0.92 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 0.933 Fit side-chains REVERT: M 58 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7912 (mp) REVERT: M 215 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.7658 (t80) REVERT: M 262 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: H 136 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8266 (mtm) REVERT: H 190 LYS cc_start: 0.7262 (mppt) cc_final: 0.6888 (mmpt) REVERT: A 21 LEU cc_start: 0.8452 (tt) cc_final: 0.8244 (tm) REVERT: N 26 MET cc_start: 0.7206 (ttp) cc_final: 0.6952 (ttm) REVERT: P 13 GLN cc_start: 0.7388 (tp40) cc_final: 0.6654 (pp30) REVERT: P 14 GLU cc_start: 0.6895 (tt0) cc_final: 0.6219 (mt-10) REVERT: S 13 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5674 (t0) REVERT: V 17 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7002 (tm-30) REVERT: W 4 ASP cc_start: 0.7450 (t70) cc_final: 0.7212 (t0) REVERT: W 7 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8264 (tptt) REVERT: X 26 MET cc_start: 0.7738 (ttp) cc_final: 0.7472 (ttm) REVERT: X 28 MET cc_start: 0.6843 (tmt) cc_final: 0.6588 (pp-130) REVERT: Z 26 MET cc_start: 0.7471 (mtp) cc_final: 0.7106 (mtp) REVERT: Z 28 MET cc_start: 0.7056 (tpp) cc_final: 0.6395 (tmt) REVERT: 2 8 THR cc_start: 0.5275 (p) cc_final: 0.4865 (m) REVERT: 7 8 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6753 (tt) REVERT: 7 10 GLN cc_start: 0.2366 (OUTLIER) cc_final: 0.1827 (mm110) REVERT: 7 22 PHE cc_start: 0.7239 (m-10) cc_final: 0.6687 (m-80) outliers start: 65 outliers final: 33 residues processed: 355 average time/residue: 0.5274 time to fit residues: 223.8000 Evaluate side-chains 337 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 296 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS L 206 GLN H 88 ASN H 103 ASN H 122 HIS K 10 GLN Z 24 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101626 restraints weight = 33959.771| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.47 r_work: 0.2921 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 27319 Z= 0.203 Angle : 0.827 24.712 37460 Z= 0.322 Chirality : 0.044 0.174 3769 Planarity : 0.005 0.053 4433 Dihedral : 18.606 179.952 4828 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 4.48 % Allowed : 11.44 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2517 helix: 2.18 (0.13), residues: 1480 sheet: -0.28 (0.89), residues: 32 loop : -0.78 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 64 TYR 0.018 0.002 TYR M 192 PHE 0.037 0.002 PHE 1 26 TRP 0.013 0.002 TRP C 168 HIS 0.010 0.002 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (27271) covalent geometry : angle 0.82700 / 0.32 (37460) hydrogen bonds : bond 0.07811 / 5.19 ( 1225) hydrogen bonds : angle 3.79292 / 2.64 ( 3429) Misc. bond : bond 0.03244 / 1.56 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 308 time to evaluate : 0.920 Fit side-chains REVERT: L 206 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7096 (mp-120) REVERT: M 215 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.7992 (t80) REVERT: M 262 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: H 136 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: H 190 LYS cc_start: 0.7261 (mppt) cc_final: 0.6893 (mmpt) REVERT: B 17 GLU cc_start: 0.7505 (tp30) cc_final: 0.7195 (tp30) REVERT: K 31 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (tp) REVERT: P 7 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.4762 (mpt) REVERT: P 13 GLN cc_start: 0.7371 (tp40) cc_final: 0.6670 (pp30) REVERT: P 14 GLU cc_start: 0.7002 (tt0) cc_final: 0.6305 (mt-10) REVERT: S 13 ASP cc_start: 0.5865 (OUTLIER) cc_final: 0.5336 (t0) REVERT: S 16 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6677 (mtt180) REVERT: T 13 ASP cc_start: 0.6849 (m-30) cc_final: 0.6640 (m-30) REVERT: W 7 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8210 (tptt) REVERT: X 26 MET cc_start: 0.7785 (ttp) cc_final: 0.7533 (ttm) REVERT: Z 26 MET cc_start: 0.7529 (mtp) cc_final: 0.7187 (mtp) REVERT: Z 28 MET cc_start: 0.7118 (tpp) cc_final: 0.6446 (tmt) REVERT: 2 8 THR cc_start: 0.5320 (p) cc_final: 0.4915 (m) REVERT: 2 13 GLN cc_start: 0.6399 (mm110) cc_final: 0.4975 (tp40) REVERT: 7 8 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6343 (tt) REVERT: 7 10 GLN cc_start: 0.2225 (OUTLIER) cc_final: 0.0924 (mm110) REVERT: 7 22 PHE cc_start: 0.7359 (m-10) cc_final: 0.6801 (m-80) REVERT: 8 19 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.6022 (t-90) outliers start: 97 outliers final: 55 residues processed: 364 average time/residue: 0.5211 time to fit residues: 225.7235 Evaluate side-chains 365 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 0 residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 139 optimal weight: 0.0060 chunk 117 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS H 103 ASN H 122 HIS J 24 GLN K 10 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104896 restraints weight = 33917.176| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.26 r_work: 0.2976 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 27319 Z= 0.157 Angle : 0.745 22.766 37460 Z= 0.288 Chirality : 0.041 0.153 3769 Planarity : 0.004 0.055 4433 Dihedral : 18.198 179.878 4825 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 4.43 % Allowed : 12.32 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.17), residues: 2517 helix: 2.33 (0.13), residues: 1480 sheet: -0.24 (0.89), residues: 32 loop : -0.74 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 12 TYR 0.017 0.002 TYR M 192 PHE 0.033 0.002 PHE 1 26 TRP 0.012 0.001 TRP C 168 HIS 0.010 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (27271) covalent geometry : angle 0.74545 / 0.29 (37460) hydrogen bonds : bond 0.06793 / 4.52 ( 1225) hydrogen bonds : angle 3.63621 / 2.53 ( 3429) Misc. bond : bond 0.02663 / 1.30 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 308 time to evaluate : 0.685 Fit side-chains REVERT: M 58 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (mp) REVERT: M 215 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.7803 (t80) REVERT: M 262 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: H 190 LYS cc_start: 0.7289 (mppt) cc_final: 0.6925 (mmpt) REVERT: F 41 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: K 31 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8365 (tp) REVERT: P 7 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.4697 (mpt) REVERT: P 13 GLN cc_start: 0.7342 (tp40) cc_final: 0.6654 (pp30) REVERT: P 14 GLU cc_start: 0.7005 (tt0) cc_final: 0.6261 (mt-10) REVERT: S 13 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.5361 (t0) REVERT: S 16 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6712 (mtt180) REVERT: T 13 ASP cc_start: 0.6834 (m-30) cc_final: 0.6570 (m-30) REVERT: V 17 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6991 (tm-30) REVERT: X 26 MET cc_start: 0.7724 (ttp) cc_final: 0.7475 (ttm) REVERT: X 28 MET cc_start: 0.6794 (tmt) cc_final: 0.6517 (pp-130) REVERT: Z 26 MET cc_start: 0.7475 (mtp) cc_final: 0.7109 (mtp) REVERT: Z 28 MET cc_start: 0.7004 (tpp) cc_final: 0.6341 (tmt) REVERT: 2 8 THR cc_start: 0.5306 (p) cc_final: 0.4925 (m) REVERT: 2 13 GLN cc_start: 0.6420 (mm110) cc_final: 0.4854 (tp40) REVERT: 7 8 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6368 (tt) REVERT: 7 10 GLN cc_start: 0.2408 (OUTLIER) cc_final: 0.1406 (mm110) REVERT: 7 22 PHE cc_start: 0.7289 (m-10) cc_final: 0.6720 (m-80) REVERT: 8 19 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.6111 (t-90) outliers start: 96 outliers final: 60 residues processed: 363 average time/residue: 0.5137 time to fit residues: 222.9677 Evaluate side-chains 372 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 0 residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 25 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS L 206 GLN H 103 ASN H 122 HIS J 24 GLN K 10 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103966 restraints weight = 33983.964| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.47 r_work: 0.2947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 27319 Z= 0.142 Angle : 0.715 21.537 37460 Z= 0.276 Chirality : 0.040 0.145 3769 Planarity : 0.004 0.055 4433 Dihedral : 17.891 179.904 4825 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.34 % Allowed : 12.46 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.17), residues: 2517 helix: 2.36 (0.13), residues: 1496 sheet: -0.22 (0.88), residues: 32 loop : -0.81 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 16 TYR 0.016 0.002 TYR M 192 PHE 0.030 0.002 PHE 1 26 TRP 0.011 0.001 TRP U 9 HIS 0.010 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (27271) covalent geometry : angle 0.71532 / 0.28 (37460) hydrogen bonds : bond 0.06360 / 4.23 ( 1225) hydrogen bonds : angle 3.56261 / 2.48 ( 3429) Misc. bond : bond 0.02490 / 1.20 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 314 time to evaluate : 0.785 Fit side-chains REVERT: L 206 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6948 (mp-120) REVERT: M 58 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8009 (mp) REVERT: M 215 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.7759 (t80) REVERT: M 262 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: H 190 LYS cc_start: 0.7289 (mppt) cc_final: 0.6908 (mmpt) REVERT: F 41 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: P 7 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.4737 (mpt) REVERT: P 13 GLN cc_start: 0.7342 (tp40) cc_final: 0.6643 (pp30) REVERT: P 14 GLU cc_start: 0.7070 (tt0) cc_final: 0.6301 (mt-10) REVERT: S 13 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5398 (t0) REVERT: S 16 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6715 (mtt180) REVERT: T 13 ASP cc_start: 0.6808 (m-30) cc_final: 0.6533 (m-30) REVERT: V 17 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7007 (tm-30) REVERT: X 26 MET cc_start: 0.7757 (ttp) cc_final: 0.7508 (ttm) REVERT: Z 26 MET cc_start: 0.7467 (mtp) cc_final: 0.7107 (mtp) REVERT: Z 28 MET cc_start: 0.7008 (tpp) cc_final: 0.6338 (tmt) REVERT: 2 8 THR cc_start: 0.5319 (p) cc_final: 0.4920 (m) REVERT: 2 13 GLN cc_start: 0.6474 (mm110) cc_final: 0.4939 (tp40) REVERT: 7 8 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6400 (tt) REVERT: 7 10 GLN cc_start: 0.2451 (OUTLIER) cc_final: 0.1429 (mm110) REVERT: 7 22 PHE cc_start: 0.7252 (m-10) cc_final: 0.6689 (m-80) REVERT: 8 19 HIS cc_start: 0.6451 (OUTLIER) cc_final: 0.6167 (t-90) outliers start: 94 outliers final: 58 residues processed: 369 average time/residue: 0.5191 time to fit residues: 228.4068 Evaluate side-chains 364 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 24 GLN Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 0 residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 189 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN L 171 HIS L 206 GLN H 103 ASN H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100887 restraints weight = 34108.742| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.26 r_work: 0.2917 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.291 27319 Z= 0.369 Angle : 1.073 23.466 37460 Z= 0.424 Chirality : 0.056 0.241 3769 Planarity : 0.006 0.082 4433 Dihedral : 19.665 179.861 4825 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.12 % Allowed : 12.51 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2517 helix: 1.64 (0.13), residues: 1464 sheet: -0.41 (0.92), residues: 32 loop : -1.08 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 12 TYR 0.024 0.004 TYR C 259 PHE 0.052 0.003 PHE 1 26 TRP 0.019 0.003 TRP C 168 HIS 0.012 0.002 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.37 (27271) covalent geometry : angle 1.07341 / 0.42 (37460) hydrogen bonds : bond 0.09925 / 6.61 ( 1225) hydrogen bonds : angle 4.10305 / 2.87 ( 3429) Misc. bond : bond 0.04611 / 2.18 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 305 time to evaluate : 0.958 Fit side-chains REVERT: M 215 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8232 (t80) REVERT: M 262 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: H 190 LYS cc_start: 0.7185 (mppt) cc_final: 0.6812 (mmpt) REVERT: F 41 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: G 34 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8031 (mt) REVERT: K 31 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8366 (tp) REVERT: P 7 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.4690 (mpt) REVERT: P 13 GLN cc_start: 0.7256 (tp40) cc_final: 0.6598 (pp30) REVERT: P 14 GLU cc_start: 0.7100 (tt0) cc_final: 0.6331 (mt-10) REVERT: P 16 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6454 (mt0) REVERT: S 16 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6512 (mtt180) REVERT: T 13 ASP cc_start: 0.6955 (m-30) cc_final: 0.6664 (m-30) REVERT: W 7 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7687 (tptt) REVERT: X 26 MET cc_start: 0.7686 (ttp) cc_final: 0.7438 (ttm) REVERT: Y 7 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: Z 26 MET cc_start: 0.7518 (mtp) cc_final: 0.7167 (mtp) REVERT: Z 28 MET cc_start: 0.7181 (tpp) cc_final: 0.6510 (tmt) REVERT: 2 8 THR cc_start: 0.5214 (p) cc_final: 0.4841 (m) REVERT: 7 10 GLN cc_start: 0.2471 (OUTLIER) cc_final: 0.1208 (mm110) REVERT: 7 22 PHE cc_start: 0.7465 (m-10) cc_final: 0.6898 (m-80) outliers start: 111 outliers final: 70 residues processed: 372 average time/residue: 0.5879 time to fit residues: 259.5393 Evaluate side-chains 377 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain S residue 27 ILE Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 34 VAL Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 0 residue 38 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 186 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS L 206 GLN H 103 ASN H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 6 24 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105238 restraints weight = 34067.952| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.32 r_work: 0.2967 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 27319 Z= 0.144 Angle : 0.733 14.935 37460 Z= 0.287 Chirality : 0.040 0.158 3769 Planarity : 0.004 0.054 4433 Dihedral : 18.345 179.932 4825 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.41 % Allowed : 14.67 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.17), residues: 2517 helix: 2.17 (0.13), residues: 1496 sheet: -0.30 (0.91), residues: 32 loop : -0.82 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 16 TYR 0.018 0.002 TYR M 192 PHE 0.033 0.002 PHE 1 26 TRP 0.013 0.001 TRP U 9 HIS 0.010 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (27271) covalent geometry : angle 0.73263 / 0.29 (37460) hydrogen bonds : bond 0.06597 / 4.39 ( 1225) hydrogen bonds : angle 3.64450 / 2.54 ( 3429) Misc. bond : bond 0.02674 / 1.31 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 0.923 Fit side-chains REVERT: L 206 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7128 (mp-120) REVERT: M 58 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (mp) REVERT: M 215 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.7787 (t80) REVERT: M 262 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: H 190 LYS cc_start: 0.7313 (mppt) cc_final: 0.6963 (mmpt) REVERT: F 41 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: P 13 GLN cc_start: 0.7360 (tp40) cc_final: 0.6674 (pp30) REVERT: P 14 GLU cc_start: 0.7098 (tt0) cc_final: 0.6294 (mt-10) REVERT: S 13 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5357 (t0) REVERT: S 16 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6669 (mtt180) REVERT: T 13 ASP cc_start: 0.6817 (m-30) cc_final: 0.6548 (m-30) REVERT: X 26 MET cc_start: 0.7666 (ttp) cc_final: 0.7397 (ttm) REVERT: X 28 MET cc_start: 0.6743 (tmt) cc_final: 0.6255 (tpt) REVERT: Z 26 MET cc_start: 0.7485 (mtp) cc_final: 0.7167 (mtp) REVERT: Z 28 MET cc_start: 0.7099 (tpp) cc_final: 0.6439 (tmt) REVERT: 2 8 THR cc_start: 0.5284 (p) cc_final: 0.4908 (m) REVERT: 2 13 GLN cc_start: 0.6414 (mm110) cc_final: 0.5059 (tp40) REVERT: 7 8 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6316 (tt) REVERT: 7 10 GLN cc_start: 0.2027 (OUTLIER) cc_final: 0.1246 (mm110) REVERT: 7 22 PHE cc_start: 0.7334 (m-10) cc_final: 0.6765 (m-80) REVERT: 8 19 HIS cc_start: 0.6536 (t70) cc_final: 0.6290 (t-90) outliers start: 74 outliers final: 48 residues processed: 356 average time/residue: 0.5438 time to fit residues: 229.7279 Evaluate side-chains 353 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 9 residue 8 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS H 103 ASN H 122 HIS J 24 GLN K 10 GLN Z 24 GLN 5 10 GLN 6 24 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106506 restraints weight = 33882.231| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.25 r_work: 0.2987 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 27319 Z= 0.128 Angle : 0.690 15.125 37460 Z= 0.268 Chirality : 0.039 0.142 3769 Planarity : 0.004 0.055 4433 Dihedral : 17.769 179.949 4823 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.23 % Allowed : 14.95 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2517 helix: 2.34 (0.13), residues: 1508 sheet: -0.16 (0.89), residues: 32 loop : -0.75 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 16 TYR 0.015 0.001 TYR M 192 PHE 0.028 0.001 PHE 1 26 TRP 0.011 0.001 TRP U 9 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27271) covalent geometry : angle 0.69044 / 0.27 (37460) hydrogen bonds : bond 0.05931 / 3.94 ( 1225) hydrogen bonds : angle 3.51078 / 2.44 ( 3429) Misc. bond : bond 0.02351 / 1.14 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 0.904 Fit side-chains REVERT: M 58 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7921 (mp) REVERT: M 215 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.7676 (t80) REVERT: M 262 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: H 190 LYS cc_start: 0.7316 (mppt) cc_final: 0.6966 (mmpt) REVERT: F 41 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: P 7 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.4655 (mpt) REVERT: P 13 GLN cc_start: 0.7354 (tp40) cc_final: 0.6680 (pp30) REVERT: P 14 GLU cc_start: 0.7016 (tt0) cc_final: 0.6238 (mt-10) REVERT: S 13 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5411 (t0) REVERT: S 16 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6643 (mtt180) REVERT: T 13 ASP cc_start: 0.6733 (m-30) cc_final: 0.6459 (m-30) REVERT: V 17 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6976 (tm-30) REVERT: X 26 MET cc_start: 0.7696 (ttp) cc_final: 0.7445 (ttm) REVERT: Y 41 GLU cc_start: 0.6965 (tt0) cc_final: 0.6699 (pm20) REVERT: Z 26 MET cc_start: 0.7445 (mtp) cc_final: 0.7173 (mtp) REVERT: Z 28 MET cc_start: 0.6963 (tpp) cc_final: 0.6297 (tmt) REVERT: 2 8 THR cc_start: 0.5322 (p) cc_final: 0.4924 (m) REVERT: 2 13 GLN cc_start: 0.6384 (mm110) cc_final: 0.4875 (tp40) REVERT: 7 8 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6255 (tt) REVERT: 7 10 GLN cc_start: 0.2538 (OUTLIER) cc_final: 0.1685 (mm110) REVERT: 7 22 PHE cc_start: 0.7223 (m-10) cc_final: 0.6700 (m-80) REVERT: 8 19 HIS cc_start: 0.6452 (OUTLIER) cc_final: 0.6211 (t-90) outliers start: 70 outliers final: 46 residues processed: 349 average time/residue: 0.5358 time to fit residues: 222.0817 Evaluate side-chains 351 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS L 206 GLN H 103 ASN H 122 HIS J 24 GLN K 10 GLN Z 24 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106943 restraints weight = 33968.398| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.27 r_work: 0.3008 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.163 27319 Z= 0.124 Angle : 0.676 14.663 37460 Z= 0.263 Chirality : 0.039 0.142 3769 Planarity : 0.004 0.055 4433 Dihedral : 17.394 179.854 4823 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.91 % Allowed : 15.41 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.17), residues: 2517 helix: 2.42 (0.13), residues: 1508 sheet: -0.11 (0.88), residues: 32 loop : -0.68 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 16 TYR 0.015 0.001 TYR M 192 PHE 0.028 0.001 PHE 1 26 TRP 0.013 0.001 TRP 7 9 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (27271) covalent geometry : angle 0.67643 / 0.26 (37460) hydrogen bonds : bond 0.05721 / 3.80 ( 1225) hydrogen bonds : angle 3.45482 / 2.39 ( 3429) Misc. bond : bond 0.02533 / 1.23 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 308 time to evaluate : 0.811 Fit side-chains REVERT: C 291 ASP cc_start: 0.7532 (m-30) cc_final: 0.7136 (p0) REVERT: L 206 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6978 (mp-120) REVERT: M 58 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7903 (mp) REVERT: M 215 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.7645 (t80) REVERT: M 262 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: H 190 LYS cc_start: 0.7317 (mppt) cc_final: 0.6997 (mmpt) REVERT: F 41 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: P 7 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.4688 (mpt) REVERT: P 13 GLN cc_start: 0.7304 (tp40) cc_final: 0.6658 (pp30) REVERT: P 14 GLU cc_start: 0.6997 (tt0) cc_final: 0.6244 (mt-10) REVERT: S 16 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6703 (mtt180) REVERT: T 13 ASP cc_start: 0.6708 (m-30) cc_final: 0.6441 (m-30) REVERT: V 17 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6995 (tm-30) REVERT: X 26 MET cc_start: 0.7690 (ttp) cc_final: 0.7418 (ttm) REVERT: Z 28 MET cc_start: 0.6940 (tpp) cc_final: 0.6319 (tmt) REVERT: 1 26 PHE cc_start: 0.7633 (t80) cc_final: 0.7222 (t80) REVERT: 2 8 THR cc_start: 0.5401 (p) cc_final: 0.4986 (m) REVERT: 2 13 GLN cc_start: 0.6402 (mm110) cc_final: 0.4955 (tp40) REVERT: 7 10 GLN cc_start: 0.2156 (OUTLIER) cc_final: 0.1362 (mm110) REVERT: 7 22 PHE cc_start: 0.7194 (m-10) cc_final: 0.6666 (m-80) REVERT: 8 19 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.6175 (t-90) outliers start: 63 outliers final: 47 residues processed: 348 average time/residue: 0.5290 time to fit residues: 218.6621 Evaluate side-chains 357 residues out of total 2171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 301 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 120 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 246 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 HIS L 206 GLN H 103 ASN H 122 HIS J 24 GLN K 10 GLN ** 1 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107016 restraints weight = 33971.900| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.25 r_work: 0.3013 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 27319 Z= 0.156 Angle : 0.815 59.196 37460 Z= 0.375 Chirality : 0.040 0.625 3769 Planarity : 0.004 0.055 4433 Dihedral : 17.396 179.851 4821 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.68 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.17), residues: 2517 helix: 2.42 (0.13), residues: 1508 sheet: -0.11 (0.88), residues: 32 loop : -0.68 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 16 TYR 0.015 0.001 TYR M 192 PHE 0.028 0.001 PHE 1 26 TRP 0.011 0.001 TRP U 9 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (27271) covalent geometry : angle 0.81452 / 0.38 (37460) hydrogen bonds : bond 0.05758 / 3.83 ( 1225) hydrogen bonds : angle 3.45530 / 2.40 ( 3429) Misc. bond : bond 0.02529 / 1.23 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9954.17 seconds wall clock time: 169 minutes 42.57 seconds (10182.57 seconds total)