Starting phenix.real_space_refine on Sat May 24 22:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdu_37465/05_2025/8wdu_37465.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 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 21 5.49 5 Mg 37 5.21 5 S 96 5.16 5 C 18084 2.51 5 N 3529 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26274 Number of models: 1 Model: "" Number of chains: 98 Chain: "C" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2429 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 283} Chain: "L" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1993 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} 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 Conformer: "B" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} 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 bond proxies already assigned to first conformer: 2041 Chain: "A" 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: "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: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" 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: "J" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 324 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} 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: 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: "R" 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: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "U" Number of atoms: 407 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 408 Chain: "V" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" 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: "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: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} 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: 359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} 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 Conformer: "B" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} 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 bond proxies already assigned to first conformer: 354 Chain: "8" 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: "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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 552 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'PGV:plan-3': 3, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 515 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'LMT': 2, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'CDL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} 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: 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: "N" 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: "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: 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: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" 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: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "T" 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: "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: 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: "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: 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: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" 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: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 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: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" 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: "0" 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: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "M" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 18.65, per 1000 atoms: 0.71 Number of scatterers: 26274 At special positions: 0 Unit cell: (132.714, 121.806, 135.138, 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 96 16.00 P 21 15.00 Mg 37 11.99 O 4496 8.00 N 3529 7.00 C 18084 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=50, symmetry=0 Number of additional bonds: simple=50, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 2.8 seconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4774 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 9 sheets defined 67.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.514A pdb=" N VAL C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 102 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 121 through 141 removed outlier: 3.538A pdb=" N VAL C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.959A pdb=" N CYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.813A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 removed outlier: 3.559A pdb=" N ALA C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.177A pdb=" N PHE C 256 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 283 removed outlier: 3.860A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 323 through 331 Proline residue: C 328 - end of helix Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 85 through 88 Processing helix chain 'L' and resid 89 through 118 Processing helix chain 'L' and resid 121 through 139 removed outlier: 3.590A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 146 Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 157 through 169 Processing helix chain 'L' and resid 170 through 171 No H-bonds generated for 'chain 'L' and resid 170 through 171' Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 176 through 205 Processing helix chain 'L' and resid 214 through 227 removed outlier: 3.667A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 256 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.711A pdb=" N TRP L 268 " --> pdb=" O GLY L 264 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP L 269 " --> pdb=" O TRP L 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 264 through 269' Processing helix chain 'L' and resid 269 through 274 Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.722A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 168 Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.801A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'M' and resid 315 through 319 removed outlier: 3.664A pdb=" N THR M 319 " --> pdb=" O PRO M 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 111 through 115 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 216 through 222 removed outlier: 3.513A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 removed outlier: 3.638A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.508A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.737A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 38 Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.526A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.761A pdb=" N LEU F 11 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 39 Processing helix chain 'G' and resid 11 through 44 Processing helix chain 'I' and resid 5 through 11 removed outlier: 4.184A pdb=" N TRP I 9 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN I 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'K' and resid 13 through 39 Processing helix chain 'N' and resid 11 through 44 removed outlier: 4.004A pdb=" N GLU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.541A pdb=" N TRP O 9 " --> pdb=" O HIS O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 39 Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 6 through 10 removed outlier: 3.903A pdb=" N TRP Q 9 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 39 Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.877A pdb=" N TRP S 9 " --> pdb=" O TRP S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 38 Processing helix chain 'T' and resid 11 through 44 Processing helix chain 'U' and resid 4 through 11 removed outlier: 3.544A pdb=" N LYS U 7 " --> pdb=" O ASP U 4 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE U 8 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 39 Processing helix chain 'V' and resid 13 through 44 removed outlier: 3.555A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.937A pdb=" N LYS W 7 " --> pdb=" O ASP W 4 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU W 10 " --> pdb=" O LYS W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 38 Processing helix chain 'X' and resid 11 through 44 removed outlier: 3.521A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 11 removed outlier: 3.803A pdb=" N LYS Y 7 " --> pdb=" O ASP Y 4 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 38 Processing helix chain 'Z' and resid 11 through 44 removed outlier: 3.564A pdb=" N GLU Z 17 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Z 20 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 12 Processing helix chain '1' and resid 13 through 39 Processing helix chain '2' and resid 11 through 44 removed outlier: 3.600A pdb=" N GLU 2 17 " --> pdb=" O GLN 2 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL 2 23 " --> pdb=" O HIS 2 19 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN 2 24 " --> pdb=" O GLY 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 13 through 39 Processing helix chain '3' and resid 43 through 47 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 7 through 12 removed outlier: 3.777A pdb=" N ILE 5 11 " --> pdb=" O LYS 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 39 Processing helix chain '5' and resid 40 through 43 removed outlier: 3.630A pdb=" N ASN 5 43 " --> pdb=" O PRO 5 40 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 40 through 43' Processing helix chain '6' and resid 11 through 44 Processing helix chain '7' and resid 5 through 11 Processing helix chain '7' and resid 13 through 39 removed outlier: 3.967A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 44 Processing helix chain '9' and resid 7 through 12 Processing helix chain '9' and resid 13 through 39 Processing helix chain '0' and resid 11 through 44 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 26 through 27 Processing sheet with id=AA3, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.788A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR H 181 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL H 172 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.518A pdb=" N VAL H 156 " --> pdb=" O ALA H 164 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3748 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: 7.58 Time building geometry restraints manager: 8.93 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: 9182 1.38 - 1.56: 17396 1.56 - 1.75: 43 1.75 - 1.93: 180 1.93 - 2.11: 156 Bond restraints: 26957 Sorted by residual: bond pdb=" CB7 CDL D 101 " pdb=" OB8 CDL D 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 407 " pdb=" OA8 CDL M 407 " 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 409 " pdb=" OA8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL L 311 " pdb=" OB8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL L 311 " pdb=" OA8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 35651 5.02 - 10.04: 1293 10.04 - 15.07: 98 15.07 - 20.09: 20 20.09 - 25.11: 12 Bond angle restraints: 37074 Sorted by residual: angle pdb=" N PRO Y 59 " pdb=" CD PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO Y 59 " pdb=" CB PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" C39 CRT V 102 " pdb=" C38 CRT V 102 " pdb=" O2 CRT V 102 " ideal model delta sigma weight residual 111.76 86.65 25.11 3.00e+00 1.11e-01 7.01e+01 angle pdb=" C40 CRT M 406 " pdb=" C38 CRT M 406 " pdb=" O2 CRT M 406 " ideal model delta sigma weight residual 111.40 86.96 24.44 3.00e+00 1.11e-01 6.64e+01 angle pdb=" C3 CRT J 103 " pdb=" C1 CRT J 103 " pdb=" C4 CRT J 103 " ideal model delta sigma weight residual 108.82 84.72 24.10 3.00e+00 1.11e-01 6.46e+01 ... (remaining 37069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 14291 36.00 - 72.00: 926 72.00 - 108.00: 179 108.00 - 144.00: 59 144.00 - 180.00: 14 Dihedral angle restraints: 15469 sinusoidal: 8098 harmonic: 7371 Sorted by residual: dihedral pdb=" C1 BCL T 101 " pdb=" CGA BCL T 101 " pdb=" O2A BCL T 101 " pdb=" CBA BCL T 101 " ideal model delta sinusoidal sigma weight residual -180.00 -74.32 -105.68 1 6.00e+00 2.78e-02 3.39e+02 dihedral pdb=" C1 BCL F 502 " pdb=" C2 BCL F 502 " pdb=" C3 BCL F 502 " pdb=" C5 BCL F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 3 101 " pdb=" C2 BCL 3 101 " pdb=" C3 BCL 3 101 " pdb=" C5 BCL 3 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.04 -179.96 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3333 0.080 - 0.160: 354 0.160 - 0.241: 65 0.241 - 0.321: 13 0.321 - 0.401: 7 Chirality restraints: 3772 Sorted by residual: chirality pdb=" CBD BCL M 403 " pdb=" CAD BCL M 403 " pdb=" CGD BCL M 403 " pdb=" CHA BCL M 403 " both_signs ideal model delta sigma weight residual False 2.62 3.02 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBD BCL R 101 " pdb=" CAD BCL R 101 " pdb=" CGD BCL R 101 " pdb=" CHA BCL R 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBD BCL V 101 " pdb=" CAD BCL V 101 " pdb=" CGD BCL V 101 " pdb=" CHA BCL V 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 3769 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 101 " 0.370 3.00e-02 1.11e+03 3.09e-01 5.30e+02 pdb=" CBA BCL 0 101 " 0.121 3.00e-02 1.11e+03 pdb=" CGA BCL 0 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL 0 101 " 0.134 3.00e-02 1.11e+03 pdb=" O2A BCL 0 101 " -0.549 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " 0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL W 101 " 0.185 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " -0.082 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.038 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " -0.493 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.354 3.00e-02 1.11e+03 2.86e-01 4.54e+02 pdb=" CBA BCL K 102 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.085 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.488 3.00e-02 1.11e+03 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 111 2.39 - 3.02: 14469 3.02 - 3.65: 42930 3.65 - 4.27: 71895 4.27 - 4.90: 112864 Nonbonded interactions: 242269 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.765 3.040 nonbonded pdb=" OE1 GLU M 96 " pdb=" O HOH M 502 " model vdw 1.806 3.040 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.031 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 401 " model vdw 2.071 2.340 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.073 2.260 ... (remaining 242264 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 10 through 47) selection = (chain '2' and resid 10 through 47) selection = (chain '4' and resid 10 through 47) selection = (chain '6' and resid 10 through 47) selection = (chain '8' and resid 10 through 47) selection = (chain 'B' and resid 10 through 47) selection = (chain 'J' and resid 10 through 47) selection = (chain 'N' and resid 10 through 47) selection = (chain 'P' and resid 10 through 47) selection = (chain 'R' and resid 10 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 21 or resid 23 through 46)) selection = (chain '5' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '7' and (resid 5 through 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) 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 21 or resid 23 through 46)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'F' and (resid 2 through 33 or resid 35 through 50 or resid 502 through 5 \ 03)) selection = (chain 'S' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'U' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) selection = (chain 'W' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) } ncs_group { reference = (chain 'E' and resid 8 through 47) selection = (chain 'G' and resid 8 through 47) selection = (chain 'T' and resid 8 through 47) selection = (chain 'V' and resid 8 through 47) selection = (chain 'X' and resid 8 through 47) selection = (chain 'Z' and resid 8 through 47) } 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: 8.020 Set stop_for_unknowns flag: 0.010 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: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.340 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.130 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.022 0.465 27007 Z= 1.428 Angle : 1.894 25.111 37074 Z= 0.819 Chirality : 0.057 0.401 3772 Planarity : 0.017 0.309 4374 Dihedral : 24.811 179.998 10695 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 18.61 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.17), residues: 2494 helix: 1.98 (0.13), residues: 1511 sheet: -0.76 (0.77), residues: 41 loop : 0.51 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 PHE 0.026 0.002 PHE V 30 TYR 0.020 0.002 TYR C 319 ARG 0.007 0.001 ARG 1 15 Details of bonding type rmsd hydrogen bonds : bond 0.18294 ( 1326) hydrogen bonds : angle 6.05960 ( 3748) covalent geometry : bond 0.01859 (26957) covalent geometry : angle 1.89430 (37074) Misc. bond : bond 0.27226 ( 50) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 2.412 Fit side-chains REVERT: H 75 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7286 (p) REVERT: F 41 GLU cc_start: 0.7606 (tp30) cc_final: 0.7252 (tp30) REVERT: I 8 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5524 (pt) REVERT: P 27 THR cc_start: 0.7498 (m) cc_final: 0.7023 (m) REVERT: X 28 MET cc_start: 0.6580 (tpt) cc_final: 0.6213 (tpt) REVERT: Y 59 PRO cc_start: 0.6371 (Cg_exo) cc_final: 0.5699 (Cg_endo) REVERT: 4 44 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7456 (ttm170) outliers start: 37 outliers final: 26 residues processed: 301 average time/residue: 1.1620 time to fit residues: 416.6693 Evaluate side-chains 284 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 206 GLN L 207 GLN L 219 ASN M 145 HIS H 71 HIS H 103 ASN H 192 ASN A 6 HIS B 4 ASN J 24 GLN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 HIS 2 16 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111432 restraints weight = 37245.250| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.42 r_work: 0.2882 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.330 27007 Z= 0.172 Angle : 0.811 16.040 37074 Z= 0.323 Chirality : 0.044 0.423 3772 Planarity : 0.005 0.068 4374 Dihedral : 21.220 179.930 6184 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 15.86 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2494 helix: 2.40 (0.12), residues: 1503 sheet: -0.77 (0.78), residues: 41 loop : 0.38 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 6 HIS 0.008 0.002 HIS R 19 PHE 0.024 0.002 PHE L 41 TYR 0.018 0.002 TYR M 193 ARG 0.005 0.001 ARG 1 15 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 1326) hydrogen bonds : angle 4.39204 ( 3748) covalent geometry : bond 0.00399 (26957) covalent geometry : angle 0.81115 (37074) Misc. bond : bond 0.07204 ( 50) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 2.560 Fit side-chains REVERT: L 208 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5332 (mppt) REVERT: H 237 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8690 (t70) REVERT: H 259 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5723 (tp) REVERT: G 21 ILE cc_start: 0.7060 (mp) cc_final: 0.6799 (mt) REVERT: I 8 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5730 (pt) REVERT: J 27 THR cc_start: 0.7404 (m) cc_final: 0.7089 (t) REVERT: O 10 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.6124 (mt0) REVERT: P 13 GLN cc_start: 0.4277 (OUTLIER) cc_final: 0.3922 (tm-30) REVERT: P 23 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.6816 (t) REVERT: P 27 THR cc_start: 0.8114 (m) cc_final: 0.7744 (m) REVERT: S 15 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.6249 (ttp-110) REVERT: S 17 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7468 (mp) REVERT: S 41 GLU cc_start: 0.8715 (mp0) cc_final: 0.8492 (mp0) REVERT: 1 7 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5621 (mmtp) REVERT: 2 27 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7302 (m) REVERT: 3 66 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6889 (ttp-170) REVERT: 4 7 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.3659 (mtm) REVERT: 4 14 GLU cc_start: 0.4017 (OUTLIER) cc_final: 0.3489 (mm-30) REVERT: 6 30 PHE cc_start: 0.7945 (m-10) cc_final: 0.7729 (m-10) outliers start: 59 outliers final: 17 residues processed: 314 average time/residue: 1.1589 time to fit residues: 434.6564 Evaluate side-chains 285 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 7 MET Chi-restraints excluded: chain 4 residue 14 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 235 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 150 HIS L 219 ASN M 74 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109218 restraints weight = 35714.774| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.22 r_work: 0.2879 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.339 27007 Z= 0.230 Angle : 0.860 17.059 37074 Z= 0.348 Chirality : 0.045 0.408 3772 Planarity : 0.005 0.067 4374 Dihedral : 20.106 179.770 6155 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.31 % Allowed : 14.97 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2494 helix: 2.18 (0.12), residues: 1497 sheet: -0.83 (0.77), residues: 41 loop : 0.19 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 9 HIS 0.008 0.002 HIS 0 37 PHE 0.029 0.002 PHE L 41 TYR 0.025 0.003 TYR C 319 ARG 0.004 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05734 ( 1326) hydrogen bonds : angle 4.46229 ( 3748) covalent geometry : bond 0.00538 (26957) covalent geometry : angle 0.86019 (37074) Misc. bond : bond 0.07499 ( 50) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 271 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5328 (mppt) REVERT: H 75 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7716 (p) REVERT: H 259 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5762 (tp) REVERT: F 41 GLU cc_start: 0.8056 (tp30) cc_final: 0.7824 (tp30) REVERT: I 8 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5664 (pt) REVERT: J 24 GLN cc_start: 0.6643 (tt0) cc_final: 0.6238 (tp40) REVERT: J 27 THR cc_start: 0.7431 (m) cc_final: 0.7134 (t) REVERT: N 26 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6020 (mtt) REVERT: P 24 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6377 (mp-120) REVERT: P 27 THR cc_start: 0.8090 (m) cc_final: 0.7704 (m) REVERT: Q 15 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7300 (mtp180) REVERT: S 15 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6229 (ttp-110) REVERT: S 17 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7478 (mp) REVERT: Y 59 PRO cc_start: 0.6778 (Cg_exo) cc_final: 0.6488 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5722 (mmtp) REVERT: 2 25 SER cc_start: 0.7142 (t) cc_final: 0.6655 (p) REVERT: 2 27 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7388 (m) REVERT: 4 14 GLU cc_start: 0.4067 (OUTLIER) cc_final: 0.3519 (mm-30) REVERT: 4 44 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7764 (ttm170) REVERT: 7 13 ASP cc_start: 0.7801 (t0) cc_final: 0.7569 (t0) outliers start: 71 outliers final: 35 residues processed: 320 average time/residue: 1.1402 time to fit residues: 436.7082 Evaluate side-chains 306 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 170 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110031 restraints weight = 33832.498| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.21 r_work: 0.2889 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.324 27007 Z= 0.202 Angle : 0.813 16.783 37074 Z= 0.329 Chirality : 0.043 0.409 3772 Planarity : 0.005 0.071 4374 Dihedral : 19.612 179.922 6155 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.54 % Allowed : 14.69 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2494 helix: 2.19 (0.12), residues: 1496 sheet: -0.89 (0.76), residues: 41 loop : 0.19 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 9 HIS 0.007 0.002 HIS 0 37 PHE 0.028 0.002 PHE L 41 TYR 0.022 0.002 TYR C 319 ARG 0.003 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 1326) hydrogen bonds : angle 4.36691 ( 3748) covalent geometry : bond 0.00471 (26957) covalent geometry : angle 0.81275 (37074) Misc. bond : bond 0.06921 ( 50) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 266 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5353 (mppt) REVERT: H 75 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7676 (p) REVERT: H 253 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6986 (mm-30) REVERT: H 259 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5744 (tp) REVERT: B 17 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: F 16 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6286 (mtt90) REVERT: I 8 ILE cc_start: 0.5927 (OUTLIER) cc_final: 0.5619 (pt) REVERT: J 24 GLN cc_start: 0.6610 (tt0) cc_final: 0.6219 (tp40) REVERT: J 27 THR cc_start: 0.7437 (m) cc_final: 0.7139 (t) REVERT: P 23 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.6808 (t) REVERT: P 24 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6357 (mp-120) REVERT: P 27 THR cc_start: 0.8103 (m) cc_final: 0.7726 (m) REVERT: Q 15 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7306 (mtp180) REVERT: S 15 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6268 (ttp-110) REVERT: S 17 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7482 (mp) REVERT: Y 59 PRO cc_start: 0.6781 (Cg_exo) cc_final: 0.6505 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5728 (mmtp) REVERT: 2 25 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6771 (p) REVERT: 2 27 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7401 (m) REVERT: 4 11 THR cc_start: 0.5129 (OUTLIER) cc_final: 0.4609 (t) REVERT: 4 14 GLU cc_start: 0.4037 (OUTLIER) cc_final: 0.3523 (mm-30) REVERT: 6 30 PHE cc_start: 0.8022 (m-10) cc_final: 0.7788 (m-10) REVERT: 7 13 ASP cc_start: 0.7779 (t0) cc_final: 0.7542 (t0) REVERT: 8 26 MET cc_start: 0.8389 (ttm) cc_final: 0.8127 (ttm) outliers start: 76 outliers final: 39 residues processed: 321 average time/residue: 1.1462 time to fit residues: 439.0141 Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113936 restraints weight = 31241.955| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.04 r_work: 0.2952 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.291 27007 Z= 0.135 Angle : 0.710 16.584 37074 Z= 0.282 Chirality : 0.039 0.400 3772 Planarity : 0.004 0.068 4374 Dihedral : 18.481 179.938 6155 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.43 % Allowed : 15.76 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.16), residues: 2494 helix: 2.53 (0.12), residues: 1496 sheet: -0.90 (0.79), residues: 41 loop : 0.33 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 6 HIS 0.005 0.001 HIS R 19 PHE 0.020 0.002 PHE L 41 TYR 0.017 0.002 TYR M 193 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 1326) hydrogen bonds : angle 4.15795 ( 3748) covalent geometry : bond 0.00311 (26957) covalent geometry : angle 0.70954 (37074) Misc. bond : bond 0.06046 ( 50) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 2.612 Fit side-chains REVERT: L 3 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: L 211 GLU cc_start: 0.7960 (pt0) cc_final: 0.7656 (mt-10) REVERT: M 45 ASP cc_start: 0.8242 (t0) cc_final: 0.7821 (m-30) REVERT: H 48 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6708 (mtp180) REVERT: H 253 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6869 (mm-30) REVERT: H 259 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5685 (tp) REVERT: I 8 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5618 (pt) REVERT: J 24 GLN cc_start: 0.6595 (tt0) cc_final: 0.6205 (tp40) REVERT: J 27 THR cc_start: 0.7413 (m) cc_final: 0.7108 (t) REVERT: P 23 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6713 (t) REVERT: P 24 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6327 (mp-120) REVERT: P 27 THR cc_start: 0.8100 (m) cc_final: 0.7759 (m) REVERT: Q 15 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7252 (mtp180) REVERT: S 15 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6208 (ttp-110) REVERT: S 17 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7429 (mp) REVERT: Y 38 SER cc_start: 0.8696 (m) cc_final: 0.8474 (p) REVERT: 1 7 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5690 (mmtp) REVERT: 2 25 SER cc_start: 0.7204 (t) cc_final: 0.6638 (p) REVERT: 2 27 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7347 (m) REVERT: 3 16 MET cc_start: 0.5769 (mmt) cc_final: 0.5377 (tpt) REVERT: 4 11 THR cc_start: 0.5060 (OUTLIER) cc_final: 0.4559 (t) REVERT: 4 14 GLU cc_start: 0.4005 (OUTLIER) cc_final: 0.3542 (mm-30) REVERT: 6 30 PHE cc_start: 0.7963 (m-10) cc_final: 0.7729 (m-10) REVERT: 7 13 ASP cc_start: 0.7706 (t0) cc_final: 0.7474 (t0) REVERT: 8 26 MET cc_start: 0.8352 (ttm) cc_final: 0.8044 (ttm) outliers start: 52 outliers final: 28 residues processed: 313 average time/residue: 1.1387 time to fit residues: 425.9923 Evaluate side-chains 297 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 139 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110144 restraints weight = 32339.956| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.16 r_work: 0.2874 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.330 27007 Z= 0.244 Angle : 0.878 16.812 37074 Z= 0.354 Chirality : 0.046 0.406 3772 Planarity : 0.005 0.067 4374 Dihedral : 19.497 179.848 6155 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.40 % Allowed : 14.97 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.16), residues: 2494 helix: 2.15 (0.12), residues: 1498 sheet: -0.93 (0.77), residues: 41 loop : 0.18 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 9 HIS 0.010 0.002 HIS 0 37 PHE 0.031 0.003 PHE L 41 TYR 0.026 0.003 TYR C 319 ARG 0.005 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 1326) hydrogen bonds : angle 4.41589 ( 3748) covalent geometry : bond 0.00571 (26957) covalent geometry : angle 0.87820 (37074) Misc. bond : bond 0.07340 ( 50) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 2.695 Fit side-chains REVERT: C 260 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8491 (ttpt) REVERT: L 208 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5319 (mppt) REVERT: M 45 ASP cc_start: 0.8342 (t0) cc_final: 0.7890 (m-30) REVERT: H 48 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6780 (mtp180) REVERT: H 75 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7744 (p) REVERT: H 253 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7015 (mm-30) REVERT: H 259 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5779 (tp) REVERT: B 13 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6615 (tp40) REVERT: D 6 TRP cc_start: 0.5560 (p-90) cc_final: 0.5321 (p-90) REVERT: F 16 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6284 (mtt90) REVERT: I 8 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5676 (pt) REVERT: J 24 GLN cc_start: 0.6581 (tt0) cc_final: 0.6196 (tp40) REVERT: J 27 THR cc_start: 0.7441 (m) cc_final: 0.7130 (t) REVERT: P 24 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6375 (mp-120) REVERT: P 27 THR cc_start: 0.8082 (m) cc_final: 0.7720 (m) REVERT: Q 15 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7321 (mtp180) REVERT: S 15 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5830 (ttp-170) REVERT: S 17 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7499 (mp) REVERT: Y 59 PRO cc_start: 0.6755 (Cg_exo) cc_final: 0.6498 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5755 (mmtp) REVERT: 1 18 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6626 (mp) REVERT: 2 25 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.6882 (p) REVERT: 4 7 MET cc_start: 0.4791 (mtm) cc_final: 0.4431 (ptm) REVERT: 4 11 THR cc_start: 0.5082 (OUTLIER) cc_final: 0.4533 (t) REVERT: 4 14 GLU cc_start: 0.4048 (OUTLIER) cc_final: 0.3536 (mm-30) REVERT: 6 30 PHE cc_start: 0.8026 (m-10) cc_final: 0.7794 (m-10) REVERT: 7 13 ASP cc_start: 0.7772 (t0) cc_final: 0.7466 (t0) REVERT: 8 26 MET cc_start: 0.8423 (ttm) cc_final: 0.8187 (ttm) outliers start: 73 outliers final: 40 residues processed: 322 average time/residue: 1.1845 time to fit residues: 453.2297 Evaluate side-chains 314 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 14 GLU Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 71 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108850 restraints weight = 35415.561| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.40 r_work: 0.2834 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 27007 Z= 0.240 Angle : 0.876 16.506 37074 Z= 0.353 Chirality : 0.046 0.413 3772 Planarity : 0.005 0.069 4374 Dihedral : 19.582 179.867 6155 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.50 % Allowed : 14.74 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 2494 helix: 2.00 (0.12), residues: 1504 sheet: -0.98 (0.76), residues: 41 loop : 0.10 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 9 HIS 0.009 0.002 HIS 0 37 PHE 0.031 0.003 PHE L 41 TYR 0.027 0.003 TYR C 319 ARG 0.004 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05621 ( 1326) hydrogen bonds : angle 4.44209 ( 3748) covalent geometry : bond 0.00563 (26957) covalent geometry : angle 0.87632 (37074) Misc. bond : bond 0.07356 ( 50) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 2.528 Fit side-chains REVERT: C 260 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8503 (ttpt) REVERT: C 304 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9045 (mtmp) REVERT: L 208 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5316 (mppt) REVERT: M 45 ASP cc_start: 0.8371 (t0) cc_final: 0.7883 (m-30) REVERT: H 48 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6770 (mtp180) REVERT: H 75 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7691 (p) REVERT: H 253 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6970 (mm-30) REVERT: H 259 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5787 (tp) REVERT: B 13 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6577 (tp40) REVERT: D 6 TRP cc_start: 0.5512 (p-90) cc_final: 0.5233 (p-90) REVERT: D 41 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: F 16 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6326 (mtt90) REVERT: I 8 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5658 (pt) REVERT: J 27 THR cc_start: 0.7433 (m) cc_final: 0.7116 (t) REVERT: P 23 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.6826 (t) REVERT: P 24 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6390 (mp-120) REVERT: P 27 THR cc_start: 0.8035 (m) cc_final: 0.7668 (m) REVERT: Q 15 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: S 15 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6321 (ttp-110) REVERT: S 17 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7466 (mp) REVERT: Y 59 PRO cc_start: 0.6689 (Cg_exo) cc_final: 0.6428 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5762 (mmtp) REVERT: 1 18 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6617 (mp) REVERT: 1 21 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7432 (tp) REVERT: 2 25 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6903 (p) REVERT: 6 30 PHE cc_start: 0.8052 (m-10) cc_final: 0.7827 (m-10) REVERT: 7 13 ASP cc_start: 0.7746 (t0) cc_final: 0.7459 (t0) REVERT: 8 26 MET cc_start: 0.8442 (ttm) cc_final: 0.8226 (ttm) outliers start: 75 outliers final: 39 residues processed: 318 average time/residue: 1.1675 time to fit residues: 442.2749 Evaluate side-chains 313 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 21 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 141 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111798 restraints weight = 28388.255| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.10 r_work: 0.2885 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 27007 Z= 0.181 Angle : 0.791 16.515 37074 Z= 0.318 Chirality : 0.042 0.407 3772 Planarity : 0.005 0.069 4374 Dihedral : 18.916 179.923 6155 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.89 % Allowed : 15.58 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2494 helix: 2.19 (0.12), residues: 1503 sheet: -0.97 (0.78), residues: 41 loop : 0.16 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 6 HIS 0.010 0.002 HIS R 19 PHE 0.027 0.002 PHE L 41 TYR 0.021 0.002 TYR C 319 ARG 0.003 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 1326) hydrogen bonds : angle 4.31995 ( 3748) covalent geometry : bond 0.00422 (26957) covalent geometry : angle 0.79122 (37074) Misc. bond : bond 0.07089 ( 50) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5344 (mppt) REVERT: M 45 ASP cc_start: 0.8309 (t0) cc_final: 0.7844 (m-30) REVERT: H 48 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6712 (mtp180) REVERT: H 253 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6920 (mm-30) REVERT: H 259 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5760 (tp) REVERT: D 6 TRP cc_start: 0.5513 (p-90) cc_final: 0.5296 (p-90) REVERT: E 16 LYS cc_start: 0.4862 (OUTLIER) cc_final: 0.4619 (mppt) REVERT: F 16 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6282 (mtt90) REVERT: J 24 GLN cc_start: 0.6585 (tt0) cc_final: 0.6206 (tp40) REVERT: J 27 THR cc_start: 0.7404 (m) cc_final: 0.7090 (t) REVERT: P 23 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.6784 (t) REVERT: P 24 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6359 (mp-120) REVERT: P 27 THR cc_start: 0.8073 (m) cc_final: 0.7726 (m) REVERT: Q 15 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: S 15 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6319 (ttp-110) REVERT: S 17 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7474 (mp) REVERT: Y 38 SER cc_start: 0.8773 (m) cc_final: 0.8530 (p) REVERT: Y 59 PRO cc_start: 0.6727 (Cg_exo) cc_final: 0.6467 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5763 (mmtp) REVERT: 1 18 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6602 (mp) REVERT: 2 25 SER cc_start: 0.7285 (OUTLIER) cc_final: 0.6916 (p) REVERT: 2 27 THR cc_start: 0.7707 (t) cc_final: 0.7392 (m) REVERT: 6 30 PHE cc_start: 0.8039 (m-10) cc_final: 0.7819 (m-10) REVERT: 7 13 ASP cc_start: 0.7785 (t0) cc_final: 0.7528 (t0) REVERT: 8 26 MET cc_start: 0.8389 (ttm) cc_final: 0.8170 (ttm) outliers start: 62 outliers final: 40 residues processed: 315 average time/residue: 1.1599 time to fit residues: 437.4585 Evaluate side-chains 313 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 132 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108174 restraints weight = 37822.582| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.41 r_work: 0.2843 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.332 27007 Z= 0.244 Angle : 0.882 16.619 37074 Z= 0.357 Chirality : 0.046 0.414 3772 Planarity : 0.005 0.067 4374 Dihedral : 19.427 179.895 6153 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.03 % Allowed : 15.72 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 2494 helix: 2.00 (0.12), residues: 1503 sheet: -1.01 (0.76), residues: 41 loop : 0.12 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 6 HIS 0.014 0.002 HIS R 19 PHE 0.031 0.003 PHE L 41 TYR 0.026 0.003 TYR C 319 ARG 0.005 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05637 ( 1326) hydrogen bonds : angle 4.44832 ( 3748) covalent geometry : bond 0.00573 (26957) covalent geometry : angle 0.88191 (37074) Misc. bond : bond 0.07323 ( 50) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: C 260 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8487 (ttpt) REVERT: L 208 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5324 (mppt) REVERT: H 48 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6746 (mtp180) REVERT: H 75 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7701 (p) REVERT: H 253 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6967 (mm-30) REVERT: H 259 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5783 (tp) REVERT: D 6 TRP cc_start: 0.5529 (p-90) cc_final: 0.5328 (p-90) REVERT: F 16 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6307 (mtt90) REVERT: I 10 GLN cc_start: 0.4987 (OUTLIER) cc_final: 0.3732 (tm-30) REVERT: J 27 THR cc_start: 0.7430 (m) cc_final: 0.7123 (t) REVERT: P 23 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.6819 (t) REVERT: P 24 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6405 (mp-120) REVERT: P 27 THR cc_start: 0.8035 (m) cc_final: 0.7671 (m) REVERT: Q 15 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7320 (mtp180) REVERT: S 15 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6345 (ttp-110) REVERT: S 17 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7470 (mp) REVERT: Y 41 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: Y 59 PRO cc_start: 0.6712 (Cg_exo) cc_final: 0.6458 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5713 (mmtp) REVERT: 1 18 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6614 (mp) REVERT: 2 25 SER cc_start: 0.7281 (OUTLIER) cc_final: 0.6948 (p) REVERT: 2 27 THR cc_start: 0.7706 (t) cc_final: 0.7371 (m) REVERT: 6 30 PHE cc_start: 0.8048 (m-10) cc_final: 0.7820 (m-10) REVERT: 7 13 ASP cc_start: 0.7777 (t0) cc_final: 0.7473 (t0) REVERT: 8 26 MET cc_start: 0.8417 (ttm) cc_final: 0.8206 (ttm) outliers start: 65 outliers final: 40 residues processed: 311 average time/residue: 1.2302 time to fit residues: 452.8443 Evaluate side-chains 309 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 143 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113384 restraints weight = 32119.864| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.20 r_work: 0.2906 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.300 27007 Z= 0.144 Angle : 0.734 16.382 37074 Z= 0.295 Chirality : 0.040 0.403 3772 Planarity : 0.004 0.069 4374 Dihedral : 18.250 179.999 6153 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.24 % Allowed : 16.70 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2494 helix: 2.38 (0.12), residues: 1499 sheet: -0.92 (0.79), residues: 41 loop : 0.26 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP S 6 HIS 0.010 0.001 HIS R 19 PHE 0.022 0.002 PHE L 41 TYR 0.018 0.002 TYR M 193 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1326) hydrogen bonds : angle 4.21494 ( 3748) covalent geometry : bond 0.00333 (26957) covalent geometry : angle 0.73416 (37074) Misc. bond : bond 0.06236 ( 50) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: L 3 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8782 (mtt) REVERT: L 208 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5314 (mppt) REVERT: L 211 GLU cc_start: 0.8011 (pt0) cc_final: 0.7703 (mt-10) REVERT: H 48 ARG cc_start: 0.6990 (mtp180) cc_final: 0.6707 (mtp180) REVERT: H 253 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6911 (mm-30) REVERT: H 259 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5738 (tp) REVERT: B 26 MET cc_start: 0.8699 (ttp) cc_final: 0.8489 (ttp) REVERT: E 47 LEU cc_start: 0.7941 (mt) cc_final: 0.7732 (mt) REVERT: J 24 GLN cc_start: 0.6595 (tt0) cc_final: 0.6216 (tp40) REVERT: J 27 THR cc_start: 0.7391 (m) cc_final: 0.7075 (t) REVERT: P 23 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6707 (t) REVERT: P 24 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6347 (mp-120) REVERT: P 27 THR cc_start: 0.8065 (m) cc_final: 0.7739 (m) REVERT: Q 15 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7288 (mtp180) REVERT: S 15 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6256 (ttp-110) REVERT: S 17 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7413 (mp) REVERT: Y 38 SER cc_start: 0.8735 (m) cc_final: 0.8482 (p) REVERT: 1 7 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5690 (mmtp) REVERT: 2 25 SER cc_start: 0.7258 (OUTLIER) cc_final: 0.6850 (p) REVERT: 2 27 THR cc_start: 0.7633 (t) cc_final: 0.7315 (m) REVERT: 3 16 MET cc_start: 0.5805 (mmt) cc_final: 0.5452 (tpt) REVERT: 4 7 MET cc_start: 0.4689 (mtm) cc_final: 0.4388 (ptm) REVERT: 6 30 PHE cc_start: 0.8022 (m-10) cc_final: 0.7803 (m-10) REVERT: 7 13 ASP cc_start: 0.7716 (t0) cc_final: 0.7483 (t0) REVERT: 8 26 MET cc_start: 0.8384 (ttm) cc_final: 0.8092 (ttm) REVERT: 0 17 GLU cc_start: 0.7741 (tt0) cc_final: 0.7536 (pt0) outliers start: 48 outliers final: 28 residues processed: 301 average time/residue: 1.1896 time to fit residues: 435.1513 Evaluate side-chains 296 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 35 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 6 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 10 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112357 restraints weight = 27381.491| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.05 r_work: 0.2888 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.323 27007 Z= 0.181 Angle : 0.788 16.359 37074 Z= 0.318 Chirality : 0.042 0.402 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.434 179.964 6149 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.10 % Allowed : 16.74 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2494 helix: 2.25 (0.12), residues: 1502 sheet: -0.88 (0.79), residues: 41 loop : 0.19 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 PHE 0.026 0.002 PHE L 41 TYR 0.021 0.002 TYR C 319 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 1326) hydrogen bonds : angle 4.29777 ( 3748) covalent geometry : bond 0.00420 (26957) covalent geometry : angle 0.78797 (37074) Misc. bond : bond 0.07149 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24535.74 seconds wall clock time: 423 minutes 2.00 seconds (25382.00 seconds total)