Starting phenix.real_space_refine on Sun Jun 22 14:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdu_37465/06_2025/8wdu_37465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdu_37465/06_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_37465/06_2025/8wdu_37465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdu_37465/06_2025/8wdu_37465.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdu_37465/06_2025/8wdu_37465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdu_37465/06_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-5710/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: 19.92, per 1000 atoms: 0.76 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: 7.93 Conformation dependent library (CDL) restraints added in 2.7 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: 1.92 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: 7.68 Time building geometry restraints manager: 9.21 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: 15.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 60.750 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.590 ------------------------------------------------------------------------------- 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 : 2.386 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: 1.2097 time to fit residues: 431.2091 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 : 2.306 ------------------------------------------------------------------------------- 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 = 37245.242| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.42 r_work: 0.2880 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 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 = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 : 2.428 Fit side-chains REVERT: L 208 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5349 (mppt) REVERT: H 237 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (t70) REVERT: H 259 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5735 (tp) REVERT: G 21 ILE cc_start: 0.7036 (mp) cc_final: 0.6775 (mt) REVERT: I 8 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5726 (pt) REVERT: J 27 THR cc_start: 0.7392 (m) cc_final: 0.7078 (t) REVERT: O 10 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.6113 (mt0) REVERT: P 13 GLN cc_start: 0.4278 (OUTLIER) cc_final: 0.3923 (tm-30) REVERT: P 23 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6798 (t) REVERT: P 27 THR cc_start: 0.8114 (m) cc_final: 0.7745 (m) REVERT: S 15 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6232 (ttp-110) REVERT: S 17 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7461 (mp) REVERT: S 41 GLU cc_start: 0.8712 (mp0) cc_final: 0.8490 (mp0) REVERT: 1 7 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5617 (mmtp) REVERT: 2 27 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7302 (m) REVERT: 3 66 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: 4 7 MET cc_start: 0.4008 (OUTLIER) cc_final: 0.3657 (mtm) REVERT: 4 14 GLU cc_start: 0.4015 (OUTLIER) cc_final: 0.3486 (mm-30) REVERT: 6 30 PHE cc_start: 0.7947 (m-10) cc_final: 0.7732 (m-10) outliers start: 59 outliers final: 17 residues processed: 314 average time/residue: 1.1587 time to fit residues: 433.1488 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 : 2.277 ------------------------------------------------------------------------------- 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: 0.8980 chunk 56 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 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: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.147748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109094 restraints weight = 35713.168| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.28 r_work: 0.2853 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.338 27007 Z= 0.237 Angle : 0.879 17.003 37074 Z= 0.356 Chirality : 0.046 0.406 3772 Planarity : 0.005 0.067 4374 Dihedral : 20.220 179.747 6155 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 1.99 (0.16), residues: 2494 helix: 2.14 (0.12), residues: 1497 sheet: -0.84 (0.76), residues: 41 loop : 0.17 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 9 HIS 0.008 0.002 HIS 0 37 PHE 0.030 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 0.05804 ( 1326) hydrogen bonds : angle 4.48399 ( 3748) covalent geometry : bond 0.00555 (26957) covalent geometry : angle 0.87859 (37074) Misc. bond : bond 0.07510 ( 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 350 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 275 time to evaluate : 2.365 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5308 (mppt) REVERT: H 75 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7753 (p) REVERT: H 259 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5787 (tp) REVERT: F 41 GLU cc_start: 0.8096 (tp30) cc_final: 0.7881 (tp30) REVERT: I 8 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5661 (pt) REVERT: J 24 GLN cc_start: 0.6652 (tt0) cc_final: 0.6255 (tp40) REVERT: J 27 THR cc_start: 0.7451 (m) cc_final: 0.7144 (t) REVERT: N 26 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.6041 (mtt) REVERT: P 24 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6406 (mp-120) REVERT: P 27 THR cc_start: 0.8082 (m) cc_final: 0.7697 (m) REVERT: Q 15 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7331 (mtp180) REVERT: S 15 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6257 (ttp-110) REVERT: S 17 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7489 (mp) REVERT: Y 59 PRO cc_start: 0.6765 (Cg_exo) cc_final: 0.6470 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5739 (mmtp) REVERT: 2 25 SER cc_start: 0.7179 (t) cc_final: 0.6698 (p) REVERT: 2 27 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7358 (m) REVERT: 4 14 GLU cc_start: 0.4062 (OUTLIER) cc_final: 0.3514 (mm-30) REVERT: 4 44 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7764 (ttm170) REVERT: 6 30 PHE cc_start: 0.7984 (m-10) cc_final: 0.7773 (m-10) REVERT: 7 13 ASP cc_start: 0.7816 (t0) cc_final: 0.7562 (t0) outliers start: 75 outliers final: 34 residues processed: 325 average time/residue: 1.2014 time to fit residues: 465.2487 Evaluate side-chains 303 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 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 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 17 ILE 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: 3.9990 chunk 41 optimal weight: 6.9990 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.148833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110308 restraints weight = 33861.033| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.23 r_work: 0.2892 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 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 = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.327 27007 Z= 0.194 Angle : 0.801 16.815 37074 Z= 0.324 Chirality : 0.043 0.410 3772 Planarity : 0.005 0.070 4374 Dihedral : 19.590 179.932 6155 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.36 % Allowed : 14.88 % Favored : 81.76 % 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: 2.08 (0.16), residues: 2494 helix: 2.21 (0.12), residues: 1496 sheet: -0.93 (0.76), residues: 41 loop : 0.20 (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 0.027 0.002 PHE L 41 TYR 0.022 0.002 TYR C 319 ARG 0.003 0.001 ARG 0 44 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 1326) hydrogen bonds : angle 4.34984 ( 3748) covalent geometry : bond 0.00453 (26957) covalent geometry : angle 0.80089 (37074) Misc. bond : bond 0.06896 ( 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 340 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 2.339 Fit side-chains REVERT: L 208 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5354 (mppt) REVERT: H 253 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6991 (mm-30) REVERT: H 259 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5741 (tp) REVERT: B 17 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: F 16 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6304 (mtt90) REVERT: I 8 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5612 (pt) REVERT: J 24 GLN cc_start: 0.6627 (tt0) cc_final: 0.6238 (tp40) REVERT: J 27 THR cc_start: 0.7442 (m) cc_final: 0.7142 (t) REVERT: P 23 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.6802 (t) REVERT: P 24 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6361 (mp-120) REVERT: P 27 THR cc_start: 0.8105 (m) cc_final: 0.7732 (m) REVERT: Q 15 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7315 (mtp180) REVERT: S 15 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6254 (ttp-110) REVERT: S 17 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7477 (mp) REVERT: Y 38 SER cc_start: 0.8776 (m) cc_final: 0.8559 (p) REVERT: Y 59 PRO cc_start: 0.6768 (Cg_exo) cc_final: 0.6488 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5733 (mmtp) REVERT: 2 25 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6764 (p) REVERT: 2 27 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7382 (m) REVERT: 4 11 THR cc_start: 0.5142 (OUTLIER) cc_final: 0.4635 (t) REVERT: 4 14 GLU cc_start: 0.4065 (OUTLIER) cc_final: 0.3514 (mm-30) REVERT: 6 30 PHE cc_start: 0.7963 (m-10) cc_final: 0.7750 (m-10) REVERT: 7 13 ASP cc_start: 0.7770 (t0) cc_final: 0.7518 (t0) outliers start: 72 outliers final: 35 residues processed: 319 average time/residue: 1.1775 time to fit residues: 447.3239 Evaluate side-chains 305 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 3.685 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 197 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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** O 10 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114987 restraints weight = 31314.629| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.04 r_work: 0.2973 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.288 27007 Z= 0.126 Angle : 0.694 16.662 37074 Z= 0.276 Chirality : 0.038 0.399 3772 Planarity : 0.004 0.067 4374 Dihedral : 18.376 179.931 6155 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.19 % Allowed : 15.95 % Favored : 81.86 % 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: 2.52 (0.16), residues: 2494 helix: 2.58 (0.12), residues: 1496 sheet: -0.86 (0.80), residues: 41 loop : 0.36 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 6 HIS 0.005 0.001 HIS R 19 PHE 0.019 0.001 PHE L 41 TYR 0.016 0.001 TYR M 193 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 1326) hydrogen bonds : angle 4.12637 ( 3748) covalent geometry : bond 0.00288 (26957) covalent geometry : angle 0.69439 (37074) Misc. bond : bond 0.05884 ( 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 323 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 2.330 Fit side-chains REVERT: L 3 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: L 211 GLU cc_start: 0.7994 (pt0) cc_final: 0.7700 (mt-10) REVERT: M 45 ASP cc_start: 0.8257 (t0) cc_final: 0.7848 (m-30) REVERT: H 48 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6738 (mtp180) REVERT: H 253 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6897 (mm-30) REVERT: H 259 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5699 (tp) REVERT: I 8 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5652 (pt) REVERT: J 27 THR cc_start: 0.7434 (m) cc_final: 0.7124 (t) REVERT: P 23 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6747 (t) REVERT: P 24 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6317 (mp-120) REVERT: P 27 THR cc_start: 0.8103 (m) cc_final: 0.7770 (m) REVERT: Q 15 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7267 (mtp180) REVERT: S 15 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.6206 (ttp-110) REVERT: S 17 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7447 (mp) REVERT: Y 38 SER cc_start: 0.8673 (m) cc_final: 0.8457 (p) REVERT: 1 7 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5662 (mmtp) REVERT: 2 25 SER cc_start: 0.7143 (t) cc_final: 0.6570 (p) REVERT: 2 27 THR cc_start: 0.7725 (t) cc_final: 0.7388 (m) REVERT: 3 16 MET cc_start: 0.5753 (mmt) cc_final: 0.5357 (tpt) REVERT: 4 11 THR cc_start: 0.5044 (OUTLIER) cc_final: 0.4572 (t) REVERT: 4 14 GLU cc_start: 0.4011 (OUTLIER) cc_final: 0.3553 (mm-30) REVERT: 8 26 MET cc_start: 0.8303 (ttm) cc_final: 0.8021 (ttm) outliers start: 47 outliers final: 27 residues processed: 311 average time/residue: 1.1446 time to fit residues: 425.2780 Evaluate side-chains 295 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 2.809 ------------------------------------------------------------------------------- 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 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 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 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 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: 6.9990 chunk 159 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.148460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110509 restraints weight = 32380.281| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.17 r_work: 0.2881 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 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 = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.006 0.344 27007 Z= 0.218 Angle : 0.840 16.902 37074 Z= 0.338 Chirality : 0.044 0.407 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.226 179.860 6151 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.03 % Allowed : 15.44 % Favored : 81.53 % 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: 2.14 (0.16), residues: 2494 helix: 2.24 (0.12), residues: 1505 sheet: -0.92 (0.77), residues: 41 loop : 0.25 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 9 9 HIS 0.009 0.002 HIS 0 37 PHE 0.030 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 0.05462 ( 1326) hydrogen bonds : angle 4.36303 ( 3748) covalent geometry : bond 0.00510 (26957) covalent geometry : angle 0.84026 (37074) Misc. bond : bond 0.07331 ( 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 334 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 2.370 Fit side-chains REVERT: C 260 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8495 (ttpt) REVERT: L 208 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5358 (mppt) REVERT: M 45 ASP cc_start: 0.8336 (t0) cc_final: 0.7895 (m-30) REVERT: H 48 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6774 (mtp180) REVERT: H 253 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7037 (mm-30) REVERT: H 259 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5785 (tp) REVERT: D 6 TRP cc_start: 0.5554 (p-90) cc_final: 0.5260 (p-90) REVERT: F 16 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6243 (mtt90) REVERT: I 8 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5627 (pt) REVERT: J 24 GLN cc_start: 0.6576 (tt0) cc_final: 0.6183 (tp40) REVERT: J 27 THR cc_start: 0.7442 (m) cc_final: 0.7128 (t) REVERT: P 24 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6345 (mp-120) REVERT: P 27 THR cc_start: 0.8076 (m) cc_final: 0.7721 (m) REVERT: Q 15 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: S 15 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5834 (ttp-170) REVERT: S 17 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7501 (mp) REVERT: Y 59 PRO cc_start: 0.6787 (Cg_exo) cc_final: 0.6527 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5743 (mmtp) REVERT: 1 18 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6591 (mp) REVERT: 2 25 SER cc_start: 0.7246 (OUTLIER) cc_final: 0.6813 (p) REVERT: 4 11 THR cc_start: 0.5085 (OUTLIER) cc_final: 0.4577 (t) REVERT: 4 14 GLU cc_start: 0.4002 (OUTLIER) cc_final: 0.3508 (mm-30) REVERT: 7 13 ASP cc_start: 0.7814 (t0) cc_final: 0.7581 (t0) outliers start: 65 outliers final: 34 residues processed: 318 average time/residue: 1.3049 time to fit residues: 494.4625 Evaluate side-chains 307 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 2.753 ------------------------------------------------------------------------------- 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 48 ARG 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 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 7 10 GLN 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108227 restraints weight = 35359.977| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.40 r_work: 0.2828 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 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 = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.335 27007 Z= 0.295 Angle : 0.965 16.691 37074 Z= 0.388 Chirality : 0.050 0.416 3772 Planarity : 0.006 0.067 4374 Dihedral : 20.144 179.835 6151 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.45 % Allowed : 15.21 % Favored : 81.34 % 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: 1.65 (0.16), residues: 2494 helix: 1.85 (0.12), residues: 1503 sheet: -1.05 (0.75), residues: 41 loop : 0.05 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP 9 9 HIS 0.011 0.003 HIS 0 37 PHE 0.033 0.003 PHE L 41 TYR 0.029 0.004 TYR C 319 ARG 0.006 0.001 ARG M 192 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 1326) hydrogen bonds : angle 4.54868 ( 3748) covalent geometry : bond 0.00696 (26957) covalent geometry : angle 0.96538 (37074) Misc. bond : bond 0.07551 ( 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 337 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 2.410 Fit side-chains revert: symmetry clash REVERT: C 260 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8467 (ttpt) REVERT: L 208 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5357 (mppt) REVERT: H 253 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6966 (mm-30) REVERT: H 259 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5767 (tp) REVERT: B 13 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6546 (tp40) REVERT: B 17 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: D 6 TRP cc_start: 0.5550 (p-90) cc_final: 0.5304 (p-90) REVERT: D 41 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: F 16 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6308 (mtt90) REVERT: I 8 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5660 (pt) REVERT: J 27 THR cc_start: 0.7436 (m) cc_final: 0.7130 (t) REVERT: P 23 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7065 (t) REVERT: P 24 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6393 (mp-120) REVERT: Q 15 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7343 (mtp180) REVERT: S 15 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6335 (ttp-110) REVERT: S 17 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7474 (mp) REVERT: Y 59 PRO cc_start: 0.6699 (Cg_exo) cc_final: 0.6450 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5759 (mmtp) REVERT: 1 18 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6624 (mp) REVERT: 2 25 SER cc_start: 0.7307 (OUTLIER) cc_final: 0.6966 (p) REVERT: 4 11 THR cc_start: 0.5010 (OUTLIER) cc_final: 0.4469 (t) REVERT: 4 14 GLU cc_start: 0.4045 (OUTLIER) cc_final: 0.3451 (mm-30) REVERT: 7 13 ASP cc_start: 0.7750 (t0) cc_final: 0.7473 (t0) outliers start: 74 outliers final: 37 residues processed: 317 average time/residue: 1.2455 time to fit residues: 467.2361 Evaluate side-chains 310 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 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 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 17 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 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 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 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 11 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 141 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.148915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111299 restraints weight = 28388.321| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.13 r_work: 0.2902 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.325 27007 Z= 0.174 Angle : 0.785 16.558 37074 Z= 0.316 Chirality : 0.042 0.406 3772 Planarity : 0.005 0.069 4374 Dihedral : 19.031 179.889 6151 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.61 % Allowed : 16.37 % Favored : 81.02 % 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: 2.03 (0.16), residues: 2494 helix: 2.17 (0.12), residues: 1504 sheet: -1.01 (0.77), residues: 41 loop : 0.17 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 6 HIS 0.010 0.002 HIS R 19 PHE 0.027 0.002 PHE L 41 TYR 0.020 0.002 TYR C 319 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.05159 ( 1326) hydrogen bonds : angle 4.31967 ( 3748) covalent geometry : bond 0.00404 (26957) covalent geometry : angle 0.78491 (37074) Misc. bond : bond 0.07088 ( 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 319 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 2.877 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5359 (mppt) REVERT: L 211 GLU cc_start: 0.8021 (pt0) cc_final: 0.7704 (mt-10) REVERT: H 253 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6863 (mm-30) REVERT: H 259 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5742 (tp) REVERT: B 13 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6524 (tp40) REVERT: F 16 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6231 (mtt90) REVERT: J 24 GLN cc_start: 0.6606 (tt0) cc_final: 0.6214 (tp40) REVERT: J 27 THR cc_start: 0.7408 (m) cc_final: 0.7105 (t) REVERT: P 23 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6794 (t) REVERT: P 24 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6325 (mp-120) REVERT: P 27 THR cc_start: 0.8054 (m) cc_final: 0.7729 (m) REVERT: Q 15 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: S 15 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6291 (ttp-110) REVERT: S 17 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7436 (mp) REVERT: Y 59 PRO cc_start: 0.6719 (Cg_exo) cc_final: 0.6458 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5706 (mmtp) REVERT: 1 18 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6593 (mp) REVERT: 2 25 SER cc_start: 0.7279 (OUTLIER) cc_final: 0.6907 (p) REVERT: 2 27 THR cc_start: 0.7680 (t) cc_final: 0.7369 (m) REVERT: 4 11 THR cc_start: 0.4900 (OUTLIER) cc_final: 0.4389 (t) REVERT: 4 14 GLU cc_start: 0.4074 (OUTLIER) cc_final: 0.3526 (mm-30) REVERT: 6 30 PHE cc_start: 0.7993 (m-10) cc_final: 0.7789 (m-10) REVERT: 7 13 ASP cc_start: 0.7776 (t0) cc_final: 0.7558 (t0) outliers start: 56 outliers final: 35 residues processed: 306 average time/residue: 1.4772 time to fit residues: 540.2045 Evaluate side-chains 300 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 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 B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 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 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 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 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 6 residue 10 LEU Chi-restraints excluded: chain 8 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: 0.9990 chunk 76 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 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 = 0.3705 r_free = 0.3705 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108168 restraints weight = 37800.003| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.41 r_work: 0.2837 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.335 27007 Z= 0.246 Angle : 0.889 16.641 37074 Z= 0.359 Chirality : 0.046 0.414 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.532 179.840 6149 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.03 % Allowed : 15.86 % Favored : 81.11 % 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: 1.80 (0.16), residues: 2494 helix: 1.98 (0.12), residues: 1503 sheet: -1.03 (0.76), residues: 41 loop : 0.09 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 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 0.05660 ( 1326) hydrogen bonds : angle 4.45941 ( 3748) covalent geometry : bond 0.00577 (26957) covalent geometry : angle 0.88893 (37074) Misc. bond : bond 0.07378 ( 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 324 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 259 time to evaluate : 2.289 Fit side-chains revert: symmetry clash REVERT: C 260 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8483 (ttpt) REVERT: L 208 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5320 (mppt) REVERT: H 253 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6959 (mm-30) REVERT: H 259 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5771 (tp) REVERT: B 13 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6511 (tp40) REVERT: D 6 TRP cc_start: 0.5528 (p-90) cc_final: 0.5268 (p-90) REVERT: F 16 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6304 (mtt90) REVERT: J 27 THR cc_start: 0.7425 (m) cc_final: 0.7115 (t) REVERT: P 23 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.6821 (t) REVERT: P 24 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6381 (mp-120) REVERT: P 27 THR cc_start: 0.8040 (m) cc_final: 0.7690 (m) REVERT: Q 15 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7301 (mtp180) REVERT: S 15 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6336 (ttp-110) REVERT: S 17 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7464 (mp) REVERT: Y 41 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: Y 59 PRO cc_start: 0.6706 (Cg_exo) cc_final: 0.6445 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5744 (mmtp) REVERT: 1 18 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6590 (mp) REVERT: 2 25 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6933 (p) REVERT: 2 27 THR cc_start: 0.7712 (t) cc_final: 0.7375 (m) REVERT: 7 13 ASP cc_start: 0.7806 (t0) cc_final: 0.7551 (t0) outliers start: 65 outliers final: 40 residues processed: 307 average time/residue: 1.2129 time to fit residues: 441.6037 Evaluate side-chains 308 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 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 B residue 13 GLN 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 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 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 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 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 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 4 residue 35 ILE 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.148835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109362 restraints weight = 31948.211| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.37 r_work: 0.2872 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1606 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= 0.177 Angle : 0.796 16.581 37074 Z= 0.321 Chirality : 0.042 0.407 3772 Planarity : 0.005 0.069 4374 Dihedral : 18.885 179.916 6149 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.57 % Allowed : 16.51 % Favored : 80.92 % 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: 1.99 (0.16), residues: 2494 helix: 2.15 (0.12), residues: 1503 sheet: -0.99 (0.77), residues: 41 loop : 0.14 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 6 HIS 0.012 0.002 HIS R 19 PHE 0.026 0.002 PHE L 41 TYR 0.022 0.002 TYR C 319 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 1326) hydrogen bonds : angle 4.33658 ( 3748) covalent geometry : bond 0.00412 (26957) covalent geometry : angle 0.79581 (37074) Misc. bond : bond 0.06963 ( 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 310 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5317 (mppt) REVERT: L 211 GLU cc_start: 0.8037 (pt0) cc_final: 0.7721 (mt-10) REVERT: H 253 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6873 (mm-30) REVERT: H 259 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5732 (tp) REVERT: B 13 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6547 (tp40) REVERT: F 16 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6235 (mtt90) REVERT: J 24 GLN cc_start: 0.6569 (tt0) cc_final: 0.6178 (tp40) REVERT: J 27 THR cc_start: 0.7377 (m) cc_final: 0.7058 (t) REVERT: P 23 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6756 (t) REVERT: P 24 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6343 (mp-120) REVERT: P 27 THR cc_start: 0.8061 (m) cc_final: 0.7728 (m) REVERT: Q 15 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7256 (mtp180) REVERT: R 10 LEU cc_start: 0.4083 (OUTLIER) cc_final: 0.3592 (tp) REVERT: S 15 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6273 (ttp-110) REVERT: S 17 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7428 (mp) REVERT: Y 59 PRO cc_start: 0.6687 (Cg_exo) cc_final: 0.6413 (Cg_endo) REVERT: 1 7 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5703 (mmtp) REVERT: 1 18 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6564 (mp) REVERT: 2 25 SER cc_start: 0.7224 (OUTLIER) cc_final: 0.6851 (p) REVERT: 2 27 THR cc_start: 0.7656 (t) cc_final: 0.7340 (m) REVERT: 7 13 ASP cc_start: 0.7755 (t0) cc_final: 0.7520 (t0) outliers start: 55 outliers final: 37 residues processed: 299 average time/residue: 1.3066 time to fit residues: 474.4305 Evaluate side-chains 304 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 307 CYS 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 B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 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 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 R residue 10 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 10 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** 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 = 0.3730 r_free = 0.3730 target = 0.149469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111860 restraints weight = 27393.243| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.99 r_work: 0.2926 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.313 27007 Z= 0.164 Angle : 0.761 16.322 37074 Z= 0.308 Chirality : 0.041 0.402 3772 Planarity : 0.005 0.068 4374 Dihedral : 18.279 179.977 6149 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.15 % Allowed : 16.88 % Favored : 80.97 % 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: 1506 sheet: -0.95 (0.78), residues: 41 loop : 0.20 (0.21), residues: 947 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 0.024 0.002 PHE L 41 TYR 0.020 0.002 TYR C 319 ARG 0.004 0.000 ARG 9 15 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 1326) hydrogen bonds : angle 4.27751 ( 3748) covalent geometry : bond 0.00381 (26957) covalent geometry : angle 0.76086 (37074) Misc. bond : bond 0.06651 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27256.29 seconds wall clock time: 470 minutes 53.79 seconds (28253.79 seconds total)