Starting phenix.real_space_refine on Sat May 24 22:23:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdv_37466/05_2025/8wdv_37466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdv_37466/05_2025/8wdv_37466.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/8wdv_37466/05_2025/8wdv_37466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdv_37466/05_2025/8wdv_37466.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdv_37466/05_2025/8wdv_37466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdv_37466/05_2025/8wdv_37466.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= 0.006 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 8 9.91 5 Fe 5 7.16 5 P 20 5.49 5 Mg 37 5.21 5 S 101 5.16 5 C 18058 2.51 5 N 3539 2.21 5 O 4493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26261 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: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 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: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} 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: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 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: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "S" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 412 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 412 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 349 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Y" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 511 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 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: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 489 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 56} 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: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 341 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 38} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "8" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 252 Unusual residues: {' CA': 1, ' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 433 Unusual residues: {'BCL': 2, 'BPH': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 72 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: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 629 Unusual residues: {' CA': 1, ' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 3, 'CRT': 1, 'LDA': 1, 'LMT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 11 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 164 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" 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: "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: 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: "K" 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: "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: 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: "Q" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 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: 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: "T" 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: "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: 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: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 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: 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: "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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 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: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" 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: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 19.08, per 1000 atoms: 0.73 Number of scatterers: 26261 At special positions: 0 Unit cell: (132.02, 122.18, 135.3, 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 8 19.99 S 101 16.00 P 20 15.00 Mg 37 11.99 O 4493 8.00 N 3539 7.00 C 18058 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: 13.16 Conformation dependent library (CDL) restraints added in 3.1 seconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 10 sheets defined 67.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 105 through 110 removed outlier: 4.150A pdb=" N ASN C 108 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS C 110 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 141 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 151 through 157 removed outlier: 4.116A 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: 3.709A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 244 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 263 through 283 removed outlier: 3.788A 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 306 through 312 removed outlier: 4.170A pdb=" N CYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) 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: 3.631A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.618A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 257 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.683A pdb=" N TRP L 268 " --> pdb=" O GLY L 264 " (cutoff:3.500A) removed outlier: 4.065A 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: 3.588A 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 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.539A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 removed outlier: 3.588A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 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: 3.586A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.839A 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 'H' and resid 10 through 35 Processing helix chain 'H' and resid 43 through 49 removed outlier: 3.519A pdb=" N SER H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) 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 215 through 222 removed outlier: 3.769A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 222 " --> pdb=" O PHE H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 250 removed outlier: 3.575A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.064A 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 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: 3.598A 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 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 39 Processing helix chain 'G' and resid 11 through 44 removed outlier: 3.531A pdb=" N ILE G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 4.186A pdb=" N ILE I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 39 Processing helix chain 'J' and resid 16 through 44 Processing helix chain 'K' and resid 7 through 12 removed outlier: 4.418A pdb=" N ILE K 11 " --> pdb=" O LYS K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 39 removed outlier: 3.584A pdb=" N VAL K 19 " --> pdb=" O ARG K 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 44 removed outlier: 3.886A pdb=" N GLN N 16 " --> pdb=" O GLU N 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.619A 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 'O' and resid 40 through 43 removed outlier: 3.693A pdb=" N ASN O 43 " --> pdb=" O PRO O 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 40 through 43' Processing helix chain 'P' and resid 11 through 44 Processing helix chain 'Q' and resid 6 through 11 Processing helix chain 'Q' and resid 13 through 39 removed outlier: 3.545A pdb=" N VAL Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 44 Processing helix chain 'S' and resid 4 through 6 No H-bonds generated for 'chain 'S' and resid 4 through 6' Processing helix chain 'S' and resid 7 through 12 removed outlier: 3.648A pdb=" N LEU S 11 " --> pdb=" O LYS S 7 " (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 2 through 11 removed outlier: 4.466A pdb=" N TRP U 6 " --> pdb=" O PRO U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 39 Processing helix chain 'V' and resid 11 through 44 Processing helix chain 'W' and resid 4 through 11 removed outlier: 4.053A pdb=" N LYS W 7 " --> pdb=" O ASP W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 39 Processing helix chain 'X' and resid 11 through 44 Processing helix chain 'Y' and resid 4 through 11 removed outlier: 3.542A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 39 Processing helix chain 'Z' and resid 11 through 44 Processing helix chain '1' and resid 5 through 11 Processing helix chain '1' and resid 13 through 39 Processing helix chain '2' and resid 11 through 44 Processing helix chain '3' and resid 6 through 12 Processing helix chain '3' and resid 13 through 39 removed outlier: 3.666A pdb=" N SER 3 39 " --> pdb=" O MET 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 47 Processing helix chain '4' and resid 11 through 44 removed outlier: 3.591A pdb=" N GLN 4 16 " --> pdb=" O GLU 4 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 4 21 " --> pdb=" O GLU 4 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 4 24 " --> pdb=" O GLY 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 10 removed outlier: 4.206A pdb=" N TRP 5 9 " --> pdb=" O HIS 5 6 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 39 Processing helix chain '5' and resid 40 through 43 removed outlier: 3.667A 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 removed outlier: 3.732A pdb=" N GLU 6 17 " --> pdb=" O GLN 6 13 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE 6 18 " --> pdb=" O GLU 6 14 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 11 removed outlier: 3.960A pdb=" N TRP 7 9 " --> pdb=" O HIS 7 6 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 39 removed outlier: 3.596A pdb=" N LEU 7 18 " --> pdb=" O PRO 7 14 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 44 removed outlier: 3.686A pdb=" N ILE 8 21 " --> pdb=" O GLU 8 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN 8 24 " --> pdb=" O GLY 8 20 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA 8 28 " --> pdb=" O GLN 8 24 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 11 Processing helix chain '9' and resid 13 through 39 removed outlier: 3.725A pdb=" N VAL 9 19 " --> pdb=" O ARG 9 15 " (cutoff:3.500A) 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 'L' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA7, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.830A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR H 181 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL H 172 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE H 179 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.567A pdb=" N VAL H 156 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR H 155 " --> pdb=" O VAL H 209 " (cutoff:3.500A) 1331 hydrogen bonds defined for protein. 3726 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: 7.26 Time building geometry restraints manager: 13.99 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: 9334 1.38 - 1.56: 17198 1.56 - 1.75: 40 1.75 - 1.93: 190 1.93 - 2.11: 156 Bond restraints: 26918 Sorted by residual: bond pdb=" CA7 CDL M 409 " pdb=" OA8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CA7 CDL M 411 " pdb=" OA8 CDL M 411 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CA7 CDL M 412 " pdb=" OA8 CDL M 412 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" CB7 CDL M 412 " pdb=" OB8 CDL M 412 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.14e+02 bond pdb=" CB7 CDL D 502 " pdb=" OB8 CDL D 502 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 ... (remaining 26913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 35599 5.00 - 10.00: 1293 10.00 - 15.00: 95 15.00 - 20.00: 14 20.00 - 25.00: 13 Bond angle restraints: 37014 Sorted by residual: angle pdb=" C40 CRT M 407 " pdb=" C38 CRT M 407 " pdb=" O2 CRT M 407 " ideal model delta sigma weight residual 111.40 86.40 25.00 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C2 CRT K 101 " pdb=" C1 CRT K 101 " pdb=" C4 CRT K 101 " ideal model delta sigma weight residual 110.24 85.73 24.51 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C39 CRT V 103 " pdb=" C38 CRT V 103 " pdb=" O2 CRT V 103 " ideal model delta sigma weight residual 111.76 87.28 24.48 3.00e+00 1.11e-01 6.66e+01 angle pdb=" C40 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.40 87.77 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" C2 CRT Q 101 " pdb=" C1 CRT Q 101 " pdb=" C4 CRT Q 101 " ideal model delta sigma weight residual 110.24 86.63 23.61 3.00e+00 1.11e-01 6.19e+01 ... (remaining 37009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 14437 35.99 - 71.98: 656 71.98 - 107.97: 165 107.97 - 143.96: 62 143.96 - 179.94: 9 Dihedral angle restraints: 15329 sinusoidal: 7933 harmonic: 7396 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 -78.00 -102.00 1 6.00e+00 2.78e-02 3.22e+02 dihedral pdb=" C1 BCL 0 102 " pdb=" CGA BCL 0 102 " pdb=" O2A BCL 0 102 " pdb=" CBA BCL 0 102 " ideal model delta sinusoidal sigma weight residual -180.00 -79.62 -100.38 1 6.00e+00 2.78e-02 3.15e+02 dihedral pdb=" C1 BCL M 404 " pdb=" C2 BCL M 404 " pdb=" C3 BCL M 404 " pdb=" C5 BCL M 404 " ideal model delta sinusoidal sigma weight residual -180.00 -0.06 -179.94 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3298 0.077 - 0.153: 373 0.153 - 0.230: 55 0.230 - 0.307: 23 0.307 - 0.383: 3 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CBD BCL M 404 " pdb=" CAD BCL M 404 " pdb=" CGD BCL M 404 " pdb=" CHA BCL M 404 " both_signs ideal model delta sigma weight residual False 2.62 3.01 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBD BCL T 101 " pdb=" CAD BCL T 101 " pdb=" CGD BCL T 101 " pdb=" CHA BCL T 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CBD BCL X 102 " pdb=" CAD BCL X 102 " pdb=" CGD BCL X 102 " pdb=" CHA BCL X 102 " both_signs ideal model delta sigma weight residual False 2.62 2.31 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 3749 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.387 3.00e-02 1.11e+03 3.17e-01 5.58e+02 pdb=" CBA BCL K 102 " -0.155 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.088 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.102 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.556 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 102 " 0.359 3.00e-02 1.11e+03 3.01e-01 5.04e+02 pdb=" CBA BCL 0 102 " 0.061 3.00e-02 1.11e+03 pdb=" CGA BCL 0 102 " -0.071 3.00e-02 1.11e+03 pdb=" O1A BCL 0 102 " 0.183 3.00e-02 1.11e+03 pdb=" O2A BCL 0 102 " -0.532 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 101 " 0.357 3.00e-02 1.11e+03 3.00e-01 4.98e+02 pdb=" CBA BCL T 101 " 0.055 3.00e-02 1.11e+03 pdb=" CGA BCL T 101 " -0.070 3.00e-02 1.11e+03 pdb=" O1A BCL T 101 " 0.186 3.00e-02 1.11e+03 pdb=" O2A BCL T 101 " -0.528 3.00e-02 1.11e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 4 2.08 - 2.78: 5582 2.78 - 3.49: 36042 3.49 - 4.19: 74566 4.19 - 4.90: 125696 Nonbonded interactions: 241890 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.372 3.040 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 402 " model vdw 1.996 2.260 nonbonded pdb="MG MG C 405 " pdb=" O HOH M 501 " model vdw 2.039 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 402 " model vdw 2.069 2.340 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.084 2.170 ... (remaining 241885 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 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '2' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '4' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '6' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'B' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'E' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'G' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'J' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'N' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'P' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'R' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'T' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'V' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'X' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'Z' and (resid 10 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) } ncs_group { reference = (chain '1' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain '5' and resid 6 through 46) selection = (chain '7' and resid 6 through 46) selection = (chain '9' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'A' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'I' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'K' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'O' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) selection = (chain 'Q' and (resid 6 or (resid 7 and (name N or name CA or name C or name O o \ r name CB )) or resid 8 through 46)) } ncs_group { reference = (chain 'D' and resid 2 through 50) selection = (chain 'F' and resid 2 through 50) selection = (chain 'S' and resid 2 through 50) selection = (chain 'U' and resid 2 through 50) selection = (chain 'W' and resid 2 through 50) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.050 Extract box with map and model: 1.140 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 63.510 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 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 0.516 26968 Z= 1.479 Angle : 1.861 25.003 37014 Z= 0.797 Chirality : 0.056 0.383 3752 Planarity : 0.018 0.317 4384 Dihedral : 22.604 179.944 10537 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.77 % Allowed : 3.82 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.38 (0.16), residues: 2500 helix: 2.32 (0.12), residues: 1477 sheet: -0.51 (1.22), residues: 20 loop : 0.60 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 9 HIS 0.008 0.001 HIS L 159 PHE 0.020 0.001 PHE L 170 TYR 0.018 0.002 TYR C 200 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.18214 ( 1329) hydrogen bonds : angle 5.95804 ( 3726) covalent geometry : bond 0.01854 (26918) covalent geometry : angle 1.86073 (37014) Misc. bond : bond 0.28756 ( 50) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 391 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.9418 (mtp) cc_final: 0.9082 (mtp) REVERT: C 308 MET cc_start: 0.9514 (tpp) cc_final: 0.9252 (tpp) REVERT: L 218 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8480 (mt-10) REVERT: M 33 LYS cc_start: 0.7803 (tppp) cc_final: 0.7267 (tppt) REVERT: M 124 MET cc_start: 0.9200 (mmp) cc_final: 0.8996 (mmm) REVERT: H 205 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7371 (mttt) REVERT: B 12 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 16 GLN cc_start: 0.7880 (tp40) cc_final: 0.7645 (tp40) REVERT: I 7 LYS cc_start: 0.8502 (mttt) cc_final: 0.8140 (mmtp) REVERT: O 15 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7939 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8167 (t0) cc_final: 0.7900 (t0) REVERT: S 16 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7598 (mtt180) REVERT: U 5 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8565 (mm) REVERT: W 16 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7462 (tpp80) REVERT: Y 5 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8514 (tt) REVERT: Y 6 TRP cc_start: 0.8898 (p-90) cc_final: 0.8402 (p-90) REVERT: Z 13 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: 3 12 PHE cc_start: 0.8006 (m-80) cc_final: 0.7779 (m-80) REVERT: 7 11 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5721 (tt) outliers start: 38 outliers final: 15 residues processed: 415 average time/residue: 1.3495 time to fit residues: 651.1934 Evaluate side-chains 371 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 352 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR 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 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN E 24 GLN J 24 GLN N 24 GLN P 13 GLN P 24 GLN T 24 GLN V 24 GLN 7 43 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082682 restraints weight = 32823.698| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.29 r_work: 0.2805 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.285 26968 Z= 0.140 Angle : 0.761 16.990 37014 Z= 0.292 Chirality : 0.041 0.240 3752 Planarity : 0.004 0.049 4384 Dihedral : 19.850 179.970 6010 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.19 % Allowed : 8.47 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.80 (0.17), residues: 2500 helix: 2.73 (0.12), residues: 1494 sheet: -0.14 (0.93), residues: 30 loop : 0.62 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.005 0.001 HIS N 37 PHE 0.017 0.001 PHE H 19 TYR 0.017 0.001 TYR M 193 ARG 0.004 0.000 ARG K 16 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 1329) hydrogen bonds : angle 4.13461 ( 3726) covalent geometry : bond 0.00333 (26918) covalent geometry : angle 0.76056 (37014) Misc. bond : bond 0.05807 ( 50) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 2.359 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9563 (mmt) cc_final: 0.9227 (mmt) REVERT: L 208 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7121 (tmtp) REVERT: M 33 LYS cc_start: 0.7888 (tppp) cc_final: 0.7086 (mptt) REVERT: M 75 MET cc_start: 0.9445 (mtt) cc_final: 0.9167 (mtp) REVERT: H 205 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7022 (mptt) REVERT: A 13 ASP cc_start: 0.8555 (t0) cc_final: 0.7964 (t0) REVERT: B 16 GLN cc_start: 0.7491 (tp40) cc_final: 0.7120 (mp10) REVERT: F 41 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: G 14 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6348 (mt-10) REVERT: I 7 LYS cc_start: 0.8510 (mttt) cc_final: 0.8007 (mmtp) REVERT: J 44 ARG cc_start: 0.8804 (ttm170) cc_final: 0.8536 (ttm170) REVERT: O 15 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7838 (ttt-90) REVERT: P 26 MET cc_start: 0.8500 (ttp) cc_final: 0.8153 (ttp) REVERT: Q 13 ASP cc_start: 0.8244 (t0) cc_final: 0.7972 (t0) REVERT: R 11 THR cc_start: 0.8164 (p) cc_final: 0.7830 (t) REVERT: R 14 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7654 (tt0) REVERT: S 16 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7759 (mtt180) REVERT: U 5 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8654 (mm) REVERT: U 16 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7395 (mtm110) REVERT: W 16 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7185 (tpp80) REVERT: Y 6 TRP cc_start: 0.8578 (p-90) cc_final: 0.8003 (p-90) REVERT: Z 17 GLU cc_start: 0.7995 (tt0) cc_final: 0.7626 (tm-30) REVERT: 3 12 PHE cc_start: 0.7478 (m-80) cc_final: 0.7224 (m-80) REVERT: 4 17 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: 4 35 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8898 (mt) REVERT: 8 24 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7446 (tp40) REVERT: 8 44 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8578 (ttm-80) outliers start: 47 outliers final: 15 residues processed: 390 average time/residue: 1.2689 time to fit residues: 578.1405 Evaluate side-chains 362 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 342 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 11 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 150 HIS L 207 GLN N 24 GLN P 13 GLN V 24 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079874 restraints weight = 32613.604| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.31 r_work: 0.2758 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.318 26968 Z= 0.188 Angle : 0.739 17.980 37014 Z= 0.293 Chirality : 0.041 0.221 3752 Planarity : 0.004 0.050 4384 Dihedral : 17.842 179.808 5997 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.37 % Allowed : 10.06 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.70 (0.16), residues: 2500 helix: 2.66 (0.12), residues: 1497 sheet: -0.17 (0.90), residues: 30 loop : 0.52 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.008 0.002 HIS L 159 PHE 0.019 0.002 PHE H 19 TYR 0.021 0.002 TYR C 200 ARG 0.008 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 1329) hydrogen bonds : angle 4.12607 ( 3726) covalent geometry : bond 0.00449 (26918) covalent geometry : angle 0.73949 (37014) Misc. bond : bond 0.06717 ( 50) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9554 (mmt) cc_final: 0.9292 (mmt) REVERT: C 308 MET cc_start: 0.9542 (tpp) cc_final: 0.9019 (tpp) REVERT: L 208 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7116 (tmtp) REVERT: M 33 LYS cc_start: 0.7940 (tppp) cc_final: 0.7157 (mptt) REVERT: H 101 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7280 (mm-30) REVERT: H 205 LYS cc_start: 0.7581 (mtmt) cc_final: 0.7022 (mptt) REVERT: A 13 ASP cc_start: 0.8574 (t0) cc_final: 0.7997 (t0) REVERT: B 16 GLN cc_start: 0.7442 (tp40) cc_final: 0.6952 (mp10) REVERT: F 41 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: G 14 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6350 (mt-10) REVERT: G 28 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7234 (tpt) REVERT: I 7 LYS cc_start: 0.8498 (mttt) cc_final: 0.8017 (mmtp) REVERT: J 12 GLU cc_start: 0.7850 (tt0) cc_final: 0.7580 (tt0) REVERT: O 15 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.8058 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8209 (t0) cc_final: 0.7951 (t0) REVERT: Q 16 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.8094 (mtt-85) REVERT: S 16 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7739 (mtt180) REVERT: U 5 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8640 (mm) REVERT: W 7 LYS cc_start: 0.8424 (mttm) cc_final: 0.8209 (mttm) REVERT: W 16 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7187 (tpp80) REVERT: X 34 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8974 (mt) REVERT: Y 5 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8348 (tt) REVERT: Y 6 TRP cc_start: 0.8568 (p-90) cc_final: 0.8017 (p-90) REVERT: Z 11 THR cc_start: 0.8378 (p) cc_final: 0.7805 (p) REVERT: Z 17 GLU cc_start: 0.8093 (tt0) cc_final: 0.7756 (tm-30) REVERT: 3 12 PHE cc_start: 0.7568 (m-80) cc_final: 0.7230 (m-80) REVERT: 4 7 MET cc_start: 0.5540 (ttm) cc_final: 0.5257 (ttp) REVERT: 4 17 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: 4 35 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8896 (mt) REVERT: 5 6 HIS cc_start: 0.5537 (OUTLIER) cc_final: 0.5262 (t-90) REVERT: 8 24 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7410 (tp40) outliers start: 51 outliers final: 26 residues processed: 370 average time/residue: 1.3569 time to fit residues: 583.1123 Evaluate side-chains 376 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 341 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 5 residue 39 SER Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 207 GLN B 24 GLN N 24 GLN P 13 GLN 2 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077237 restraints weight = 32905.690| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.30 r_work: 0.2707 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.339 26968 Z= 0.339 Angle : 0.875 16.283 37014 Z= 0.346 Chirality : 0.048 0.206 3752 Planarity : 0.005 0.056 4384 Dihedral : 18.275 179.956 5997 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.89 % Allowed : 10.24 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2500 helix: 2.29 (0.12), residues: 1507 sheet: -0.50 (0.89), residues: 31 loop : 0.38 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 252 HIS 0.010 0.002 HIS P 37 PHE 0.023 0.002 PHE L 170 TYR 0.023 0.003 TYR C 200 ARG 0.009 0.001 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 1329) hydrogen bonds : angle 4.32278 ( 3726) covalent geometry : bond 0.00816 (26918) covalent geometry : angle 0.87548 (37014) Misc. bond : bond 0.07688 ( 50) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 348 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 308 MET cc_start: 0.9512 (tpp) cc_final: 0.9182 (tpp) REVERT: L 208 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7254 (tmtp) REVERT: M 33 LYS cc_start: 0.8023 (tppp) cc_final: 0.7254 (mptt) REVERT: M 124 MET cc_start: 0.9175 (mmm) cc_final: 0.8917 (mmm) REVERT: H 101 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7323 (mm-30) REVERT: H 205 LYS cc_start: 0.7541 (mtmt) cc_final: 0.6985 (mptt) REVERT: A 13 ASP cc_start: 0.8583 (t0) cc_final: 0.8203 (t0) REVERT: B 12 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7930 (mm-30) REVERT: B 16 GLN cc_start: 0.7531 (tp40) cc_final: 0.7102 (tp40) REVERT: F 41 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: G 14 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6336 (mt-10) REVERT: G 23 THR cc_start: 0.8410 (m) cc_final: 0.8198 (m) REVERT: G 28 MET cc_start: 0.8268 (mtp) cc_final: 0.7643 (tpt) REVERT: I 7 LYS cc_start: 0.8469 (mttt) cc_final: 0.8031 (mmtp) REVERT: O 15 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.7822 (ttt-90) REVERT: P 10 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (mp) REVERT: Q 13 ASP cc_start: 0.8164 (t0) cc_final: 0.7926 (t0) REVERT: S 16 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7744 (mtt180) REVERT: W 4 ASP cc_start: 0.7459 (t0) cc_final: 0.7216 (t0) REVERT: W 7 LYS cc_start: 0.8673 (mttm) cc_final: 0.8383 (mttm) REVERT: W 16 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7209 (tpp80) REVERT: Y 5 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8423 (tt) REVERT: Y 6 TRP cc_start: 0.8630 (p-90) cc_final: 0.7965 (p-90) REVERT: Z 17 GLU cc_start: 0.8092 (tt0) cc_final: 0.7529 (tm-30) REVERT: 3 12 PHE cc_start: 0.7722 (m-80) cc_final: 0.7393 (m-80) REVERT: 4 7 MET cc_start: 0.5472 (ttm) cc_final: 0.5194 (ttp) REVERT: 4 17 GLU cc_start: 0.8026 (tt0) cc_final: 0.7755 (tm-30) REVERT: 5 8 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7235 (mp) outliers start: 62 outliers final: 34 residues processed: 372 average time/residue: 1.4156 time to fit residues: 609.1289 Evaluate side-chains 380 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 8 ILE Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 5 residue 39 SER Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 27 VAL Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 52 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.080862 restraints weight = 32625.438| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.31 r_work: 0.2768 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.294 26968 Z= 0.151 Angle : 0.690 14.711 37014 Z= 0.274 Chirality : 0.039 0.151 3752 Planarity : 0.004 0.049 4384 Dihedral : 17.245 179.979 5993 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.23 % Allowed : 11.36 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.64 (0.16), residues: 2500 helix: 2.62 (0.12), residues: 1503 sheet: -0.50 (0.91), residues: 31 loop : 0.48 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.010 0.001 HIS 8 19 PHE 0.017 0.001 PHE H 19 TYR 0.019 0.002 TYR M 193 ARG 0.009 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 1329) hydrogen bonds : angle 4.03799 ( 3726) covalent geometry : bond 0.00356 (26918) covalent geometry : angle 0.68993 (37014) Misc. bond : bond 0.06466 ( 50) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 351 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9510 (mmt) cc_final: 0.9111 (mmt) REVERT: C 308 MET cc_start: 0.9506 (tpp) cc_final: 0.9172 (tpp) REVERT: L 208 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7185 (tmtp) REVERT: M 33 LYS cc_start: 0.8029 (tppp) cc_final: 0.7289 (mptt) REVERT: M 124 MET cc_start: 0.9141 (mmm) cc_final: 0.8673 (mmp) REVERT: H 101 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7303 (mm-30) REVERT: H 205 LYS cc_start: 0.7518 (mtmt) cc_final: 0.6939 (mptt) REVERT: A 13 ASP cc_start: 0.8532 (t0) cc_final: 0.8078 (t0) REVERT: B 16 GLN cc_start: 0.7509 (tp40) cc_final: 0.6953 (mp10) REVERT: F 41 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: G 14 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6289 (mt-10) REVERT: I 7 LYS cc_start: 0.8456 (mttt) cc_final: 0.7898 (mmtp) REVERT: J 12 GLU cc_start: 0.7828 (tt0) cc_final: 0.7575 (tt0) REVERT: O 15 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7960 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8221 (t0) cc_final: 0.7979 (t0) REVERT: S 16 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7769 (mtt180) REVERT: T 17 GLU cc_start: 0.8562 (tt0) cc_final: 0.8341 (tt0) REVERT: V 24 GLN cc_start: 0.8531 (tt0) cc_final: 0.7855 (mt0) REVERT: W 7 LYS cc_start: 0.8599 (mttm) cc_final: 0.8393 (mttm) REVERT: Y 6 TRP cc_start: 0.8605 (p-90) cc_final: 0.7975 (p-90) REVERT: Y 11 LEU cc_start: 0.8270 (mt) cc_final: 0.7991 (mt) REVERT: Z 17 GLU cc_start: 0.8072 (tt0) cc_final: 0.7751 (tm-30) REVERT: 3 12 PHE cc_start: 0.7525 (m-80) cc_final: 0.7234 (m-80) REVERT: 4 7 MET cc_start: 0.5386 (ttm) cc_final: 0.5106 (ttp) REVERT: 4 17 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: 5 6 HIS cc_start: 0.5568 (OUTLIER) cc_final: 0.5335 (t70) outliers start: 48 outliers final: 24 residues processed: 371 average time/residue: 1.3705 time to fit residues: 592.4634 Evaluate side-chains 370 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 342 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 5 residue 39 SER Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 209 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.081487 restraints weight = 32606.620| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.27 r_work: 0.2775 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.286 26968 Z= 0.151 Angle : 0.679 14.545 37014 Z= 0.272 Chirality : 0.039 0.150 3752 Planarity : 0.004 0.049 4384 Dihedral : 16.814 179.965 5993 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.33 % Allowed : 11.87 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.72 (0.16), residues: 2500 helix: 2.73 (0.12), residues: 1499 sheet: -0.64 (0.81), residues: 35 loop : 0.46 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.011 0.001 HIS 8 19 PHE 0.017 0.001 PHE H 19 TYR 0.019 0.002 TYR M 193 ARG 0.008 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 1329) hydrogen bonds : angle 3.99381 ( 3726) covalent geometry : bond 0.00358 (26918) covalent geometry : angle 0.67924 (37014) Misc. bond : bond 0.06312 ( 50) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 354 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9551 (mmt) cc_final: 0.9200 (mmt) REVERT: C 308 MET cc_start: 0.9499 (tpp) cc_final: 0.9160 (tpp) REVERT: M 33 LYS cc_start: 0.7966 (tppp) cc_final: 0.7235 (mptt) REVERT: M 75 MET cc_start: 0.9489 (mtt) cc_final: 0.9178 (mtp) REVERT: M 124 MET cc_start: 0.9123 (mmm) cc_final: 0.8628 (mmp) REVERT: H 101 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7213 (mm-30) REVERT: H 204 LYS cc_start: 0.7473 (mttp) cc_final: 0.6957 (mptt) REVERT: H 205 LYS cc_start: 0.7513 (mtmt) cc_final: 0.6911 (mptt) REVERT: A 13 ASP cc_start: 0.8527 (t0) cc_final: 0.8021 (t0) REVERT: B 16 GLN cc_start: 0.7469 (tp40) cc_final: 0.6910 (mp10) REVERT: F 41 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: G 14 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6268 (mt-10) REVERT: G 28 MET cc_start: 0.8093 (mtp) cc_final: 0.7252 (tpt) REVERT: I 7 LYS cc_start: 0.8472 (mttt) cc_final: 0.7880 (mmtp) REVERT: J 12 GLU cc_start: 0.7841 (tt0) cc_final: 0.7588 (tt0) REVERT: N 14 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6104 (mm-30) REVERT: O 15 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7718 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8177 (t0) cc_final: 0.7935 (t0) REVERT: S 16 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7657 (mtt180) REVERT: V 24 GLN cc_start: 0.8548 (tt0) cc_final: 0.7830 (mt0) REVERT: W 4 ASP cc_start: 0.7370 (t0) cc_final: 0.7153 (t0) REVERT: W 7 LYS cc_start: 0.8548 (mttm) cc_final: 0.8200 (mttm) REVERT: W 19 ILE cc_start: 0.8689 (mm) cc_final: 0.8403 (mt) REVERT: Y 6 TRP cc_start: 0.8553 (p-90) cc_final: 0.8050 (p-90) REVERT: Y 11 LEU cc_start: 0.8217 (mt) cc_final: 0.7950 (mt) REVERT: Z 17 GLU cc_start: 0.8074 (tt0) cc_final: 0.7461 (tt0) REVERT: 4 7 MET cc_start: 0.5321 (ttm) cc_final: 0.5060 (ttp) REVERT: 4 17 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7701 (tm-30) outliers start: 50 outliers final: 22 residues processed: 374 average time/residue: 1.3597 time to fit residues: 590.4034 Evaluate side-chains 364 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 340 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 239 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN P 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082746 restraints weight = 32689.424| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.31 r_work: 0.2808 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 26968 Z= 0.122 Angle : 0.639 14.294 37014 Z= 0.258 Chirality : 0.037 0.157 3752 Planarity : 0.004 0.047 4384 Dihedral : 16.438 179.995 5993 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 12.29 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.87 (0.16), residues: 2500 helix: 2.85 (0.12), residues: 1502 sheet: -0.62 (0.81), residues: 35 loop : 0.53 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.011 0.001 HIS 8 19 PHE 0.015 0.001 PHE H 19 TYR 0.018 0.001 TYR M 193 ARG 0.009 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1329) hydrogen bonds : angle 3.89519 ( 3726) covalent geometry : bond 0.00287 (26918) covalent geometry : angle 0.63945 (37014) Misc. bond : bond 0.05466 ( 50) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 351 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9460 (mmt) cc_final: 0.9211 (mmt) REVERT: C 308 MET cc_start: 0.9480 (tpp) cc_final: 0.9118 (tpp) REVERT: M 33 LYS cc_start: 0.7973 (tppp) cc_final: 0.7269 (mptt) REVERT: M 75 MET cc_start: 0.9483 (mtt) cc_final: 0.9169 (mtp) REVERT: H 101 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7177 (mm-30) REVERT: H 204 LYS cc_start: 0.7457 (mttp) cc_final: 0.6959 (mptt) REVERT: H 205 LYS cc_start: 0.7533 (mtmt) cc_final: 0.6910 (mptt) REVERT: A 13 ASP cc_start: 0.8460 (t0) cc_final: 0.7947 (t0) REVERT: B 16 GLN cc_start: 0.7448 (tp40) cc_final: 0.6909 (mp10) REVERT: D 6 TRP cc_start: 0.7552 (p-90) cc_final: 0.7207 (p-90) REVERT: F 41 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: G 14 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6323 (mt-10) REVERT: G 28 MET cc_start: 0.8074 (mtp) cc_final: 0.7291 (tpt) REVERT: I 7 LYS cc_start: 0.8367 (mttt) cc_final: 0.7856 (mmtp) REVERT: I 10 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: J 12 GLU cc_start: 0.7877 (tt0) cc_final: 0.7612 (tt0) REVERT: N 14 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6028 (mm-30) REVERT: O 7 LYS cc_start: 0.8589 (mtmp) cc_final: 0.7996 (mttt) REVERT: O 15 ARG cc_start: 0.8227 (ttt-90) cc_final: 0.7938 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8200 (t0) cc_final: 0.7992 (t0) REVERT: S 16 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7701 (mtt180) REVERT: V 24 GLN cc_start: 0.8551 (tt0) cc_final: 0.7888 (mt0) REVERT: W 19 ILE cc_start: 0.8714 (mm) cc_final: 0.8427 (mt) REVERT: X 16 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7538 (mtpp) REVERT: Y 6 TRP cc_start: 0.8567 (p-90) cc_final: 0.8064 (p-90) REVERT: Y 11 LEU cc_start: 0.8213 (mt) cc_final: 0.7941 (mt) REVERT: Z 17 GLU cc_start: 0.8069 (tt0) cc_final: 0.7774 (tt0) REVERT: 3 16 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6557 (ttm) REVERT: 4 7 MET cc_start: 0.5312 (ttm) cc_final: 0.5047 (ttp) REVERT: 4 17 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: 8 24 GLN cc_start: 0.7860 (tp40) cc_final: 0.7459 (tp40) REVERT: 0 17 GLU cc_start: 0.7108 (tp30) cc_final: 0.6895 (tp30) outliers start: 44 outliers final: 22 residues processed: 371 average time/residue: 1.3364 time to fit residues: 575.4758 Evaluate side-chains 360 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 334 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 253 CYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain 3 residue 16 MET Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN B 24 GLN P 13 GLN 0 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.081567 restraints weight = 32450.721| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.30 r_work: 0.2785 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.276 26968 Z= 0.143 Angle : 0.661 14.564 37014 Z= 0.268 Chirality : 0.038 0.149 3752 Planarity : 0.004 0.048 4384 Dihedral : 16.402 179.996 5991 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.96 % Allowed : 12.43 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.83 (0.16), residues: 2500 helix: 2.82 (0.12), residues: 1501 sheet: -0.57 (0.80), residues: 35 loop : 0.50 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.011 0.001 HIS 8 19 PHE 0.016 0.001 PHE H 19 TYR 0.018 0.001 TYR M 193 ARG 0.009 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 1329) hydrogen bonds : angle 3.93931 ( 3726) covalent geometry : bond 0.00338 (26918) covalent geometry : angle 0.66109 (37014) Misc. bond : bond 0.06085 ( 50) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 344 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9509 (mmt) cc_final: 0.9212 (mmt) REVERT: C 308 MET cc_start: 0.9486 (tpp) cc_final: 0.9133 (tpp) REVERT: M 33 LYS cc_start: 0.7990 (tppp) cc_final: 0.7269 (mptt) REVERT: M 75 MET cc_start: 0.9501 (mtt) cc_final: 0.9193 (mtp) REVERT: M 124 MET cc_start: 0.9115 (mmm) cc_final: 0.8811 (mmp) REVERT: H 101 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7203 (mm-30) REVERT: H 204 LYS cc_start: 0.7447 (mttp) cc_final: 0.7019 (mptt) REVERT: H 205 LYS cc_start: 0.7501 (mtmt) cc_final: 0.6887 (mptt) REVERT: A 13 ASP cc_start: 0.8533 (t0) cc_final: 0.7980 (t0) REVERT: B 16 GLN cc_start: 0.7457 (tp40) cc_final: 0.6897 (mp10) REVERT: D 6 TRP cc_start: 0.7537 (p-90) cc_final: 0.7188 (p-90) REVERT: F 41 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: G 14 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6314 (mt-10) REVERT: G 28 MET cc_start: 0.8098 (mtp) cc_final: 0.7315 (tpt) REVERT: I 7 LYS cc_start: 0.8393 (mttt) cc_final: 0.7895 (mmtp) REVERT: J 12 GLU cc_start: 0.7836 (tt0) cc_final: 0.7587 (tt0) REVERT: N 14 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6039 (mm-30) REVERT: O 7 LYS cc_start: 0.8595 (mtmp) cc_final: 0.7985 (mttt) REVERT: O 15 ARG cc_start: 0.8234 (ttt-90) cc_final: 0.7949 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8203 (t0) cc_final: 0.7999 (t0) REVERT: S 16 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7702 (mtt180) REVERT: V 24 GLN cc_start: 0.8574 (tt0) cc_final: 0.7911 (mt0) REVERT: W 7 LYS cc_start: 0.8514 (mttm) cc_final: 0.8109 (mttm) REVERT: W 19 ILE cc_start: 0.8715 (mm) cc_final: 0.8428 (mt) REVERT: Y 6 TRP cc_start: 0.8550 (p-90) cc_final: 0.8060 (p-90) REVERT: Y 11 LEU cc_start: 0.8219 (mt) cc_final: 0.7956 (mt) REVERT: Z 17 GLU cc_start: 0.8148 (tt0) cc_final: 0.7449 (tt0) REVERT: 3 16 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6582 (ttm) REVERT: 4 7 MET cc_start: 0.5315 (ttm) cc_final: 0.5055 (ttp) REVERT: 4 17 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: 8 24 GLN cc_start: 0.7860 (tp40) cc_final: 0.7455 (tp40) outliers start: 42 outliers final: 23 residues processed: 365 average time/residue: 1.3319 time to fit residues: 565.6249 Evaluate side-chains 358 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 332 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain Q residue 6 HIS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 16 MET Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 9 residue 7 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 219 optimal weight: 0.0020 chunk 8 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 243 optimal weight: 7.9990 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN B 24 GLN P 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085238 restraints weight = 32815.014| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.30 r_work: 0.2851 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.213 26968 Z= 0.110 Angle : 0.619 14.213 37014 Z= 0.254 Chirality : 0.037 0.142 3752 Planarity : 0.004 0.046 4384 Dihedral : 15.957 179.949 5991 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.54 % Allowed : 13.08 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.99 (0.17), residues: 2500 helix: 2.96 (0.12), residues: 1502 sheet: -0.76 (0.74), residues: 47 loop : 0.56 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 252 HIS 0.011 0.001 HIS 8 19 PHE 0.013 0.001 PHE L 170 TYR 0.017 0.001 TYR M 193 ARG 0.008 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 1329) hydrogen bonds : angle 3.80985 ( 3726) covalent geometry : bond 0.00258 (26918) covalent geometry : angle 0.61922 (37014) Misc. bond : bond 0.04719 ( 50) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 2.357 Fit side-chains revert: symmetry clash REVERT: L 13 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7574 (ptm160) REVERT: M 33 LYS cc_start: 0.7971 (tppp) cc_final: 0.7237 (mptt) REVERT: M 75 MET cc_start: 0.9468 (mtt) cc_final: 0.9148 (mtp) REVERT: M 124 MET cc_start: 0.9082 (mmm) cc_final: 0.8762 (mmp) REVERT: H 101 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7111 (tp30) REVERT: H 204 LYS cc_start: 0.7382 (mttp) cc_final: 0.7015 (mptt) REVERT: H 205 LYS cc_start: 0.7513 (mtmt) cc_final: 0.6895 (mptt) REVERT: A 13 ASP cc_start: 0.8490 (t0) cc_final: 0.7900 (t0) REVERT: B 16 GLN cc_start: 0.7418 (tp40) cc_final: 0.6895 (mp10) REVERT: D 6 TRP cc_start: 0.7498 (p-90) cc_final: 0.7121 (p-90) REVERT: F 17 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8158 (mp) REVERT: F 41 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: G 14 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6373 (mt-10) REVERT: G 28 MET cc_start: 0.8008 (mtp) cc_final: 0.7289 (tpt) REVERT: I 7 LYS cc_start: 0.8364 (mttt) cc_final: 0.7900 (mmtp) REVERT: J 12 GLU cc_start: 0.7816 (tt0) cc_final: 0.7575 (tt0) REVERT: N 14 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6071 (mm-30) REVERT: O 7 LYS cc_start: 0.8586 (mtmp) cc_final: 0.8015 (mttt) REVERT: O 15 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7947 (ttt-90) REVERT: S 16 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7710 (mtt180) REVERT: V 24 GLN cc_start: 0.8543 (tt0) cc_final: 0.7914 (mt0) REVERT: W 19 ILE cc_start: 0.8690 (mm) cc_final: 0.8421 (mt) REVERT: Y 6 TRP cc_start: 0.8546 (p-90) cc_final: 0.8056 (p-90) REVERT: Y 11 LEU cc_start: 0.8194 (mt) cc_final: 0.7899 (mt) REVERT: Z 17 GLU cc_start: 0.8075 (tt0) cc_final: 0.7672 (tm-30) REVERT: 4 7 MET cc_start: 0.5420 (ttm) cc_final: 0.5153 (ttp) REVERT: 4 16 GLN cc_start: 0.6858 (mt0) cc_final: 0.6432 (mp10) REVERT: 4 17 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: 8 24 GLN cc_start: 0.7862 (tp40) cc_final: 0.7447 (tp40) outliers start: 33 outliers final: 19 residues processed: 367 average time/residue: 1.2922 time to fit residues: 554.2396 Evaluate side-chains 355 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 333 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain Q residue 6 HIS Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 192 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN B 24 GLN P 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081542 restraints weight = 32464.559| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.32 r_work: 0.2778 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.283 26968 Z= 0.156 Angle : 0.676 14.814 37014 Z= 0.278 Chirality : 0.039 0.176 3752 Planarity : 0.004 0.048 4384 Dihedral : 16.135 179.995 5991 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.58 % Allowed : 13.45 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.87 (0.16), residues: 2500 helix: 2.83 (0.12), residues: 1505 sheet: -0.72 (0.73), residues: 47 loop : 0.57 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 252 HIS 0.012 0.001 HIS 8 19 PHE 0.017 0.001 PHE H 19 TYR 0.018 0.002 TYR M 193 ARG 0.009 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1329) hydrogen bonds : angle 3.93723 ( 3726) covalent geometry : bond 0.00369 (26918) covalent geometry : angle 0.67580 (37014) Misc. bond : bond 0.06738 ( 50) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 333 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: C 308 MET cc_start: 0.9561 (tpp) cc_final: 0.9107 (tpp) REVERT: M 33 LYS cc_start: 0.7974 (tppp) cc_final: 0.7242 (mptt) REVERT: M 124 MET cc_start: 0.9147 (mmm) cc_final: 0.8814 (mmp) REVERT: H 204 LYS cc_start: 0.7412 (mttp) cc_final: 0.7046 (mptt) REVERT: H 205 LYS cc_start: 0.7510 (mtmt) cc_final: 0.6888 (mptt) REVERT: A 13 ASP cc_start: 0.8559 (t0) cc_final: 0.8030 (t0) REVERT: B 16 GLN cc_start: 0.7449 (tp40) cc_final: 0.6888 (mp10) REVERT: D 6 TRP cc_start: 0.7534 (p-90) cc_final: 0.7147 (p-90) REVERT: F 17 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8172 (mp) REVERT: F 41 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: G 14 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6325 (mt-10) REVERT: G 28 MET cc_start: 0.8085 (mtp) cc_final: 0.7363 (tpt) REVERT: I 7 LYS cc_start: 0.8376 (mttt) cc_final: 0.7888 (mmtp) REVERT: J 12 GLU cc_start: 0.7827 (tt0) cc_final: 0.7559 (tt0) REVERT: N 14 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6013 (mm-30) REVERT: O 7 LYS cc_start: 0.8566 (mtmp) cc_final: 0.7968 (mttt) REVERT: O 15 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7962 (ttt-90) REVERT: Q 16 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.8111 (mtt-85) REVERT: S 16 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7722 (mtt180) REVERT: V 24 GLN cc_start: 0.8578 (tt0) cc_final: 0.7921 (mt0) REVERT: W 7 LYS cc_start: 0.8159 (mttm) cc_final: 0.7870 (mttm) REVERT: W 19 ILE cc_start: 0.8724 (mm) cc_final: 0.8437 (mt) REVERT: Y 6 TRP cc_start: 0.8560 (p-90) cc_final: 0.8093 (p-90) REVERT: Y 11 LEU cc_start: 0.8232 (mt) cc_final: 0.7963 (mt) REVERT: 3 16 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6595 (ttm) REVERT: 4 7 MET cc_start: 0.5328 (ttm) cc_final: 0.5056 (ttp) REVERT: 4 17 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: 8 24 GLN cc_start: 0.7869 (tp40) cc_final: 0.7401 (tp40) outliers start: 34 outliers final: 23 residues processed: 351 average time/residue: 1.4056 time to fit residues: 579.5842 Evaluate side-chains 357 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 330 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain Q residue 6 HIS Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain 3 residue 16 MET Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 194 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 223 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN B 24 GLN P 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083423 restraints weight = 32621.695| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.32 r_work: 0.2820 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.254 26968 Z= 0.121 Angle : 0.639 14.363 37014 Z= 0.263 Chirality : 0.037 0.174 3752 Planarity : 0.004 0.046 4384 Dihedral : 15.939 179.987 5991 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.63 % Allowed : 13.50 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 2.92 (0.16), residues: 2500 helix: 2.90 (0.12), residues: 1502 sheet: -0.72 (0.73), residues: 47 loop : 0.55 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 252 HIS 0.012 0.001 HIS 8 19 PHE 0.020 0.001 PHE 1 26 TYR 0.018 0.001 TYR M 193 ARG 0.009 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1329) hydrogen bonds : angle 3.87047 ( 3726) covalent geometry : bond 0.00284 (26918) covalent geometry : angle 0.63903 (37014) Misc. bond : bond 0.05967 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27914.45 seconds wall clock time: 479 minutes 11.45 seconds (28751.45 seconds total)