Starting phenix.real_space_refine on Mon Aug 25 06:48:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdv_37466/08_2025/8wdv_37466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdv_37466/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wdv_37466/08_2025/8wdv_37466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdv_37466/08_2025/8wdv_37466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wdv_37466/08_2025/8wdv_37466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdv_37466/08_2025/8wdv_37466.map" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1, 'PGV:plan-3': 3} 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: 6.88, per 1000 atoms: 0.26 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: 2.91 Conformation dependent library (CDL) restraints added in 936.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.74 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: 4.75 Time building geometry restraints manager: 3.58 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.450 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- 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 : 11.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 129 TYR 0.018 0.002 TYR C 200 PHE 0.020 0.001 PHE L 170 TRP 0.014 0.002 TRP S 9 HIS 0.008 0.001 HIS L 159 Details of bonding type rmsd covalent geometry : bond 0.01854 (26918) covalent geometry : angle 1.86073 (37014) hydrogen bonds : bond 0.18214 ( 1329) hydrogen bonds : angle 5.95804 ( 3726) 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 : 0.951 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: 0.7098 time to fit residues: 340.3123 Evaluate side-chains 370 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 351 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0470 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- 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 E 24 GLN J 24 GLN N 24 GLN P 13 GLN P 24 GLN T 24 GLN V 24 GLN ** 2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 ASN 0 16 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080566 restraints weight = 32766.098| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.31 r_work: 0.2763 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 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 = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.305 26968 Z= 0.177 Angle : 0.792 17.907 37014 Z= 0.306 Chirality : 0.042 0.242 3752 Planarity : 0.004 0.048 4384 Dihedral : 20.355 179.918 6010 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.19 % Allowed : 8.66 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.16), residues: 2500 helix: 2.64 (0.12), residues: 1494 sheet: -0.17 (0.91), residues: 30 loop : 0.59 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 16 TYR 0.018 0.002 TYR M 193 PHE 0.019 0.002 PHE H 19 TRP 0.015 0.001 TRP M 252 HIS 0.006 0.001 HIS L 159 Details of bonding type rmsd covalent geometry : bond 0.00420 (26918) covalent geometry : angle 0.79212 (37014) hydrogen bonds : bond 0.05019 ( 1329) hydrogen bonds : angle 4.21744 ( 3726) Misc. bond : bond 0.06798 ( 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 410 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 363 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9560 (mmt) cc_final: 0.9245 (mmt) REVERT: C 308 MET cc_start: 0.9488 (tpp) cc_final: 0.9253 (tpp) REVERT: L 208 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7119 (tmtp) REVERT: M 33 LYS cc_start: 0.7902 (tppp) cc_final: 0.7095 (mptt) REVERT: M 75 MET cc_start: 0.9479 (mtt) cc_final: 0.9168 (mtp) REVERT: H 205 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7018 (mptt) REVERT: A 13 ASP cc_start: 0.8553 (t0) cc_final: 0.8110 (t0) REVERT: B 16 GLN cc_start: 0.7472 (tp40) cc_final: 0.7026 (mp10) REVERT: F 41 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: G 14 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6255 (mt-10) REVERT: I 7 LYS cc_start: 0.8523 (mttt) cc_final: 0.8014 (mmtp) REVERT: J 12 GLU cc_start: 0.7742 (tt0) cc_final: 0.7494 (tt0) REVERT: J 44 ARG cc_start: 0.8784 (ttm170) cc_final: 0.8489 (ttm170) REVERT: K 16 ARG cc_start: 0.7037 (mtp-110) cc_final: 0.6386 (mmt90) REVERT: O 15 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7838 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8224 (t0) cc_final: 0.7948 (t0) REVERT: R 11 THR cc_start: 0.8173 (p) cc_final: 0.7838 (t) REVERT: R 14 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7635 (tt0) REVERT: S 16 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7764 (mtt180) REVERT: U 5 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8649 (mm) REVERT: U 16 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7399 (mtm110) REVERT: W 16 ARG cc_start: 0.7768 (mtt-85) cc_final: 0.7209 (tpp80) REVERT: Y 5 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8390 (tt) REVERT: Y 6 TRP cc_start: 0.8604 (p-90) cc_final: 0.8029 (p-90) REVERT: Z 17 GLU cc_start: 0.8009 (tt0) cc_final: 0.7672 (tm-30) REVERT: 3 12 PHE cc_start: 0.7524 (m-80) cc_final: 0.7238 (m-80) REVERT: 4 17 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: 4 35 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8908 (mt) REVERT: 8 24 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7457 (tp40) outliers start: 47 outliers final: 14 residues processed: 381 average time/residue: 0.6449 time to fit residues: 285.5788 Evaluate side-chains 361 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 341 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 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 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 93 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 157 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN N 24 GLN P 13 GLN T 24 GLN V 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082543 restraints weight = 32965.276| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.31 r_work: 0.2801 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 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 = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 26968 Z= 0.131 Angle : 0.674 17.047 37014 Z= 0.266 Chirality : 0.038 0.204 3752 Planarity : 0.004 0.050 4384 Dihedral : 17.538 179.838 5999 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 10.06 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.16), residues: 2500 helix: 2.79 (0.12), residues: 1499 sheet: -0.06 (0.92), residues: 30 loop : 0.55 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 8 TYR 0.018 0.001 TYR M 193 PHE 0.015 0.001 PHE H 19 TRP 0.014 0.001 TRP M 252 HIS 0.007 0.001 HIS Q 6 Details of bonding type rmsd covalent geometry : bond 0.00307 (26918) covalent geometry : angle 0.67431 (37014) hydrogen bonds : bond 0.04524 ( 1329) hydrogen bonds : angle 3.99829 ( 3726) Misc. bond : bond 0.05464 ( 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 403 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9451 (mmt) cc_final: 0.9227 (mmt) REVERT: L 13 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7824 (ptm160) REVERT: L 208 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7093 (tmtp) REVERT: M 33 LYS cc_start: 0.7939 (tppp) cc_final: 0.7156 (mptt) REVERT: M 75 MET cc_start: 0.9474 (mtt) cc_final: 0.9177 (mtp) REVERT: M 124 MET cc_start: 0.9125 (mmm) cc_final: 0.8729 (mmp) REVERT: H 101 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7210 (tp30) REVERT: H 205 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7021 (mptt) REVERT: A 13 ASP cc_start: 0.8583 (t0) cc_final: 0.8069 (t0) REVERT: B 16 GLN cc_start: 0.7481 (tp40) cc_final: 0.7061 (mp10) REVERT: E 12 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: F 41 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: G 14 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6336 (mt-10) REVERT: G 28 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7195 (tpt) REVERT: I 7 LYS cc_start: 0.8485 (mttt) cc_final: 0.8013 (mmtp) REVERT: K 16 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6353 (mmt90) REVERT: O 7 LYS cc_start: 0.8441 (mttp) cc_final: 0.7908 (mttt) REVERT: O 15 ARG cc_start: 0.8259 (ttt-90) cc_final: 0.8050 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8241 (t0) cc_final: 0.7988 (t0) REVERT: Q 16 ARG cc_start: 0.8397 (mtt-85) cc_final: 0.8117 (mtt-85) REVERT: R 11 THR cc_start: 0.8214 (p) cc_final: 0.7860 (t) REVERT: R 14 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7587 (tt0) REVERT: S 16 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7791 (mtt180) REVERT: U 5 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8669 (mm) REVERT: W 19 ILE cc_start: 0.8781 (mm) cc_final: 0.8513 (mt) REVERT: X 16 LYS cc_start: 0.8063 (mtpm) cc_final: 0.7530 (mtpp) REVERT: X 34 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8992 (mt) REVERT: Y 6 TRP cc_start: 0.8553 (p-90) cc_final: 0.8003 (p-90) REVERT: Y 11 LEU cc_start: 0.8203 (mt) cc_final: 0.7985 (mt) REVERT: Z 11 THR cc_start: 0.8425 (p) cc_final: 0.7872 (p) REVERT: Z 17 GLU cc_start: 0.8115 (tt0) cc_final: 0.7827 (tm-30) REVERT: 3 12 PHE cc_start: 0.7498 (m-80) cc_final: 0.7217 (m-80) REVERT: 4 17 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: 4 35 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8888 (mt) REVERT: 5 6 HIS cc_start: 0.5547 (OUTLIER) cc_final: 0.4416 (p90) REVERT: 8 24 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7398 (tp40) outliers start: 47 outliers final: 20 residues processed: 376 average time/residue: 0.6108 time to fit residues: 267.5136 Evaluate side-chains 375 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 ASP 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 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 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 E residue 12 GLU 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 S residue 4 ASP Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain X residue 34 ILE 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 7 residue 11 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 P 13 GLN P 24 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 = 0.3597 r_free = 0.3597 target = 0.117877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.078612 restraints weight = 32640.942| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.30 r_work: 0.2722 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 26968 Z= 0.257 Angle : 0.798 16.298 37014 Z= 0.316 Chirality : 0.044 0.183 3752 Planarity : 0.004 0.049 4384 Dihedral : 17.752 179.833 5996 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.79 % Allowed : 10.15 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.16), residues: 2500 helix: 2.52 (0.12), residues: 1501 sheet: -0.35 (0.89), residues: 31 loop : 0.44 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 8 TYR 0.023 0.002 TYR C 200 PHE 0.021 0.002 PHE H 19 TRP 0.015 0.002 TRP M 252 HIS 0.009 0.002 HIS P 37 Details of bonding type rmsd covalent geometry : bond 0.00617 (26918) covalent geometry : angle 0.79826 (37014) hydrogen bonds : bond 0.05144 ( 1329) hydrogen bonds : angle 4.20078 ( 3726) Misc. bond : bond 0.07466 ( 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 409 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.9572 (mmt) cc_final: 0.9324 (mmt) REVERT: C 308 MET cc_start: 0.9526 (tpp) cc_final: 0.9169 (tpp) REVERT: L 21 ASP cc_start: 0.7727 (t0) cc_final: 0.7507 (m-30) REVERT: L 208 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7174 (tmtp) REVERT: M 33 LYS cc_start: 0.7976 (tppp) cc_final: 0.7199 (mptt) REVERT: M 309 GLU cc_start: 0.8723 (tt0) cc_final: 0.8473 (tt0) REVERT: H 205 LYS cc_start: 0.7540 (mtmt) cc_final: 0.6975 (mptt) REVERT: A 13 ASP cc_start: 0.8574 (t0) cc_final: 0.8162 (t0) REVERT: B 16 GLN cc_start: 0.7468 (tp40) cc_final: 0.7099 (tp40) REVERT: E 12 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: F 41 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: G 14 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6294 (mt-10) REVERT: G 23 THR cc_start: 0.8357 (m) cc_final: 0.8149 (m) REVERT: G 28 MET cc_start: 0.8202 (mtp) cc_final: 0.7484 (tpt) REVERT: I 7 LYS cc_start: 0.8491 (mttt) cc_final: 0.8047 (mmtp) REVERT: J 12 GLU cc_start: 0.7836 (tt0) cc_final: 0.7542 (tt0) REVERT: K 16 ARG cc_start: 0.6967 (mtp-110) cc_final: 0.6352 (mmt90) REVERT: O 15 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7761 (ttt-90) REVERT: Q 13 ASP cc_start: 0.8167 (t0) cc_final: 0.7906 (t0) REVERT: S 16 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7740 (mtt180) REVERT: Y 6 TRP cc_start: 0.8608 (p-90) cc_final: 0.7995 (p-90) REVERT: Y 11 LEU cc_start: 0.8264 (mt) cc_final: 0.8021 (mt) REVERT: Z 17 GLU cc_start: 0.8116 (tt0) cc_final: 0.7850 (tm-30) REVERT: 3 12 PHE cc_start: 0.7593 (m-80) cc_final: 0.7281 (m-80) REVERT: 4 7 MET cc_start: 0.5364 (ttm) cc_final: 0.5091 (ttp) REVERT: 4 17 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: 5 6 HIS cc_start: 0.5490 (OUTLIER) cc_final: 0.5209 (t-90) REVERT: 8 24 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7417 (tp40) outliers start: 60 outliers final: 29 residues processed: 373 average time/residue: 0.6113 time to fit residues: 265.1081 Evaluate side-chains 374 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 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 E residue 12 GLU 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 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 17 ILE Chi-restraints excluded: chain U residue 18 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 6 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 74 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 207 GLN P 13 GLN P 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079628 restraints weight = 32522.112| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.30 r_work: 0.2743 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.308 26968 Z= 0.198 Angle : 0.729 14.651 37014 Z= 0.292 Chirality : 0.041 0.164 3752 Planarity : 0.004 0.048 4384 Dihedral : 17.287 179.954 5994 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.70 % Allowed : 10.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.16), residues: 2500 helix: 2.60 (0.12), residues: 1497 sheet: -0.45 (0.89), residues: 31 loop : 0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 8 TYR 0.020 0.002 TYR C 200 PHE 0.019 0.002 PHE L 170 TRP 0.014 0.001 TRP M 252 HIS 0.009 0.002 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00474 (26918) covalent geometry : angle 0.72869 (37014) hydrogen bonds : bond 0.04790 ( 1329) hydrogen bonds : angle 4.10222 ( 3726) Misc. bond : bond 0.06592 ( 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 404 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 308 MET cc_start: 0.9506 (tpp) cc_final: 0.9181 (tpp) REVERT: L 13 ARG cc_start: 0.8350 (ptm160) cc_final: 0.8125 (ptm160) REVERT: L 208 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7171 (tmtp) REVERT: M 33 LYS cc_start: 0.8012 (tppp) cc_final: 0.7258 (mptt) REVERT: H 205 LYS cc_start: 0.7531 (mtmt) cc_final: 0.6958 (mptt) REVERT: A 13 ASP cc_start: 0.8581 (t0) cc_final: 0.8069 (t0) REVERT: B 16 GLN cc_start: 0.7475 (tp40) cc_final: 0.7099 (tp40) REVERT: E 12 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: F 41 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: G 10 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6998 (mt) REVERT: G 14 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6323 (mt-10) REVERT: G 28 MET cc_start: 0.8189 (mtp) cc_final: 0.7506 (tpt) REVERT: I 7 LYS cc_start: 0.8468 (mttt) cc_final: 0.7913 (mmtp) REVERT: J 44 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8536 (ttm170) REVERT: K 16 ARG cc_start: 0.7010 (mtp-110) cc_final: 0.6786 (mtp-110) REVERT: O 7 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7807 (mttt) REVERT: O 15 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: Q 7 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8698 (mtpt) REVERT: Q 13 ASP cc_start: 0.8215 (t0) cc_final: 0.7978 (t0) REVERT: S 16 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7776 (mtt180) REVERT: V 24 GLN cc_start: 0.8534 (tt0) cc_final: 0.7862 (mt0) REVERT: X 34 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8994 (mt) REVERT: Y 6 TRP cc_start: 0.8627 (p-90) cc_final: 0.8122 (p-90) REVERT: Y 11 LEU cc_start: 0.8281 (mt) cc_final: 0.8019 (mt) REVERT: Z 17 GLU cc_start: 0.8122 (tt0) cc_final: 0.7871 (tt0) REVERT: 3 12 PHE cc_start: 0.7510 (m-80) cc_final: 0.7198 (m-80) REVERT: 4 7 MET cc_start: 0.5353 (ttm) cc_final: 0.5070 (ttp) REVERT: 4 17 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: 5 6 HIS cc_start: 0.5487 (OUTLIER) cc_final: 0.4493 (p90) REVERT: 5 8 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7246 (mp) REVERT: 8 24 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7398 (tp40) outliers start: 58 outliers final: 31 residues processed: 369 average time/residue: 0.5895 time to fit residues: 252.9075 Evaluate side-chains 377 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 208 LYS Chi-restraints excluded: chain L residue 210 GLU 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 E residue 12 GLU Chi-restraints excluded: chain E residue 17 GLU 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 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 17 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain X residue 34 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 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 6 HIS 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 0 residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 241 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 207 GLN P 13 GLN P 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080299 restraints weight = 32605.423| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.31 r_work: 0.2756 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 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 = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.301 26968 Z= 0.173 Angle : 0.700 14.604 37014 Z= 0.281 Chirality : 0.040 0.157 3752 Planarity : 0.004 0.048 4384 Dihedral : 17.025 179.993 5994 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.98 % Allowed : 11.13 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.16), residues: 2500 helix: 2.66 (0.12), residues: 1498 sheet: -0.82 (0.80), residues: 36 loop : 0.46 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 8 TYR 0.020 0.002 TYR M 193 PHE 0.018 0.002 PHE L 170 TRP 0.014 0.001 TRP M 252 HIS 0.010 0.001 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00412 (26918) covalent geometry : angle 0.69992 (37014) hydrogen bonds : bond 0.04621 ( 1329) hydrogen bonds : angle 4.05113 ( 3726) Misc. bond : bond 0.06428 ( 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 416 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9487 (mmt) cc_final: 0.9086 (mmt) REVERT: C 308 MET cc_start: 0.9499 (tpp) cc_final: 0.9164 (tpp) REVERT: L 13 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7965 (ptm160) REVERT: L 208 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7147 (tmtp) REVERT: M 25 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (mttt) REVERT: M 33 LYS cc_start: 0.8041 (tppp) cc_final: 0.7301 (mptt) REVERT: M 124 MET cc_start: 0.9130 (mmm) cc_final: 0.8771 (mmp) REVERT: H 204 LYS cc_start: 0.7519 (mttp) cc_final: 0.6993 (mptt) REVERT: H 205 LYS cc_start: 0.7503 (mtmt) cc_final: 0.6920 (mptt) REVERT: A 13 ASP cc_start: 0.8552 (t0) cc_final: 0.8062 (t0) REVERT: B 16 GLN cc_start: 0.7507 (tp40) cc_final: 0.6939 (mp10) REVERT: D 6 TRP cc_start: 0.7610 (p-90) cc_final: 0.7142 (p-90) REVERT: E 12 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: F 41 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: G 14 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6329 (mt-10) REVERT: G 28 MET cc_start: 0.8109 (mtp) cc_final: 0.7495 (tpt) REVERT: I 7 LYS cc_start: 0.8425 (mttt) cc_final: 0.7882 (mmtp) REVERT: K 16 ARG cc_start: 0.7006 (mtp-110) cc_final: 0.6759 (mtp-110) REVERT: N 14 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6105 (mm-30) REVERT: O 7 LYS cc_start: 0.8526 (mtmm) cc_final: 0.7821 (mttt) REVERT: O 15 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7984 (ttt-90) REVERT: P 10 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7919 (mp) REVERT: Q 7 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8633 (mtpt) REVERT: Q 13 ASP cc_start: 0.8234 (t0) cc_final: 0.7988 (t0) REVERT: S 16 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7777 (mtt180) REVERT: V 24 GLN cc_start: 0.8555 (tt0) cc_final: 0.7850 (mt0) REVERT: Y 6 TRP cc_start: 0.8610 (p-90) cc_final: 0.8118 (p-90) REVERT: Y 11 LEU cc_start: 0.8241 (mt) cc_final: 0.7976 (mt) REVERT: Z 17 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: 2 44 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7533 (ttp-170) REVERT: 3 12 PHE cc_start: 0.7476 (m-80) cc_final: 0.7257 (m-80) REVERT: 4 7 MET cc_start: 0.5328 (ttm) cc_final: 0.5044 (ttp) REVERT: 4 17 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: 5 6 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.4539 (p90) REVERT: 5 8 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7260 (mp) REVERT: 8 24 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7397 (tp40) REVERT: 0 17 GLU cc_start: 0.7237 (tp30) cc_final: 0.7028 (tp30) outliers start: 64 outliers final: 29 residues processed: 375 average time/residue: 0.5746 time to fit residues: 249.2773 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 : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 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 25 LYS 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 E residue 12 GLU 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 P residue 10 LEU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain S residue 5 LEU 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 Z residue 17 GLU 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 8 ILE Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 8 residue 24 GLN Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 207 GLN P 13 GLN P 24 GLN 0 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.081801 restraints weight = 32450.951| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.29 r_work: 0.2789 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 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 = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 26968 Z= 0.134 Angle : 0.653 14.386 37014 Z= 0.263 Chirality : 0.038 0.146 3752 Planarity : 0.004 0.047 4384 Dihedral : 16.632 179.987 5994 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.33 % Allowed : 11.73 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.16), residues: 2500 helix: 2.78 (0.12), residues: 1501 sheet: -0.63 (0.81), residues: 35 loop : 0.51 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 8 TYR 0.018 0.001 TYR M 193 PHE 0.016 0.001 PHE L 170 TRP 0.014 0.001 TRP M 252 HIS 0.009 0.001 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00317 (26918) covalent geometry : angle 0.65284 (37014) hydrogen bonds : bond 0.04347 ( 1329) hydrogen bonds : angle 3.94990 ( 3726) Misc. bond : bond 0.05802 ( 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 396 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9477 (mmt) cc_final: 0.9214 (mmt) REVERT: C 308 MET cc_start: 0.9485 (tpp) cc_final: 0.9134 (tpp) REVERT: L 13 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7948 (ptm160) REVERT: M 25 LYS cc_start: 0.7909 (mptp) cc_final: 0.7707 (mttt) REVERT: M 33 LYS cc_start: 0.7993 (tppp) cc_final: 0.7272 (mptt) REVERT: M 66 MET cc_start: 0.9211 (tpp) cc_final: 0.8975 (tpt) REVERT: M 124 MET cc_start: 0.9117 (mmm) cc_final: 0.8726 (mmp) REVERT: H 204 LYS cc_start: 0.7464 (mttp) cc_final: 0.6963 (mptt) REVERT: H 205 LYS cc_start: 0.7544 (mtmt) cc_final: 0.6929 (mptt) REVERT: A 13 ASP cc_start: 0.8542 (t0) cc_final: 0.8035 (t0) REVERT: B 16 GLN cc_start: 0.7503 (tp40) cc_final: 0.6963 (mp10) REVERT: D 6 TRP cc_start: 0.7629 (p-90) cc_final: 0.7188 (p-90) REVERT: E 12 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: F 41 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: G 14 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6347 (mt-10) REVERT: G 28 MET cc_start: 0.8086 (mtp) cc_final: 0.7444 (tpt) REVERT: I 7 LYS cc_start: 0.8394 (mttt) cc_final: 0.7892 (mmtp) REVERT: I 10 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: J 12 GLU cc_start: 0.7866 (tt0) cc_final: 0.7617 (tt0) REVERT: K 16 ARG cc_start: 0.6968 (mtp-110) cc_final: 0.6720 (mtp-110) REVERT: N 14 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6058 (mm-30) REVERT: O 7 LYS cc_start: 0.8564 (mtmm) cc_final: 0.7879 (mttt) REVERT: O 15 ARG cc_start: 0.8204 (ttt-90) cc_final: 0.7936 (ttt-90) REVERT: Q 7 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8481 (mtpp) REVERT: Q 13 ASP cc_start: 0.8219 (t0) cc_final: 0.7988 (t0) REVERT: S 16 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7712 (mtt180) REVERT: V 24 GLN cc_start: 0.8552 (tt0) cc_final: 0.7850 (mt0) REVERT: W 19 ILE cc_start: 0.8723 (mm) cc_final: 0.8440 (mt) REVERT: Y 6 TRP cc_start: 0.8583 (p-90) cc_final: 0.8090 (p-90) REVERT: Y 11 LEU cc_start: 0.8243 (mt) cc_final: 0.7980 (mt) REVERT: Z 17 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: 3 12 PHE cc_start: 0.7423 (m-80) cc_final: 0.7221 (m-80) REVERT: 4 7 MET cc_start: 0.5373 (ttm) cc_final: 0.5130 (ttp) REVERT: 4 16 GLN cc_start: 0.6717 (mt0) cc_final: 0.6340 (mp10) REVERT: 4 17 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: 5 6 HIS cc_start: 0.5561 (OUTLIER) cc_final: 0.4476 (p90) REVERT: 8 24 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7367 (tp40) outliers start: 50 outliers final: 22 residues processed: 367 average time/residue: 0.6961 time to fit residues: 296.1220 Evaluate side-chains 366 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 337 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 E residue 12 GLU 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 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 Z residue 17 GLU 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 7 residue 11 ILE Chi-restraints excluded: chain 8 residue 24 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 89 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 P 24 GLN ** 6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078239 restraints weight = 32630.524| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.31 r_work: 0.2711 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.340 26968 Z= 0.276 Angle : 0.799 14.965 37014 Z= 0.323 Chirality : 0.044 0.184 3752 Planarity : 0.005 0.052 4384 Dihedral : 17.406 179.995 5994 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 12.01 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.16), residues: 2500 helix: 2.48 (0.12), residues: 1504 sheet: -0.82 (0.80), residues: 36 loop : 0.42 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 8 TYR 0.023 0.002 TYR C 200 PHE 0.023 0.002 PHE M 65 TRP 0.015 0.002 TRP M 252 HIS 0.011 0.002 HIS P 37 Details of bonding type rmsd covalent geometry : bond 0.00664 (26918) covalent geometry : angle 0.79874 (37014) hydrogen bonds : bond 0.05109 ( 1329) hydrogen bonds : angle 4.19802 ( 3726) Misc. bond : bond 0.07466 ( 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 396 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9592 (mmt) cc_final: 0.9323 (mmt) REVERT: C 308 MET cc_start: 0.9499 (tpp) cc_final: 0.9156 (tpp) REVERT: L 13 ARG cc_start: 0.8344 (ptm160) cc_final: 0.8061 (ptm160) REVERT: M 25 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7736 (mttt) REVERT: M 33 LYS cc_start: 0.8025 (tppp) cc_final: 0.7277 (mptt) REVERT: M 309 GLU cc_start: 0.8769 (tt0) cc_final: 0.8531 (tt0) REVERT: H 204 LYS cc_start: 0.7478 (mttp) cc_final: 0.6937 (mptt) REVERT: H 205 LYS cc_start: 0.7506 (mtmt) cc_final: 0.6910 (mptt) REVERT: A 13 ASP cc_start: 0.8591 (t0) cc_final: 0.8183 (t0) REVERT: B 12 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 16 GLN cc_start: 0.7509 (tp40) cc_final: 0.7084 (tp40) REVERT: E 12 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: F 41 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: G 10 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6976 (mt) REVERT: G 14 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6375 (mt-10) REVERT: G 28 MET cc_start: 0.8160 (mtp) cc_final: 0.7603 (tpt) REVERT: I 7 LYS cc_start: 0.8493 (mttt) cc_final: 0.7985 (mmtp) REVERT: N 14 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6041 (mm-30) REVERT: O 15 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7950 (ttt-90) REVERT: P 10 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7976 (mp) REVERT: Q 7 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8523 (mtpp) REVERT: Q 13 ASP cc_start: 0.8196 (t0) cc_final: 0.7976 (t0) REVERT: S 16 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7714 (mtt180) REVERT: V 26 MET cc_start: 0.8689 (ttp) cc_final: 0.8434 (ttp) REVERT: Y 6 TRP cc_start: 0.8590 (p-90) cc_final: 0.8098 (p-90) REVERT: Y 11 LEU cc_start: 0.8331 (mt) cc_final: 0.8061 (mt) REVERT: Z 17 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: 3 12 PHE cc_start: 0.7581 (m-80) cc_final: 0.7298 (m-80) REVERT: 4 7 MET cc_start: 0.5322 (ttm) cc_final: 0.5088 (ttp) REVERT: 4 17 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: 5 6 HIS cc_start: 0.5570 (OUTLIER) cc_final: 0.4688 (p90) REVERT: 5 8 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7270 (mp) REVERT: 8 24 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7372 (tp40) outliers start: 55 outliers final: 25 residues processed: 365 average time/residue: 0.6208 time to fit residues: 262.4456 Evaluate side-chains 372 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 337 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 210 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 25 LYS 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 E residue 12 GLU 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 R residue 12 GLU 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 Z residue 17 GLU 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 8 ILE Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 8 residue 24 GLN Chi-restraints excluded: chain 0 residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 187 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082687 restraints weight = 32605.202| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.31 r_work: 0.2805 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 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 = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.264 26968 Z= 0.126 Angle : 0.653 14.249 37014 Z= 0.266 Chirality : 0.038 0.141 3752 Planarity : 0.004 0.046 4384 Dihedral : 16.597 179.976 5994 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.72 % Allowed : 12.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.16), residues: 2500 helix: 2.80 (0.12), residues: 1499 sheet: -0.63 (0.80), residues: 35 loop : 0.50 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 8 TYR 0.019 0.001 TYR M 193 PHE 0.016 0.001 PHE L 170 TRP 0.012 0.001 TRP M 252 HIS 0.012 0.001 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00295 (26918) covalent geometry : angle 0.65335 (37014) hydrogen bonds : bond 0.04261 ( 1329) hydrogen bonds : angle 3.94787 ( 3726) Misc. bond : bond 0.05388 ( 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 382 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 345 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9426 (mmt) cc_final: 0.9204 (mmt) REVERT: C 308 MET cc_start: 0.9480 (tpp) cc_final: 0.9130 (tpp) REVERT: L 13 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7961 (ptm160) REVERT: L 208 LYS cc_start: 0.8050 (tttm) cc_final: 0.7650 (mmtm) REVERT: M 25 LYS cc_start: 0.7920 (mptp) cc_final: 0.7661 (mmtt) REVERT: M 33 LYS cc_start: 0.7997 (tppp) cc_final: 0.7268 (mptt) REVERT: M 75 MET cc_start: 0.9496 (mtt) cc_final: 0.9178 (mtp) REVERT: M 124 MET cc_start: 0.9077 (mmm) cc_final: 0.8835 (mmp) REVERT: H 204 LYS cc_start: 0.7477 (mttp) cc_final: 0.6983 (mptt) REVERT: H 205 LYS cc_start: 0.7511 (mtmt) cc_final: 0.6890 (mptt) REVERT: A 13 ASP cc_start: 0.8575 (t0) cc_final: 0.8052 (t0) REVERT: B 16 GLN cc_start: 0.7470 (tp40) cc_final: 0.6914 (mp10) REVERT: F 41 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: G 14 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6336 (mt-10) REVERT: G 28 MET cc_start: 0.8110 (mtp) cc_final: 0.7467 (tpt) REVERT: I 7 LYS cc_start: 0.8396 (mttt) cc_final: 0.7946 (mmtp) REVERT: K 16 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6412 (mmt90) REVERT: N 14 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5981 (mm-30) REVERT: O 15 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7927 (ttt-90) REVERT: Q 7 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8482 (mttp) REVERT: Q 13 ASP cc_start: 0.8237 (t0) cc_final: 0.8023 (t0) REVERT: Q 16 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8229 (mtt-85) REVERT: S 16 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7734 (mtt180) REVERT: V 24 GLN cc_start: 0.8496 (tt0) cc_final: 0.7864 (mt0) REVERT: V 26 MET cc_start: 0.8586 (ttp) cc_final: 0.8332 (ttp) REVERT: W 19 ILE cc_start: 0.8742 (mm) cc_final: 0.8461 (mt) REVERT: Y 6 TRP cc_start: 0.8568 (p-90) cc_final: 0.8094 (p-90) REVERT: Y 11 LEU cc_start: 0.8266 (mt) cc_final: 0.7959 (mt) REVERT: Z 17 GLU cc_start: 0.8132 (tt0) cc_final: 0.7856 (tm-30) REVERT: 4 7 MET cc_start: 0.5384 (ttm) cc_final: 0.5138 (ttp) REVERT: 4 17 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: 5 6 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.4659 (p90) REVERT: 8 24 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7383 (tp40) outliers start: 37 outliers final: 20 residues processed: 360 average time/residue: 0.5923 time to fit residues: 247.0338 Evaluate side-chains 357 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 333 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 6 HIS Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 8 residue 24 GLN 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 219 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 GLN L 207 GLN B 24 GLN P 13 GLN P 24 GLN ** 6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.078693 restraints weight = 32569.917| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.30 r_work: 0.2724 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.326 26968 Z= 0.250 Angle : 0.773 14.667 37014 Z= 0.315 Chirality : 0.043 0.176 3752 Planarity : 0.004 0.049 4384 Dihedral : 17.105 179.971 5994 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.96 % Allowed : 12.80 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.16), residues: 2500 helix: 2.56 (0.12), residues: 1502 sheet: -0.77 (0.80), residues: 36 loop : 0.48 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 8 TYR 0.022 0.002 TYR C 200 PHE 0.021 0.002 PHE M 65 TRP 0.015 0.002 TRP M 252 HIS 0.014 0.002 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00599 (26918) covalent geometry : angle 0.77304 (37014) hydrogen bonds : bond 0.04954 ( 1329) hydrogen bonds : angle 4.15729 ( 3726) Misc. bond : bond 0.07471 ( 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 371 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: C 236 MET cc_start: 0.9580 (mmt) cc_final: 0.9309 (mmt) REVERT: C 308 MET cc_start: 0.9499 (tpp) cc_final: 0.9152 (tpp) REVERT: L 208 LYS cc_start: 0.8048 (tttm) cc_final: 0.7615 (mmtm) REVERT: M 25 LYS cc_start: 0.7940 (mptp) cc_final: 0.7728 (mttt) REVERT: M 33 LYS cc_start: 0.8027 (tppp) cc_final: 0.7295 (mptt) REVERT: M 309 GLU cc_start: 0.8739 (tt0) cc_final: 0.8495 (tt0) REVERT: H 204 LYS cc_start: 0.7543 (mttp) cc_final: 0.6974 (mptt) REVERT: H 205 LYS cc_start: 0.7494 (mtmt) cc_final: 0.6898 (mptt) REVERT: A 13 ASP cc_start: 0.8567 (t0) cc_final: 0.8031 (t0) REVERT: B 16 GLN cc_start: 0.7481 (tp40) cc_final: 0.7074 (tp40) REVERT: F 41 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: G 10 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6937 (mt) REVERT: G 14 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6359 (mt-10) REVERT: G 28 MET cc_start: 0.8165 (mtp) cc_final: 0.7549 (tpt) REVERT: I 7 LYS cc_start: 0.8438 (mttt) cc_final: 0.7978 (mmtp) REVERT: N 14 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6041 (mm-30) REVERT: O 15 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7951 (ttt-90) REVERT: Q 7 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8500 (mttp) REVERT: Q 13 ASP cc_start: 0.8211 (t0) cc_final: 0.7985 (t0) REVERT: S 16 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7698 (mtt180) REVERT: V 26 MET cc_start: 0.8691 (ttp) cc_final: 0.8447 (ttp) REVERT: Y 6 TRP cc_start: 0.8571 (p-90) cc_final: 0.8097 (p-90) REVERT: Y 11 LEU cc_start: 0.8308 (mt) cc_final: 0.8026 (mt) REVERT: Z 17 GLU cc_start: 0.8149 (tt0) cc_final: 0.7834 (tm-30) REVERT: 4 7 MET cc_start: 0.5354 (ttm) cc_final: 0.5111 (ttp) REVERT: 4 17 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: 5 6 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.4683 (p90) REVERT: 8 24 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7410 (tp40) outliers start: 42 outliers final: 24 residues processed: 351 average time/residue: 0.6685 time to fit residues: 271.9137 Evaluate side-chains 356 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 327 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 P residue 21 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 54 THR Chi-restraints excluded: chain 4 residue 17 GLU Chi-restraints excluded: chain 5 residue 6 HIS Chi-restraints excluded: chain 5 residue 8 ILE Chi-restraints excluded: chain 5 residue 11 ILE Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 8 residue 24 GLN 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 192 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080733 restraints weight = 32483.383| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.27 r_work: 0.2756 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 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 = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.303 26968 Z= 0.178 Angle : 0.713 14.402 37014 Z= 0.291 Chirality : 0.040 0.159 3752 Planarity : 0.004 0.068 4384 Dihedral : 16.893 179.995 5994 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.68 % Allowed : 13.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.16), residues: 2500 helix: 2.64 (0.12), residues: 1498 sheet: -0.78 (0.80), residues: 36 loop : 0.44 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 16 TYR 0.020 0.002 TYR M 193 PHE 0.018 0.002 PHE 1 26 TRP 0.014 0.001 TRP M 252 HIS 0.013 0.002 HIS 8 19 Details of bonding type rmsd covalent geometry : bond 0.00426 (26918) covalent geometry : angle 0.71259 (37014) hydrogen bonds : bond 0.04632 ( 1329) hydrogen bonds : angle 4.09163 ( 3726) Misc. bond : bond 0.06601 ( 50) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13988.26 seconds wall clock time: 237 minutes 43.21 seconds (14263.21 seconds total)